title: virus-cured M. restricta KCTC 27540

status: Public on Aug 18 2020

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Salmonella enterica serivar Typhimurium 14028s whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
Mapped reads were counted by featureCounts in Subread package v1.4.3 and the relative transcript abundance was TPM-normalized.
Genome_build: Malassezia restricta KCTC 27527 (GCA_003290485.1)
Supplementary_files_format_and_content: Excel file including TPM values and locus_tags of M. restricta.

organism: Malassezia restricta

source_name: Clinical isolate

growth_protocol: M. restricta KCTC 27540 cells were cultured in LNA medium at 34ºC for 3 days and harvested for RNA extraction of virus-infected cell. The strain was transferred to fresh LNA medium, cultured for 3 or 4 days, passaged eight times for virus-curing and harvested for RNA extraction of virus-cured cell.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiqagen, Cat#74104).
Illumina Stranded TruSeq mRNA Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using manufacturer's protocols.

tag: infection status

value: virus-cured


title: Rp_A_2M_01

status: Public on Aug 19 2020

type: SRA

city: Dunedin

first: Eddy

last: Dowle

address: 270 Gt King St

department: Department of Anatomy

country: New Zealand

institute: University of Otago

description: Pool of 10 CNS

library_source: transcriptomic

data_processing:
Reads were mapped to the Rhagoletis zephyria genome using STAR
Read counts were estimated in RSEM
Genome_build: NCBI Assembly: GCA_001687245.1, Rhagoletis_zephyria_1.0
Supplementary_files_format_and_content: RSEM output file - counts per gene

molecule: polyA RNA

organism: Rhagoletis pomonella

source_name: Central Nervous System CNS

growth_protocol: Infested apple and hawthorn fruits were collected from Urbana, IL in the late summer and fall of 2014. Infested fruit were returned to the laboratory at the University of Florida, emerging larvae were collected and held at ~24C 14:10 LD for 10 days to complete pupation and enter diapause, then pupae were transferred to 3.5C at 95% Relative Humidity (RH). At monthly intervals from 2 to 6 months we dissected out the Central Nervous System (CNS), homogenized pools of 10 CNS, and extracted RNA (5 samples per time point per host). RNA sequencing libraries were prepared using Illumina’s tru-seq stranded mRNA kit and sequenced using 100bp single end Illumina HiSeq 2500. Cleaned reads were mapped to the R. zephyria genome using STAR, and read counts were generated using RSEM.

extract_protocol:
Flies were disected and CNS removed, extractions consisted of pools of 10 fly CNS, RNA extraction
Illumina mRNA tru-seq stranded

tag: host

value: Apple Tree

tag: diapause age

value: 2 Months diapause

tag: location

value: USA:Urbana Illinois

tag: lifestage

value: Pupa

tag: collection year


title: ATACseq-EryD-Rep2

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
ATAC-seq reads were trimmed for adapter sequences and low alignment quality using Cutadapt (Martin, 2011), with the parameters -q 30 --minimum-length 36. Paired-end reads were aligned to the mm10 reference genome by using Bowtie2 (Langmead et al., 2009), with the parameter -X 2000 allowing fragments of up to 2 kb to be aligned (Buenrostro et al., 2015). ATAC-seq peaks were called using MACS2 (Zhang et al., 2008) with following parameters (--nomodel --nolambda --keep-dup all --call-summits) (Buenrostro et al., 2015). Peak calling was done in two biological replicates respectively with the same parameter settings. One replicate of each cell type was used for subsequent analysis. We then extended the summits to 500-bp window (±250 bp) as peaks and filtered using the consensus excludable ENCODE blacklist (Consortium, 2012).
HiChIP datasets were processed using HiC-Pro (Mumbach et al., 2016; Mumbach et al., 2017; Servant et al., 2015) with default settings. Specifically, HiChIP paired-end reads were aligned using Bowtie2 with –very-sensitive -L 30 –score-min L, -0.6, -0.2 --end-to-end –reorder. The restriction sites were obtained by scanning MboI restriction fragments across mouse genome (mm10). Specific configuration file (config-hicpro.txt) can be found at https://bitbucket.org/qzhu/wenqing-hichip/src/default/hicpro/config-hicpro.txt. Valid interactions pairs (named valid Pairs) were converted to a .hic file using hicpro2juicebox.sh script (utility tool of HiC-Pro). The generated .hic file contains interaction matrices at fragment and base pair resolutions. Interaction maps were visualized with Juicebox (Durand et al., 2016a). The HiCCUPS function of Juicer-tools 1.7.6 was used to call high-confidence loops based on a .hic file (Rao et al., 2014). We set -m 512 -r 5000,10000,25000 -f 0.2,0.2,0.2 -p 4,2,1 -k VC_SQRT -i 7,5,3 -d 20000,20000,50000 --ignore_sparsity -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y -t 0.02,1.5,1.75,2. This combination of settings finds loops at the 5-kb, 10-kb, and 25-kb resolutions using the interaction matrices at matched resolutions, and also applied the appropriate normalization step for interaction matrix (vanilla coverage square-root, VC SQRT). Loops at these resolutions were subsequently merged.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig  generated using macs2 pileup, following by bedGraphToBigWig; Peak  were called using MACS2

molecule: genomic DNA

organism: Mus musculus

source_name: Definitive erythroblast

growth_protocol: EryP was collected from peripheral blood of E10.5 mouse embryos in HBSS supplemented with 10% FBS and 0.25% EDTA. EryD was collected by mechanically dissociation of E13.5 whole fetal liver. All mouse embryos were obtained from C57BL/6 mouse. MEL cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2mM L-glutamine and Penicillin and Streptomycin. 2% DMSO in culture medium was used to induce MEL cells differentiation. Medium was changed on differentiation day 3.

extract_protocol:
HiChIP was performed as previously described (Mumbach et al 2016) using the Gata1 antibody (ab11852, Abcam). In brief, 15 million of either peripheral blood cells of E10.5 mouse embryos or single cells of E14.5 fetal liver were cross-linked with 1% v/v formaldehyde at room temperature for 10 minutes, and were quenched with 0.125 M Glycine for 5minutes. Crosslinked cells were lysed in cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40, 1x Roche protease inhibitors) and followed by 1 U/ul MboI (NEB) digestion at 37oC for 6 h, fill-in of overhangs with biotin-dATP (Thermo Fisher) at 37oC for 1.5 h, and ligation with 4 U/ul T4 DNA Ligase (NEB) at room temperature for 6 h. The nuclear pellet was sheared using a Covaris E220 with following parameters: Duty Factor = 5.0, Peak Power = 140, Cycle/Burst = 200, Time = 240 seconds. Chromatin extracts were immunoprecipitated with Gata1 antibodies overnight at 4oC, and then incubated with protein A Dynabeads (Invitrogen) for another 4 hours. ChIP complexes were eluted and cross-linking reversed by heating at 65oC overnight. DNA was extracted with DNA Clean and Concentrator columns (Zymo Research).
ATAC-seq was performed as described (Buenrostro et al., 2013) on FACS isolated EryP and EryD cells. 2.5 x 104 cells were used per sample. 2.5 l Tn5 Transposases (Illuminar) was used to make the transposition reaction. Libraries were generated using Ad1_noMX and Ad2.1-2.4 barcoded primers (Buenrostro et al., 2013) and were amplified for 6-9 total cycles. All libraries were sequenced on Illumina HiSeq2000 with 100 bp paired-end reads. HiChIP was performed as previously described (Mumbach et al., 2016) using the Gata1 antibody (ab11852, Abcam). In brief, 15 million of either peripheral blood cells of E10.5 mouse embryos or single cells of E14.5 fetal liver were cross-linked with 1% v/v formaldehyde at room temperature for 10 minutes, and were quenched with 0.125 M Glycine for 5minutes. Crosslinked cells were lysed in cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40, 1x Roche protease inhibitors) and followed by 1 U/l MboI (NEB) digestion at 37oC for 6 h, fill-in of overhangs with biotin-dATP (Thermo Fisher) at 37oC for 1.5 h, and ligation with 4 U/l T4 DNA Ligase (NEB) at room temperature for 6 h. The nuclear pellet was sheared using a Covaris E220 with following parameters: Duty Factor = 5.0, Peak Power = 140, Cycle/Burst = 200, Time = 240 seconds. Chromatin extracts were immunoprecipitated with Gata1 antibodies overnight at 4oC, and then incubated with protein A Dynabeads (Invitrogen) for another 4 hours. ChIP complexes were eluted and cross-linking reversed by heating at 65oC overnight. DNA was extracted with DNA Clean and Concentrator columns (Zymo Research).   For library preparation, Biotin labeled post-ChIP DNA was captured by 5 l Streptavidin C-1 beads (Thermo Fisher), and followed by Tn5 treatment. The amount of Tn5 used and the number of PCR cycles performed was based on the post-ChIP Qubit amounts, as previously described (Mumbach et al., 2016). HiChIP libraries were size-selected for 300-800bp fragments. All libraries were sequenced on the Illumina Nextseq 500 to an average depth of 200 million total reads.

tag: cell type

value: erythroblast

tag: developmental stage

tag: chip antibody


title: virus-infected M. restricta KCTC 27540

city: Seoul

country: South Korea

molecule: total RNA

tag: strain

value: virus-infected


title: CEP #6

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: spinal paraganglioma tumor tissue

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.28.4) in R. The detection p-value for each sample was computed. All samples had detection p values less than 0.005. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: spinal paraganglioma tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25).  Genomic DNA was extracted from these punches using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

tag: tissue

value: spinal paraganglioma tumor

tag: age at diagnosis

tag: gender

value: Male


title: CEP #10

description: spinal paraganglioma tumor tissue


title: CEP #1

description: spinal paraganglioma tumor tissue


title: CEP #3

description: spinal paraganglioma tumor tissue

value: Female


title: MDA_R20B_3

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

data_processing: R package ChAMP v2.9.9

source_name: taxol-resistant TNBC cells, Paclitaxel 20nM

label_protocol: Standard Illumina Protocol

extract_protocol: nor provided

tag: cell line

value: Triple-negative breast cancer (TNBC)


title: MDA_R20A_1


title: CEP #5

description: spinal paraganglioma tumor tissue


title: MDA_parental_4

source_name: parental TNBC cells, DMSO


title: CEP #2

description: spinal paraganglioma tumor tissue


title: MDA_parental_5


title: MDA_R20B_1


title: CEP #4

description: spinal paraganglioma tumor tissue


title: MDA_parental_3


title: CEP #8

description: spinal paraganglioma tumor tissue


title: MDA_R20C_3


title: MDA_R20C_4


title: CEP #9

description: spinal paraganglioma tumor tissue


title: CEP #11

description: spinal paraganglioma tumor tissue


title: MDA_R20A_3


title: ce_male_tail_rep2

city: Irvine

first: Ali

last: Mortazavi

address: 2300 Biological Sciences 3

department: Developmental and cell biology

institute: University of California, Irvine

description: PolyA RNA  unstranded, paired-end, read_length= 43 bp

data_processing:
Unstranded, paired-end 43 bp RNA-seq reads for each worm were mapped to the S. carpocapsae genome using Bowtie 1.0.0 with the following options: -X 1500 -a -m 200 --S -- seedlen 25 -n 2 --offrate 1 -p 64 -v 3  (Langmead et al. 2009). After Bowtie, gene expression was quantified with RSEM with the following options: rsem-calculate-expression -- bam -- paired-end. Gene expression for S. carpocapsae were performed as previously described (Lu et al. 2017) and reported in Transcripts Per Million (TPM). We used counts for differential gene expression analysis.
The Transcript per million (TPM) generated by rsem-calculate-expression for S. carpocapsae samples were normalized according to groups using the R package limma (Ritchie et al., 2015) because samples were collected, processed and sequenced in different batches.

organism: Caenorhabditis elegans

source_name: grown on lawn of Esherichia coli (op50)

growth_protocol: For S.carpocapse as described in Serra L, Chang DZ, Macchietto M, et al. Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq. Bio-protocol. 2018;8(4). doi:10.21769/BioProtoc.2729. For C.elegans as described in Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974;77(1):71-94. http://www.ncbi.nlm.nih.gov/pubmed/4366476.

extract_protocol:
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.

treatment_protocol: S. carpocapsae IJs were cultured with Xenorhabdus nematophila and collected at the IJ or young adult stage. C. elegans strain him-8 young adults were grown on Escherichia coli (op50) and collected at young adult stage. C.elegans strain N2 dauers were starved for 16 weeks at 25° C, confirmed phenotypically and collected.

tag: genotype

value: young adult

value: tail


title: MDA_R20C_2


title: MDA_R20A_2


title: MDA_R20B_2


title: ce_male_head_rep2

value: head


title: ce_male_head_rep3


title: ce_male_whole_rep3

value: whole body


title: ce_male_whole_rep2


title: ce_hermaphrodite_tail_rep3


title: ce_male_head_rep1


title: ce_hermaphrodite_tail_rep1


title: MDA_R20C_1


title: ce_male_tail_rep3


title: ce_male_whole_rep1


title: MDA_R20B_5


title: ce_hermaphrodite_tail_rep2


title: MDA_R20A_5


title: MDA_R20A_4


title: ce_hermaphrodite_head_rep1


title: ce_hermaphrodite_whole_rep2


title: ce_hermaphrodite_whole_rep3


title: CEP #7

description: spinal paraganglioma tumor tissue


title: ce_dauer_tail_rep3

source_name: grown on lawn of Esherichia coli (op50) and starved for 16 weeks

value: wildtype

value: dauer


title: ce_dauer_tail_rep2


title: ce_male_tail_rep1


title: ce_dauer_tail_rep1


title: ce_dauer_head_rep3


title: ce_hermaphrodite_head_rep3


title: ce_dauer_head_rep2


title: CEP #12

description: spinal paraganglioma tumor tissue


title: MDA_R20B_4


title: ce_dauer_whole_rep3


title: ce_dauer_head_rep1


title: ce_dauer_whole_rep1


title: MDA_R20C_5


title: ce_hermaphrodite_whole_rep1


title: ce_dauer_whole_rep2


title: ce_hermaphrodite_head_rep2


title: O4 treatment, replicate 2

type: RNA

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: gene expression data from myelinating cultures 24 DIV treated with O4

hyb_protocol: hybridized to Affymetrix Rat Gene 2.1 ST Arrays using manufacturer's protocols using Fluidics Station 450

scan_protocol: Gene Array Scanner 3000-7G

data_processing: Partek Genomics Suite (version 6.6), probeset level data were normalised using GCRMA normalisation and summarised to transcript cluster level using One-Step Tukey's Biweight method.

label: biotin

organism: Rattus norvegicus

source_name: myelinating cultures, 24 DIV

label_protocol: labelled with biotin using Ambion WT Expression Kit following the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol

growth_protocol: Neurospheres were generated from striata of P1 Sprague-Dawley rats by resuspending enzymatically dissociated cells in 20ml neurosphere media [DMEM/F12 (1:1, DMEM containing 4,500 mg/L glucose), supplemented with 0.105 % NaHCO3, 2 mM glutamine, 5,000 IU/ml penicillin, 5µg/ml streptomycin, 5.0mM HEPES, 0.0001% bovine serum albumin, (all from Invitrogen), 25 µg/ml insulin, 100 µg/ml apotransferrin, 60M putrescine, 20nM progesterone, and 30nM sodium selenite (all from Sigma)] and plating them into a 75 cm3 tissue culture flask. The culture was supplemented with 20ng/ml mouse submaxillary gland epidermal growth factor (R&D Systems) and maintained at 37ºC in a humidified atmosphere of 7% CO2/93% air. Every 2-3 days, 5 ml NSM and 4 µl EGF were added to the flask. Neurosphere-derived astrocytes (NsAs) were obtained by triturating neurospheres and plating them onto Poly-L lysine (PLL, 13g/ml, Sigma) -coated coverslips (13 mm diameter, VWR International, Leicestershire, UK) in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine (Sigma) until they formed confluent monolayer.      Myelinating spinal cord cultures were derived from E15.5 Sprague-Dawley (SD) embryos. Spinal cords were dissected out, cleared of meninges, minced with a scalpel blade and enzymatically dissociated with 2.5% trypsin (Invitrogen) and 1.33% collagenase (ICN Pharmaceuticals, UK). Enzymatic activity was stopped by adding 1 ml of a solution containing 0.52 mg/ml soybean trypsin inhibitor, 3.0 mg/ml bovine serum albumin, and 0.04 mg/ml DNase (Sigma). The tissue was then triturated, centrifuged and resuspended in plating medium (PM, 50% DMEM, 25% horse serum, 25% HBSS) and 150,000 cells per 100 µl plated on cover slips coated with a confluent monolayer of NsAs. Coverslips were placed in 35-mm Petri dishes (3 per dish) and left in the incubator to attach for 2 hours, after which 300 µl of PM and 500 µl of differentiation medium (DM) [DMEM (4,500 mg/ml glucose), 10 ng/ml biotin, 0.5% hormone mixture (1 mg/ml apotransferrin, 20 mM Putrescine, 4 μM progesterone, and 6 μM selenium; formulation based on Bottenstein and Sato, 197940), 50 nM hydrocortisone, and 0.1 μg/ml insulin (all reagents from Sigma) ] were added. Cultures were fed every 2 days by removing 500 µl of media and replacing it with fresh DM media, after 12 days insulin was removed from the DM used to feed the cultures.  The effect of O4 antibody in the presence or absence of serum on these in vitro myelinating cultures was investigated by adding to the culture media from day 24 for 24 hours in vitro.

extract_protocol: RNA was extracted using the Qiagen Rneasy Micro kit according to manufacturer's instructions

treatment_protocol: The in vitro myelinating cultures were either untreated or treated with 2% serum alone, IgM isotpye or O4 in the absence or presence of serum. Samples were collected at 24 hours from the untreated and treated myelinating cultures.

value: Sprague-Dawley

value: myelinating culture

tag: treatment


title: O4 treatment, replicate 1


title: O4 plus serum, replicate 1

description: gene expression data from myelinating cultures 24 DIV treated with O4 and serum

value: O4 plus serum


title: O4 plus serum, replicate 3


title: IgM isotyope Control, replicate 2

description: gene expression data from myelinating cultures 24 DIV treated with IgM

value: IgM


title: IgM isotyope Control, replicate 1


title: S_wt_12: somatotropinoma_wild-type_AIP_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from somatotropinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 5

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: miRNA QC tool (Affymetrix, version 1.0.33.0)

label_protocol: FlashTag Biotin HSR kit (Genisphere)

extract_protocol: RNeasy FFPE Kit (#73504, Qiagen N.V., Venlo, Netherlands)

tag: Sex

value: f

value: aryl hydrocarbon receptor interacting protein (wild-type)

value: somatotropinoma


title: S_wt_08: somatotropinoma_wild-type_AIP_rep4

description: Gene expression data from somatotropinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 4

scan_protocol: According to the Affymetrix expression protocol


title: S_wt_03: somatotropinoma_wild-type_AIP_rep1

description: Gene expression data from somatotropinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 1


title: O4 treatment, replicate 3


title: Control plus serum, replicate 3

description: gene expression data from myelinating cultures 24 DIV treated with 2% rabbit serumm

value: serum


title: Control, replicate 3

description: gene expression data from myelinating cultures 24 DIV untreated

value: Control


title: S_R271W_21: somatotropinoma_mutant_AIP_rep4

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (R271W), replicate 4

value: m


title: Control, replicate 1


title: O4 plus serum, replicate 2


title: S_R271W_13b: somatotropinoma_mutant_AIP_tech_rep6

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (R271W), technical replicate of rep6


title: S_R271W_13a: somatotropinoma_mutant_AIP_rep6

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (R271W), replicate 6


title: S_R271W_15: somatotropinoma_mutant_AIP_rep5

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (R271W), replicate 5


title: S_wt_07: somatotropinoma_wild-type_AIP_rep3

description: Gene expression data from somatotropinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 3


title: S_wt_04: somatotropinoma_wild-type_AIP_rep2

description: Gene expression data from somatotropinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 2


title: IgM isotyope Control, replicate 3


title: Control plus serum, replicate 1


title: Control, replicate 2


title: S_Q146S_18: somatotropinoma_mutant_AIP_rep2

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (Q146S), replicate 2


title: S_L115W_22: somatotropinoma_mutant_AIP_rep1

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (L115W), replicate 1


title: Control plus serum, replicate 2


title: S_R128H_24: somatotropinoma_mutant_AIP_rep3

description: Gene expression data from somatotropinoma expressing mutant aryl hydrocarbon receptor interacting protein (R128H), replicate 3


title: MDA_parental_1

value: Triple-negative breast cancer (TNBC)


title: P_wt_29: prolactinoma_wild-type_AIP_rep4

description: Gene expression data from prolactinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 4

value: prolactinoma


title: P_R56C_16: prolactinoma_mutant_AIP_rep2

description: Gene expression data from prolactinoma expressing mutant aryl hydrocarbon receptor interacting protein (R56C), replicate 2


title: P_wt_19: prolactinoma_wild-type_AIP_rep1

description: Gene expression data from prolactinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 1


title: Lyve1_LPS_HA_4

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Kim et al SOURCE file  07082020.xlsx
Lyve1 SS vs. LPS.xlsx

data_processing:
UTAP analysis (https://doi.org/10.1186/s12859-019-2728-2)
Demultiplexing
Low-quality trimmng
UMI counting
Normalization
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene above 5 reads number and every sample

source_name: Mouse brain

extract_protocol:
Half brain homogenization and antibody treatment for IP
Mars-seq (DOI: 10.1126/science.1247651)

treatment_protocol: 2.5mg/kg LPS injection

value: Brain

value: Lyve1+ macrophage

value: 12h post LPS i.p

tag: ip antibody

value: anti-HA (Merk, Cat#:H9658)


title: Lyve1_IgG_4

value: Steady state

value: anti-IgG (Merk, Cat#:PP100)


title: Lyve1_LPS_HA_3


title: Lyve1_IgG_6


title: Lyve1_LPS_IgG_2


title: Lyve1_LPS_IgG_1


title: Lyve1_LPS_HA_2


title: P_wt_31: prolactinoma_wild-type_AIP_rep5

description: Gene expression data from prolactinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 5


title: P_R271W_14b: prolactinoma_mutant_AIP_tech_rep3

description: Gene expression data from prolactinoma expressing mutant aryl hydrocarbon receptor interacting protein (R271W), technical replicate of replicate 3


title: P_wt_20: prolactinoma_wild-type_AIP_rep2

description: Gene expression data from prolactinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 2


title: P_F290F_17: prolactinoma_mutant_AIP_rep1

description: Gene expression data from prolactinoma expressing mutant aryl hydrocarbon receptor interacting protein (F290F), replicate 1


title: Lyve1_LPS_IgG_3


title: Lyve1_IgG_3


title: Lyve1_LPS_IgG_4


title: Lyve1_LPS_HA_1


title: P_R271W_14a: prolactinoma_mutant_AIP_rep3

description: Gene expression data from prolactinoma expressing mutant aryl hydrocarbon receptor interacting protein (R271W), replicate 3


title: Lyve1_HA_6


title: Lyve1_HA_5


title: Lyve1_HA_4


title: Lyve1_HA_3


title: Lyve1_IgG_5


title: P_wt_28: prolactinoma_wild-type_AIP_rep3

description: Gene expression data from prolactinoma expressing wild-type aryl hydrocarbon receptor interacting protein, replicate 3


title: Lyve1_HA_1


title: MDA_parental_2


title: Lyve1_IgG_2


title: Sall1_LPS_IgG_2

description: Kim et al SOURCE file  07082020.xlsx

value: Sall1+ microglia


title: Sall1_LPS_IgG_1

description: Kim et al SOURCE file  07082020.xlsx


title: Lyve1_IgG_1


title: Sall1_LPS_HA_2

description: Kim et al SOURCE file  07082020.xlsx


title: Sall1_IgG_5

description:
Kim et al SOURCE file  07082020.xlsx
Sall1 vs. Lyve1.xlsx


title: Sall1_LPS_HA_1

description: Kim et al SOURCE file  07082020.xlsx


title: Sall1_IgG_4


title: Sall1_IgG_1


title: Sall1_HA_2


title: Sall1_HA_4


title: Sall1_IgG_2


title: Sall1_HA_3


title: Sall1_IgG_3


title: Sall1_HA_6


title: Sall1_IgG_6


title: Lyve1_HA_2


title: Sall1_HA_5


title: WTMB21_A

city: Kaohsiung

first: Daniel

middle: Esguerra

last: Gracilla

state: Taiwan

address: Institution of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, TAIWAN

department: Biomedical Science

country: Taiwan

institute: National Sun Yat Sen University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CAL27_Wild Type

growth_protocol: DMEM, 1% PS 10%FBS with G418 selction drug

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

treatment_protocol: Stable Cell lines GFP fused proteins

value: oral adenosquamous carcinoma cell line

tag: genotype/variation

value: Constitutive Wild type form expression


title: EmpVec_B

value: Contains Empty Vector


title: EmpVec_A


title: Q311E_A

value: Constitutive Q311E form expression


title: Sall1_HA_1


title: Q311E_B


title: WTMB21_B


title: PSPPH_2469_cycle2_Rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A  (GCF_000012205.01)
Supplementary_files_format_and_content: xls file was summary of position weight matrix for all motifs; txt file was genome wide target sites result of TFs.

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary TableX and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary TableX, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer.

treatment_protocol: 1 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce each TF expression at 16 °C for 16 h.

value: wide type

tag: growth phase

value: exponential phase


title: PSPPH_2469_cycle3_Rep1

organism: Pseudomonas savastanoi pv. phaseolicola 1448A


title: PSPPH_2469_cycle1_Rep1


title: PSPPH_2448_cycle4_Rep1


title: PSPPH_2432_cycle4_Rep1


title: PSPPH_2448_cycle2_Rep1


title: PSPPH_2448_cycle3_Rep1


title: PSPPH_2432_cycle3_Rep1


title: PSPPH_2448_cycle1_Rep1


title: PSPPH_2432_cycle2_Rep1


title: PSPPH_2338_cycle4_Rep1


title: PSPPH_2338_cycle1_Rep1


title: PSPPH_2328_cycle3_Rep1


title: PSPPH_2338_cycle2_Rep1


title: PSPPH_2328_cycle4_Rep1


title: PSPPH_2315_cycle4_Rep1


title: PSPPH_2338_cycle3_Rep1


title: PSPPH_2328_cycle2_Rep1


title: PSPPH_2315_cycle1_Rep1


title: PSPPH_2432_cycle1_Rep1


title: PSPPH_2315_cycle2_Rep1


title: PSPPH_2315_cycle3_Rep1


title: PSPPH_1737_cycle3_Rep1


title: PSPPH_1737_cycle2_Rep1


title: PSPPH_1737_cycle4_Rep1


title: PSPPH_1737_cycle1_Rep1


title: PSPPH_1244_cycle2_Rep1


title: PSPPH_1244_cycle3_Rep1


title: PSPPH_1244_cycle4_Rep1


title: PSPPH_1233_cycle4_Rep1


title: PSPPH_1244_cycle1_Rep1


title: PSPPH_1233_cycle2_Rep1


title: PSPPH_1233_cycle3_Rep1


title: PSPPH_2328_cycle1_Rep1


title: PSPPH_1233_cycle1_Rep1


title: PSPPH_1195_cycle4_Rep1


title: PSPPH_1195_cycle2_Rep1


title: PSPPH_1187_cycle1_Rep1


title: PSPPH_1187_cycle2_Rep1


title: PSPPH_1195_cycle1_Rep1


title: PSPPH_0676_cycle4_Rep1


title: PSPPH_1187_cycle3_Rep1


title: PSPPH_0676_cycle2_Rep1


title: PSPPH_0676_cycle3_Rep1


title: PSPPH_0676_cycle1_Rep1


title: PSPPH_1187_cycle4_Rep1


title: PSPPH_0589_cycle3_Rep1


title: sh-JAML

city: Jinan

first: Yi

last: Fu

address: West Wenhua Road

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: podocytes

growth_protocol: The conditionally immortalized murine podocyte cell line (MPC) was cultured under growth permissive conditions at 33 C in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 20 U/ml mouse recombinant interferon-γ , and 100 U/ml penicillin plus 0.1 mg/ml streptomycin. To induce differentiation, podocytes were maintained in non-permissive conditions at 37 C without IFN-γ for 7 days and used for the experiments

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: High glucose (D-glucose at a final concentration of  40 mmol/L in culture medium)

value: MPC

tag: induction

value: sh-JAML


title: sh-NC

value: sh-NC


title: sh-JAML/HG

value: D-glucose at a final concentration of  40 mmol/L


title: PSPPH_0589_cycle4_Rep1


title: PSPPH_0589_cycle1_Rep1


title: sh-NC/HG


title: PSPPH_0190_cycle3_Rep1


title: PSPPH_0190_cycle2_Rep1


title: Liver CD45- cells derived from mice fed a standard diet for 36 weeks

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 3.1.0 mkfastq
Demultiplexed data was then processed using the Cell Ranger 3.1.0 count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) for each sample

source_name: Liver

extract_protocol: All Methods listed in Remmerie et al.  Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in MAFLD.. Immunity. 2020.

tag: diet

value: standard diet

value: CD45- cells

tag: time point

tag: platform

value: 10x Genomics – v3

tag: number of cells


title: Liver CD45- cells derived from mice fed a western diet for 36 weeks

value: western diet

tag: cell type


title: PSPPH_1195_cycle3_Rep1


title: Lin- iAdFASNKO

city: Worcester

first: Michael

last: Czech

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: Lin- cells have -2 tag in barcode

data_processing:
10X Genomics Cell Ranger Software v.3.1.0 was used to de-multiplex the paired-end and index fastq files.  It then  aligned, quality filtered, and aggregated the Lin- and Lin+ samples (for WT and KO separately).
10X Genomics Cell Ranger Software v.3.1.0 was used to perform k-means clustering.
10X Genomics Loupe Cell Browser v.3.1.1 was used for visualization and to aid manual sub-clustering.
Seurat v 3.0 was to produce violin plots of expression levels.
clusterProfiler 3.14.0  determined Gene Ontology fpr DE genes.
Genome_build: refdata-cellranger-mm10-3.0.0.tar.gz
Supplementary_files_format_and_content: 10X Genomics Cell Ranger v.3.1.0 produced the barcodes, features, and matrix files found in its   outs/filtered_feature_bc_matrix directory.  It also produced the cloupe files (typically called cloupe.cloupe   in the outs/ directory). If you strip the prefix from the barcodes, features, and matrix files, and place the 3 files   in a directory then they can be read in using Seurat's Read10X function.  10X Genomics Loupe Browser will  display and allow interactive analysis of the cloupe files.

source_name: iWAT SVF

extract_protocol:
Fat pads were cut and minced in digestion buffer and incubated in a 37°C water bath for 45 min. The digested tissue was passed through a 100-μm-pore-size cell strainer and centrifuged at 600g for 10 min. The pelleted cells were collected as the SVF, and red blood cells were lysed by incubation with red blood cell lysis buffer for 5 min. The SVF was centrifuged again, and the cell pellet was resuspended in 1 ml of PBS. This final cell suspension solution was passed through a 40um cell strainer to discard debris and get single cells for Drop-Seq application.
Single cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X Genomics) according to the manufacturer’s protocol.
The SVF of iWAT from control and iAdFASNKO mice were isolated and subjected to single-cell RNA-seq analysis. To better resolve the relatively low numbers of immune cells present in the SVF, the cells were isolated and fractionated into lineage marker-positive (Lin+), mostly immune cells, and all other stromal cells (Lin-) using magnetic bead cell sorting. Thus, four different libraries were prepared from an estimated approximately 6,000 cells per condition (Control and iAdFASNKO, Lin+ and Lin-), and were subjected to sequencing using Illumina NovaSeq 6000.

value: iWAT SVF

tag: immune lineage

value: lineage negative

value: iAdFASNKO


title: Lin+ iAdFASNKO

description: Lin+ cells have -1 tag in barcode

value: lineage positive


title: PSPPH_0190_cycle1_Rep1


title: cycle0_FL-0726

source_name: no protein

value: no protein


title: Lin+ control

description: Lin+ cells have -1 tag in barcode

value: control


title: cycle0_FL-0724


title: Lin- control

description: Lin- cells have -2 tag in barcode


title: PSPPH_0589_cycle2_Rep1


title: PSPPH_0190_cycle4_Rep1


title: cycle0_FL-0683


title: E12

city: Los Angeles

last: Xu

address: 2250 Alcazar Street, CSA 106

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

data_processing:
raw data analysis using 10XGenomics Cell Ranger Software
matrix files are imported to R studio (seurat packages) for further analysis.

source_name: E12.5 Tbx18-Cre; YFP/+

extract_protocol:
TrypLE digestion
10X Genomics Chromium v2 kit
single cell RNA-seq

tag: tissue

value: heart

tag: developmental stage

value: Tbx18-Cre; YFP/+


title: cycle0_FL-0716


title: C11_2

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
CITE-Seq files:ADTs: C11_2_ADT_S2_L001
Hashing files: HTOs: C11_2_HTO_S2_L001

data_processing:
Data were analyzed using Cell Ranger™ v3.0.1 pipelines which is available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

source_name: CITEseq/Multiplex Blood and heart

extract_protocol:
8 to 10-week-old C57BL6/J mice were subjected to myocardial infarction induced by permanent ligation of the left descendant coronary artery, or to sham surgery (i.e. mice underwent the exact same surgical procedure without coronary artery ligation). Cells were isolated from blood or ischemic heart of C57BL6/J mice in the following conditions: no surgery control (n=3), sham surgery day 1 (n=3), sham surgery day 3 (n=3), myocardial infarction day 1 (n=5), myocardial infarction day 3 (n=5). Venous blood was collected in EDTA containing collection tubes by retroorbital puncture using heparinized hematocrit capillaries and kept on ice with agitation until further processing. Red blood cells were removed by performing erythrocyte lysis in ACK buffer for 5’ on ice twice. Ischemic cardiac tissue from mice with 1 and 3 days old infarcts was mechanically dissociated using a 12-Well Tissue Disaggregator plate (ScienceWare, Bel-Art Products).  Cells were labeled with hashtag antibodies 1 to 7 (TotalSeqA hashtag antibodies, Biolegend, at a final concentration of 2µg/ml), Fixable Viability Staining e780 (1:1000), B220-PE-Cy7 (clone RA3-6B2), NK1.1 PE-Cy7 (clone PK136), Ter119-PE-Cy7 (clone Ter119), CD11b-PercpCy5.5 (M1/70), Ly6G-PacificBlue (1A8), SiglecF-Biotin (clone EA798). At this step, CITE-seq antibodies against Ly6G (1.25µg/ml) and CD11b (1.25µg/ml) were also included in the labeling mix to avoid epitopes being inaccessible in the second CITE-seq labeling. Viable Ter119-B220-NK1.1-CD11b+ cells were sorted using a FACS Aria III (BD Biosciences) with a 100µm nozzle. The final content of Ly6G+ neutrophils and Ly6G- non-neutrophils in the sorted cells was adjusted to approximately 1:1 proportions. After sorting, cells were washed once and cells from each sample were pooled together (the volume of each sample used to pool cells was adjusted based on the number of sorted events, to ensure an approximately equal proportion of cells from each sample in the final single-cell RNA-seq data). Pooled cells were labeled with TotalSeq-A antibodies (Biolegend) directed against CD64 (5µg/ml), CD54/ICAM1 (5µg/ml), CD49d (5µg/ml), anti-biotin (2.5µg/ml), CD115 (2.5µg/ml), CD62L (1.67µg/ml), Ly6C (1µg/ml), IA-IE (1.25µg/ml), MSR1(5µg/ml), Fcer1a (5µg/ml), CCR3 (5µg/ml) and CXCR4 (5µg/ml), washed twice in PBS/0.04% BSA.  Hashtags/Sample list: Hashtag-1: blood cells, no operation control; Hashtag-2: blood cells, day 1 post sham surgery; Hashtag-3: blood cells, day 3 post sham surgery; hashtag-4: blood cells, day 1 post myocardial infarction surgery; hashtag-5: blood cells, day 3 post myocardial infarction surgery; hashtag-6: heart cells, day 1 post myocardial infarction surgery; hashtag-7: heart cells, day 1 post myocardial infarction surgery.
Cells were loaded in the 10X Genomics Chromium at a concentration of 1700 cells/µl with the aim of recovering 15,000 cells. Libraries were generated with the Chromium Single Cell 3’ Reagents Kit v3 Chemistry. Libraries were prepared with Chromium Single Cell 3’ Reagents Kit v3 Chemistry and prepared for CITE-Seq/Hashing according to the manual until the cDNA amplification step in which 1 μl (0.2 μM) ADT PCR additive primer to capture Antibody-derived tags (ADTs) and 1 μl (0.1 μM) HTO PCR additive primer to capture Hashtag oligos (HTOs) were added. After cDNA amplification 60 μl (0.6x) SPRI beads (Beckman Coulter) were added to separate the supernatant fraction that contains the ADT/HTO-derived cDNAs (<180bp) and the bead fraction that contains the mRNA-derived cDNAs (>300bp). The mRNA-derived cDNAs (bead fraction) were processed following the standard 10x Genomics protocol. The ADT/HTO-derived cDNAs (supernatant fraction) were purified twice with 2x SPRI. After the two purifications half amount of the eluted cDNAs were amplified for ADTs and half for hashtags. In the same reactions, the ADTs were indexed using TruSeq Small RNA primers and the hashtags using modified TruSeq DNA primers. The libraries were purified once more with 1.6x SPRI (160 μl). The detailed protocol including the oligo sequences can be accessed here: https://cite-seq.com/protocol.
Chromium single cell 3´v3 (10XGenomics)

tag: strain

tag: condition

value: Myocardial infarction

tag: sample type

value: mixed sample of blood and heart


title: H10

description:
CITE-Seq files: ADTs: H10_ADTs_S3_L002_R1_001.fastq.gz
Hashing files: HTOs: H10_HTOs_S4_L002_R1_001.fastq.gz

data_processing:
Data were analyzed using Cell Ranger™ v3.0.1 pipelines which is available in 10x Genomics website.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: h5: Contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: *tsv, *mtx: Gene barcode matrices and feature barcode matrix.

source_name: CITEseq/Multiplexed Day1-3-5

extract_protocol:
Cells were isolated from the heart of mice at 1 (n=5), 3 (n=5) and 5 days post-MI (n=3) as described above. Fc-Block was performed (10µg/ml purified rat anti-mouse CD16/CD32, Biolegend TruStain FcX anti-mouse), after which cells were stained with Fixable Viability Staining e780 (1:1000) and CD11b (M1/70) antibodies: CD11b-BV510 (Day 1 cells, 1:300, BD Biosciences), CD11b-Percp-Cy5.5 (Day 3 cells, 1:300, BD Biosciences) or CD11b-PE (Day 5 cells, 1:300, BD Biosciences) for 25 minutes at 4°C in PBS containing 1% FCS. Cells were washed once, resuspended in 1ml of PBS-1%FCS, pooled and centrifuged once more (8’, 350rcf). Viable/CD45.2 (intravenous)-negative cells labeled with CD11b-BV510, CD11b-Percp-Cy5.5 and CD11b-PE were separately sorted using a FACS Aria III (BD Biosciences). After sorting, cells were washed once in 1ml of PBS-1%FCS (8’, 350rcf). Cells were then separately labeled with hashtag antibodies (Biolegend TotalSeq-A antibodies, Day 1: Hashtag 1, Day 3: Hashtag 2, Day 5: Hashtag 3) and CITE-Seq antibodies (Biolegend TotalSeq-A against mouse Ly6C, Ly6G, CD64, F4/80, CD11c, MSR1, IA/IE, TIM4, CX3CR1, and CCR2). Labeling was performed for 30 minutes at 4°C in 150µl PBS/1%FCS containing 1.5µg of each antibody. Cells were washed with 2ml PBS/1%FCS once (8’, 350rcf), resuspended in PBS supplemented with 0.04% BSA, pooled and centrifuged again (8’, 350rcf). The cells were resuspended in 150µl PBS/0.04% BSA, filtered through a 40µm cell strainer and counted before loading in the 10X Genomics Chromium.
Cells were loaded in the 10X Genomics Chromium at concentrations recommended by the manufacturer. Libraries were prepared with Chromium Single Cell 3’ Reagents Kit v3 Chemistry and prepared for CITE-Seq/Hashing according to the manual until the cDNA amplification step in which 1 μl (0.2 μM) ADT PCR additive primer to capture Antibody-derived tags (ADTs) and 1 μl (0.1 μM) HTO PCR additive primer to capture Hashtag oligos (HTOs) were added. After cDNA amplification 60 μl (0.6x) SPRI beads (Beckman Coulter) were added to separate the supernatant fraction that contains the ADT/HTO-derived cDNAs (<180bp) and the bead fraction that contains the mRNA-derived cDNAs (>300bp). The mRNA-derived cDNAs (bead fraction) were processed following the standard 10x Genomics protocol. The ADT/HTO-derived cDNAs (supernatant fraction) were purified twice with 2x SPRI. After the two purifications half amount of the eluted cDNAs were amplified for ADTs and half for hashtags. In the same reactions, the ADTs were indexed using TruSeq Small RNA primers and the hashtags using modified TruSeq DNA primers. The libraries were purified once more with 1.6x SPRI (160 μl). The detailed protocol including the oligo sequences can be accessed here: https://cite-seq.com/protocol

treatment_protocol: Mice were anesthetized with isoflurane (4.0%), received an intravenous injection of 5µg of anti-CD45.2-APC (clone 104, ThermoFisher Scientific) in 100µl of PBS, and left under isoflurane anesthesia for 5-10 minutes before being killed by cervical dislocation. Induction of myocardial infarction was macroscopically confirmed and mice received an intracardiac perfusion of PBS and the hearts were collected. The right ventricle was removed as well as the viable myocardium right above the ligature site, so that the infarcted area, its border zone and the adjacent viable myocardium were processed. A similar part of the left ventricle was processed for non-infarcted hearts. The excised hearts were rinsed in 4°C RPMI and gently massaged to expel excess blood, minced with surgery scissors and digested in RPMI containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) for 1 hour at 37°C in a Thermomixer (Eppendorf) with shaking set at 1000rpm. The resulting cell suspension was filtered through a 70µm cell strainer, and incompletely digested pieces of myocardium were gently dissociated using a syringe plunger. Cells were then washed in 50ml 4°C PBS containing 1% Fetal Bovine Serum (centrifugation 8 minutes at 300rcf).

value: Male

value: CD11b+ myeloid cells from heart

value: mixed sample (non-demultiplexed)


title: M12 (mutant)

source_name: E12.5 Tbx18-Cre; Prmt1 fl/fl;YFP/+

tag: genotype

value: Tbx18-Cre; Prmt1 fl/fl;YFP/+


title: cycle0_FL-0095


title: F9

source_name: day 7

extract_protocol:
Cardiac cells were collected at different time points after myocardial infarction (no infarct/Day 0: n=5; Day 1: n=5; Day 3: n=5, Day 5: n=5; Day 7: n=3) as described above. Cell suspensions were incubated for 10 minutes at 4°C with 10μg/ml Fc Block (purified rat anti-mouse CD16/CD32, Biolegend TruStain FcX anti-mouse) to block non-specific binding of antibodies to Fc Receptors and then incubated at 4°C for 30 minutes with anti-CD45-PE (1:300, Thermofisher Scientific, Clone 30-F11), anti-Ly6G-V450 (1:300, BD Biosciences, Clone 1A8) and Fixable Viability Staining e780 (1:1000, Thermofisher Scientific). All staining and washing steps were performed in PBS containing 1% FCS, except the last wash and sorting that were made in PBS supplemented with 0.04% BSA (Sigma Aldrich, SRE0036). Right before sorting, cells were passed through a 40µm cell strainer. In this experiment, a neutrophil reduction step was performed to increase the proportion of monocyte/macrophages at early time points. Viable CD45.2 (intravenous)-negative/CD45+ cells were sorted using a FACS-Aria III (BD Biosciences) with a 100µm nozzle, counted and loaded into the 10X Genomics Chromium.
Cells were loaded in the 10X Genomics Chromium at concentrations recommended by the manufacturer. Libraries were prepared with Chromium Single Cell 3’ Reagents Kit v2 Chemistry.

tag: Sex

value: CD45+ total leukocytes from heart

value: Day 7


title: cycle0_FL-0682


title: F11

source_name: day 1

value: Day 1


title: cycle0_FL-0086


title: cycle0_FL-0088


title: cycle0_FL-0096


title: cycle0_FL-0081


title: cycle0_FL-0082


title: F8

source_name: steady state heart

value: Steady state


title: cycle0_FL-0077


title: cycle0_FL-0069


title: cycle0_FL-0072


title: cycle0_FL-0080


title: ODE_Virulent_rep2

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
The strand-specific reads were mapped on to Bovine genome (bosTau7; Btau_4.6.1; GCF_000003205.5) using Tophat2 (-g 1 --library-type fr-firststrand). The samples with respective replicates were analyzed further for differential gene expression by three different tools, baySeq, DESeq2 (fitType ="local") and CuffDiff2 with default parameters unless mentioned specifically. The count values for DESeq2 and baySeq were calculated from BAM files using HTSeq-count tool.  The transcriptome quality plots were generated by cummeRbund package (v2.14.0).
Genome_build: Bos taurus4.6.1 (bosTau7)

organism: Bos taurus

growth_protocol: Bovine BL3, TBL3, BL20, TBL20  B lymphocytes, and Ode macrophages were cultured in RPMI 1640 medium supplemented with 2 mM of L-glutamine (Lonza, catalogue number 12-702F) and 10 mM Hepes (Lonza, catalogue number 17-737E), 10 % heat-inactivated FBS (Gibco, catalogue number 10082147), 100 units/ml of Penicillin and 100 μg/ml of streptomycin (Lonza, catalogue number 17-602E) and 10mM beta-mercaptoethanol (Sigma-Aldrich, catalogue number M6250) for BL3/TBL3 and BL20/TBL20. The virulent (Vir) hyper-disseminating Ode cell line was used at low passage (53-71), while its attenuated (Att) poorly disseminating vaccine counterpart corresponded to passages 309-317. The OCI-LY19 cell line (DSMZ, ACC 528) was cultured in Minimum Essential Medium Eagle - Alpha Modification (Gibco, catalog number 12000063) supplemented with 2.2g/L of sodium bicarbonate (Thermofisher Scientific, catalog number 25080094), 20% FBS, 10 mM Hepes and 100 units/ml of Penicillin and 100 μg/ml of streptomycin. The RI-1 cell line (DSMZ, ACC 585) was cultured in RPMI1640 and supplemented with 10% FBS, 100 units/ml of Penicillin and 100 μg/ml of streptomycin and 10 mM Hepes. All cell lines were incubated at 37°C with 5% CO2 and were regularly tested for mycoplasma contamination.

extract_protocol:
Cells were seeded in 3 biological replicates at a density of 2.5x105 cell/ml. RNA extraction was performed using the PureLink RNA Mini Kit (Life technologies, catalogue number 12183018A) following the manufacturer’s instructions. Briefly, cells were pelleted, lysed and homogenized using a 21-gauge needle, then 70% ethanol was added to cell lysates and samples loaded onto spin cartridges to bind RNA. After 3 washes RNA was eluted in RNase-free water. The quality of extracted RNA was verified using a Bioanalyzer 2100 and quantification carried using Qubit (Invitrogen, catalogue number Q10210).
Strand-specific RNA-sequencing (ssRNA-seq) libraries were prepared using the Illumina Truseq Stranded mRNA Sample Preparation Kit (Illumina, catalogue number RS-122-2101) following the manufacturer’s instructions. Briefly, 1ug of total RNA was used to purify mRNA using poly-T oligo-attached magnetic beads. mRNA was then fragmented and cDNA was synthesized using SuperScript III reverse transcriptase (Thermofisher, catalogue number 18080044), followed by adenylation of the 3’-end, barcoding and adapter ligation. The adapter ligated cDNA fragments were then enriched and cleaned with Agencourt Ampure XP beads (Agencourt, catalogue number A63880). Libraries validation was conducted using the 1000 DNA kit on 2100 Bioanalyzer (Agilent Technologies, catalogue number 5067-1504) and quantified using qubit (Thermofisher, catalogue number Q32850). ssRNA libraries were sequenced on Illumina Hiseq2000 and Hiseq4000.

value: Ode macrophages


title: ODE_Attenuated_TGFb_rep3


title: ODE_Virulent_rep1


title: ODE_Attenuated_TGFb_rep2


title: cycle0_FL-0719


title: cycle0_FL-0067


title: cycle0_FL-0066


title: ODE_Attenuated_TGFb_rep1


title: cycle0_FL-0065


title: ODE_Attenuated_rep3


title: ODE_Attenuated_rep2


title: cycle0_FL-0049


title: cycle0_FL-0051


title: cycle0_FL-0045


title: ODE_Virulent_rep3


title: ODE_Attenuated_rep1


title: cycle0_FL-0040


title: PSPPH_1160_cycle2_Rep1

value: wide type

value: exponential phase


title: PSPPH_1160_cycle1_Rep1


title: PSPPH_0857_cycle2_Rep2


title: PSPPH_0857_cycle3_Rep2


title: cycle0_FL-0037

value: no protein


title: cycle0_FL-0038


title: PSPPH_0857_cycle1_Rep2


title: PSPPH_0778_cycle4_Rep1


title: cycle0_FL-0035


title: cycle0_FL-0032


title: cycle0_FL-0033


title: PSPPH_0778_cycle3_Rep1


title: cycle0_FL-0031


title: PSPPH_0778_cycle1_Rep1


title: cycle0_FL-0030


title: PSPPH_0642_cycle4_Rep1


title: cycle0_FL-0027


title: PSPPH_0642_cycle2_Rep1


title: PSPPH_0642_cycle3_Rep1


title: cycle0_FL-0028


title: cycle0_FL-0026


title: cycle0_FL-0043


title: PSPPH_0857_cycle4_Rep2


title: PSPPH_0642_cycle1_Rep1


title: cycle0_FL-0024


title: PSPPH_0263_cycle4_Rep1


title: PSPPH_0263_cycle3_Rep1


title: cycle0_FL-0021


title: cycle0_FL-0025


title: cycle0_FL-0019


title: PSPPH_0263_cycle1_Rep1


title: cycle0_FL-0176


title: cycle0_FL-0175


title: PSPPH_0778_cycle2_Rep1


title: cycle0_FL-0174


title: cycle0_FL-0018


title: cycle0_FL-0010


title: cycle0_FL-0015


title: cycle0_FL-0169


title: cycle0_FL-0008


title: cycle0_FL-0168


title: cycle0_FL-0167


title: cycle0_FL-0005


title: cycle0_FL-0004


title: cycle0_FL-0003


title: PSPPH_0263_cycle2_Rep1


title: cycle0_FL-0023


title: cycle0_FL-0160


title: cycle0_FL-0154


title: cycle0_FL-0165


title: cycle0_FL-0148


title: PSPPH_3645_cycle4_Rep1

description:
processed data file: 5TFs_6motifs_pwm_summary.xls
processed data file: 5TFs_PWM_genome_wide_target_sites_results.txt

data_processing:
Library strategy: HT-SELEX
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A (GCF_000012205.1, ASM1220v1)
Supplementary_files_format_and_content: all_motifs_pwm_summary.xls: Excel file includes summary of position weight matrix for all motifs.
Supplementary_files_format_and_content: all_TF_PWM_genome_wide_target_sites_filtered_results.txt: Tab-delimited text file includes genome-wide target sites result of TFs.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system. The ligand libraries were produced by PCR amplification using the primers in Supplementary TableX and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq Xten sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul Promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary TableX, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq Xten sequencer.

value: wild type


title: cycle0_FL-0146


title: PSPPH_3645_cycle3_Rep1


title: cycle0_FL-0001


title: PSPPH_3645_cycle1_Rep1


title: cycle0_FL-0141


title: cycle0_FL-0145


title: PSPPH_3244_cycle3_Rep1


title: PSPPH_3244_cycle4_Rep1


title: cycle0_FL-0139


title: cycle0_FL-0007


title: cycle0_FL-0138


title: PSPPH_3244_cycle2_Rep1


title: PSPPH_2004_cycle4_Rep1


title: cycle0_FL-0137


title: PSPPH_3244_cycle1_Rep1


title: cycle0_FL-0166


title: cycle0_FL-0131


title: PSPPH_2004_cycle3_Rep1


title: cycle0_FL-0164


title: PSPPH_2004_cycle2_Rep1


title: cycle0_FL-0129


title: PSPPH_2004_cycle1_Rep1


title: cycle0_FL-0124


title: cycle0_FL-0115


title: PSPPH_3645_cycle2_Rep1


title: PSPPH_0857_cycle3_Rep1


title: PSPPH_0857_cycle4_Rep1


title: cycle0_FL-0109


title: PSPPH_0857_cycle1_Rep1


title: PSPPH_0736_cycle4_Rep1


title: cycle0_FL-0133


title: PSPPH_5193_cycle4_Rep1


title: PSPPH_5193_cycle3_Rep1


title: PSPPH_5193_cycle2_Rep1


title: PSPPH_5193_cycle1_Rep1


title: PSPPH_0736_cycle2_Rep1


title: PSPPH_0736_cycle1_Rep1


title: NC_NgCtrl1_cycle3_Rep1

source_name: Negative Control


title: PSPPH_5057_cycle2_Rep1


title: NC_NgCtrl1_cycle2_Rep1


title: NC_NgCtrl1_cycle1_Rep1


title: PSPPH_5057_cycle1_Rep1


title: phyB_5_R

city: Seattle

first: Jennifer

last: Nemhauser

state: WA

address: department of biology, university of washington, box 351800

department: Biology

institute: University of Washington

data_processing:
Base calling was performed by bcl2fastq v 2.17.1.14.
A Python library (clipper.py, https://github.com/mfcovington/clipper) was used to trim off the first 8 nucleotides of each read to remove potential mismatches to the reference sequence caused by annealing of a random hexamer required for library synthesis.
Trimmomatic v0.36 (http://www.usadellab.org/cms/?page=trimmomatic) was used to remove adapter sequences and trim or filter reads based on quality The parameters used for Trimmomatic were ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Preprocessed reads were mapped to the Brassica rapa v2.5 genomic reference sequence (http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V2.0/V2.5/Chr/BrapaV2.5_Chr.fa.gz) using bowtie2.
Read counts for each gene in the gene annotation file (http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V2.0/V2.5/Chr/BrapaV2.5_Chr.gene.gff.gz) were calculated using htseq-count (with the -s yes parameter to enforce strand-specific alignment) from the HTSeq Python library (https://academic.oup.com/bioinformatics/article/31/2/166/2366196; http://htseq.readthedocs.io/en/master/index.html).
Genome_build: BrapaV2.5 from BRAD (http://brassicadb.org/brad/)
Supplementary_files_format_and_content: comma-delimited text file, rows are genes, columns are samples, values are transcript read counts.

organism: Brassica rapa

source_name: BrphyB_3 mutant_recovery_leaf tissue

growth_protocol: The B. rapa wild-type R-o-18 and BrphyB mutants were originally from the John Innes Center’s RevGenUK resource. Seeds were planted directly into our standard soil mix of 1:1 Sunshine Mix #4 (SunGro Horticulture):vermiculite. Plants were grown in 2.6 liter square pots (McConkey Grower Products; Sumner, WA, USA) and bottom-watered daily in long day conditions (16 h light, 8 h dark, ~115 µmol.m-2.s-1 light intensity) in a Percival E-30B growth chamber (https://www.percival-scientific.com/) set to 20°C.

extract_protocol:
Tissue disruption, mRNA isolation, library synthesis, sequencing, and fastq processing were conducted by Amaryllis Nucleics (Oakland, CA). Leaf tissue was disrupted with Zirconia/Silica beads for 1 minute in a MiniBeadbeater-96 (BioSpec Products, Inc.) while frozen. After adding 500 µL of Lysis/Binding Buffer to each sample and vortexing until homogeneous, samples were run on the MiniBeadbeater-96 for an additional minute. Following tissue disruption samples were centrifuged at 16,000 x g for 10 minutes at 20 ºC. For each sample, a 50 µL aliquot of the supernatant was added to 50 µL of NEB RNA binding buffer and mRNA isolated as per the NEBNext® Poly(A) mRNA Magnetic Isolation Module manual.
RNA-seq libraries were prepared by using the Full Transcript mode YourSeq Dual (FT & 3’-DGE) RNAseq Library Kit (Amaryllis Nucleics). A Bioanalyzer 2100 (Agilent, High Sensitivity DNA Kit) was used for library quality control, to determine average library size, and together with concentration data from a Qubit 2.0 Fluorometer (Life Technologies, dsDNA High Sensitivity Assay Kit) to determine individual library molarity and pooled library molarity. Pooled libraries were sequenced on a NextSeq 500 (Illumina, High Output v2 75 cycle kit) to yield single-read 80 bp reads.

treatment_protocol: Two developmentally matched leaves from each wild-type and BrphyB-3 plant were tagged that corresponded to the first and second true leaves. Samples were collected at 5 ZT using a standard whole punch (28 mm2 of leaf tissue) with symmetrical harvest for chlorophyll assay, chloroplast measurements and transcriptome analysis. Tissue from 3 plants was combined to make one biological replicate. At 3 weeks of age the “Pre” sample was collected from the first leaf while the second one was covered with tinfoil. 24 hours later the “24hr” sample were harvested from the uncovered leaf, the same leaf that provided the “Pre” sample. Then, 48 hours later the tinfoil was removed from the covered leaf and the “dark” samples were similarly collected. Finally, 24 hours later the “recovery” samples were collected from this same leaf. Samples were immediately frozen in liquid nitrogen.

value: BrphyB_3 mutant

value: recovery

tag: replicate

value: leaf tissue


title: PSPPH_4858_cycle4_Rep1


title: phyB_4_R


title: phyB_3_R


title: PSPPH_5204_cycle4_Rep1


title: PSPPH_0857_cycle2_Rep1


title: phyB_4_D

source_name: BrphyB_3 mutant_dark_leaf tissue

value: dark


title: phyB_5_D


title: PSPPH_4858_cycle3_Rep1


title: cycle0_FL-0098


title: PSPPH_5204_cycle3_Rep1


title: phyB_3_D


title: PSPPH_0736_cycle3_Rep1


title: NC_NgCtrl1_cycle4_Rep1


title: PSPPH_5057_cycle4_Rep1


title: PSPPH_5204_cycle2_Rep1


title: PSPPH_5057_cycle3_Rep1


title: PhyB_5_24

source_name: BrphyB_3 mutant_24hr_leaf tissue


title: PSPPH_4828_cycle4_Rep1


title: PSPPH_5204_cycle1_Rep1


title: PhyB_3_24


title: PhyB_4_24


title: PSPPH_5171_cycle4_Rep1


title: phyB_4_P

source_name: BrphyB_3 mutant_pre_leaf tissue

value: pre


title: phyB_3_P


title: PSPPH_4828_cycle3_Rep1


title: WT_6_R

source_name: wild type_recovery_leaf tissue


title: PSPPH_5171_cycle3_Rep1


title: WT_5_R


title: PSPPH_5171_cycle2_Rep1


title: WT_4_R


title: PSPPH_4828_cycle2_Rep1


title: PSPPH_4828_cycle1_Rep1


title: WT_3_R


title: WT_6_D

source_name: wild type_dark_leaf tissue


title: PSPPH_4858_cycle2_Rep1


title: PSPPH_5171_cycle1_Rep1


title: PSPPH_4858_cycle1_Rep1


title: PSPPH_4730_cycle4_Rep1


title: WT_4_D


title: PSPPH_5145_cycle4_Rep1


title: phyB_5_P


title: WT_3_D


title: WT_5_D


title: PSPPH_4730_cycle2_Rep1


title: PSPPH_5145_cycle2_Rep1


title: WT_5_24

source_name: wild type_24hr_leaf tissue


title: WT_6_24


title: PSPPH_5145_cycle3_Rep1


title: PSPPH_4730_cycle3_Rep1


title: PSPPH_4730_cycle1_Rep1


title: PSPPH_5145_cycle1_Rep1


title: WT_4_24


title: PSPPH_3800_cycle4_Rep1


title: WT_3_24


title: PSPPH_4612_cycle4_Rep1


title: WT_6_P

source_name: wild type_pre_leaf tissue


title: PSPPH_3800_cycle3_Rep1


title: PSPPH_3800_cycle2_Rep1


title: PSPPH_4612_cycle2_Rep1


title: PSPPH_4612_cycle3_Rep1


title: WT_5_P


title: PSPPH_3800_cycle1_Rep1


title: PSPPH_4612_cycle1_Rep1


title: WT_3_P


title: PSPPH_3779_cycle3_Rep1


title: PSPPH_4419_cycle4_Rep1


title: G39-12: mouse GSCs, Hx D, biological rep3

city: Tokyo

first: Oltea

last: Sampetrean

address: 35 Shinanomachi Shinjuku-ku

department: Division of Gene Regulation

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array. GeneChips were washed and stained in the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 3000 7G (Thermo Fisher Scientific)

data_processing: Data were processed using the Transcriptome Analysis Console (TAC) 4.0.1 Software (Thermo Fisher Scientific)

source_name: murine GSCs treated with 3 mM doranidazole under hypoxic conditions for 24 h

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, Affymetrix). Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Cells were maintained in serum-free Dulbecco’s modified Eagles medium (DMEM)–F12 supplemented with recombinant human epidermal growth factor and basic fibroblast growth factor at 20 ng/ml, heparan sulfate at 200 ng/ml, and B27 supplement without vitamin A.

extract_protocol: Total RNA was extracted by RNeasy kit (QIAGEN) according to manufacturer's protocol.

treatment_protocol: Cells were treated with PBS (control) or 3 mM doranidazole under normoxic conditions (21%O2) or hypoxic (1%O2) conditions for 24 h.

value: Murine glioma stem cells (GSCs)

value: Ink4a/Arf-null NSCs overexpressing H-Rasv12


title: PSPPH_3779_cycle2_Rep1


title: ∆lsd1 N5555 bisulfite-seq rep1

city: Eugene

first: Eric

middle: U

last: Selker

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy (Afgan et al., 2018) were used to map mRNA-sequencing reads (intron size < 1kb) (Dobin et al, 2012) against the corrected N. crassa OR74A (NC12) genome (Galazka et al., 2016), count the number of reads per gene (Dobin et al., 2012) and determine differentially expressed genes with DESeq2 (Love et al, 2014).
Bisulfite-seq processing: The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping. BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged. The average 5mC level was determined for 25bp step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/). The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp.
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 replicates each of wild type (Klocko et al. 2016; GSE82222) and ∆lsd1 and the output file from DESeq2 (Love et al., 2014) with pairwise comparisons of 2 biological replicates from each genotype.
Supplementary_files_format_and_content: Bisulfite-seq processed data files are .igv files displaying the % methylation over 25bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region.  Values in between 0 and 1.0 represent partial methylation of a region.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Cultures were grown in Vogel's medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32˚C. Genomic DNA was isolated using a protocol modified from (Pomraning et al, 2009). Genomic DNA (1µg) was treated with bisulfite and libraries were prepared for sequencing using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370; NEB) and EpiMark Bisulfite Conversion Kit (E3318; NEB). The library was purified with Agencourt AMPure XP beads (Beckman Coulter), quantified using a Qubit HS Assay (Life Technologies), visualized on the Fragment AnalyzerTM (Advanced Analytical), and sequenced on a Illumina HiSeq 4000

value: mat a delta_lsd1::hph

value: germinated conidia


title: PSPPH_3779_cycle4_Rep1


title: PSPPH_4419_cycle3_Rep1


title: PSPPH_4419_cycle1_Rep1


title: PSPPH_3779_cycle1_Rep1


title: G39-10: mouse GSCs, Hx D, biological rep1


title: WT_4_P


title: PSPPH_3654_cycle4_Rep1


title: PSPPH_3654_cycle3_Rep1


title: PSPPH_4209_cycle3_Rep1


title: G39-11: mouse GSCs, Hx D, biological rep2


title: G39-9: mouse GSCs, Hx P, biological rep3

source_name: murine GSCs treated with PBS under hypoxic conditions for 24 h


title: PSPPH_4209_cycle2_Rep1


title: PSPPH_3654_cycle2_Rep1


title: PSPPH_4419_cycle2_Rep1


title: PSPPH_3654_cycle1_Rep1


title: G39-7: mouse GSCs, Hx P, biological rep1


title: G39-4: mouse GSCs, Nx D, biological rep1

source_name: murine GSCs treated with 3 mM doranidazole under normoxic conditions for 24 h


title: Input for ssDRIP of human induced pluripotent stem cells (hiPSCs)

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Library strategy: ssDRIP-Seq
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 software.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were calculated and corrected by HMMcopy (version 1.25.0) in each 0.5-Mb bin size

extract_protocol:
genomic DNA were isolated using DNeasy Blood & Tissue Kit (Qiagen).
Libraries were then constructed with the Next DNA Library Prep Reagent Sets (NEB) following the manufacturer’s instructions

value: induced pluripotent stem cells (hiPSCs)

value: WT

tag: passage


title: G39-5: mouse GSCs, Nx D, biological rep2


title: G39-8: mouse GSCs, Hx P, biological rep2


title: G39-6: mouse GSCs, Nx D, biological rep3


title: Input for ssDRIP of human neural stem cells (hNSCs)

source_name: human neural stem cells (hNSCs)

value: neural stem cells (hNSCs)


title: PSPPH_4209_cycle1_Rep1

tag: growth phase


title: PSPPH_3547_cycle4_Rep1


title: Input for ssDRIP of human vascular smooth muscle cells (hVSMCs)

value: vascular smooth muscle cells (hVSMCs)


title: PSPPH_4209_cycle4_Rep1

value: wide type


title: Input for ssDRIP of human mesenchymal stem cells (hMSCs)

source_name: human mesenchymal stem cells (hMSCs)

value: mesenchymal stem cells (hMSCs)


title: G39-2: mouse GSCs, Nx P, biological rep2

source_name: murine GSCs treated with PBS under normoxic conditions for 24 h


title: PSPPH_4062_cycle4_Rep2

value: exponential phase


title: PSPPH_3547_cycle3_Rep1


title: PSPPH_4062_cycle3_Rep2


title: PSPPH_3547_cycle2_Rep1


title: PSPPH_4062_cycle2_Rep2


title: Input for ssDRIP of human vascular endothelial cells (hVECs)

value: vascular endothelial cells (hVECs)


title: G39-1: mouse GSCs, Nx P, biological rep1


title: PSPPH_3547_cycle1_Rep1


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T08

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T08

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Experimental procedures of the cold-acclimation study have been previously published (PMID: 26147760). In this study samples of seven overweight male individuals with type 2 diabetes (age 59 ± 6 years, BMI 29.9 ± 3.1 kg/m2; average ± SD) were included.

extract_protocol: Total RNA was isolated using Trizol and further purified using Rneasy columns. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Subjects underwent a 10-day cold acclimation intervention. Prior to the cold acclimation, a muscle biopsy was taken from the vastus lateralis muscle following an overnight fast. During the 10-day cold acclimation protocol, subjects were exposed to an environmental temperature of 14–15 °C for 10 consecutive days: 2 h on day 1, 4 h on day 2, and 6 h on days 3 through 10. On day 10, after an overnight fast, a skeletal muscle biopsy was taken. See Hanssen et al. (Nat Med. 2015;21(8):863-5. doi: 10.1038/nm.3891, PMID: 26147760) for more details.

tag: subject id

tag: disease

value: type 2 diabete

value: male


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T07

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T07

tag: time point


title: PSPPH_4062_cycle1_Rep2


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T04

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T04


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T08

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T08


title: PSPPH_3297_cycle4_Rep2


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T04

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T04


title: PSPPH_4020_cycle4_Rep1


title: PSPPH_3297_cycle3_Rep2


title: G39-3: mouse GSCs, Nx P, biological rep3


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T07

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T07


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T03

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T03


title: BMDC SIP-H3K4me3 4

first: Pranitha

last: Vangala

address: 55 Lake Avenue North

institute: University of Massachussets Medical School

data_processing:
Library strategy: SPRITE
SPRITE barcodes were identified by parsing the first DNA tag sequence from the beginning of Read 1 (DPM) and the remainder of the tags were parsed from Read 2. We identified these tag sequences corresponding to the DPM, Odd, Even, and Terminal tags that were added to these samples. The tags and their sequences were identified by software available at: https://github.com/GuttmanLab/sprite-pipeline/wiki/1.-Barcode-Identification. The configuration files required for this software are available on the series record.  We aligned each read to the appropriate reference genome (mm10) using Bowtie2 (v2.3.1). We trimmed the 11 base pair tag sequence (DPM) from Read 1 using the --trim5 11 parameter and used a local alignment search (--local).  We filtered the alignments for low quality reads, multimappers, and repetitive sequences. First, we removed all alignments with a MAPQ score less than 10 or 30. Second, we removed all reads that had >2 mismatches to the reference genome.
To define SPRITE clusters, all reads that have the same barcode sequence were grouped into a single cluster. To remove possible PCR duplicates, all reads starting at the same genomic position with identical barcodes were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments. When multiple positions are listed, these regions are in physical contact with each other. If only one position is listed, either that fragment exists on its own as a singleton, or the other constituent pieces were not sequenced.

source_name: BMDC

growth_protocol: Mouse dendritic cells were derived from bone marrow harvested from 6-8 week old female C57BL/6 mice. Bone marrow was then dissociated into single cells and filtered through a 70um cell strainer. The cells were then incubated with the red blood cell lysis buffer for 5 minutes. To differentiate bone marrow to dendritic cells, bone marrow cells were plated at 200,000 cells/mL in untreated tissue culture plates. These cells were supplemented with media on day 2 and day 7. On day 5 cells were harvested and resuspended in fresh media. On day 8 all the floating cells were collected as mouse bone-marrow-derived dendritic cells. The media used for culturing and differentiating contains RPMI (Gibco) supplemented with 10% heat-inactivated FBS (Gibco), β-mercaptoethanol (50uM, Gibco), MEM non-essential amino acids (1X, Gibco), sodium pyruvate (1mM, Gibco), and GM-CSF (20 ng/ml; Miltenyi).

extract_protocol: Cells were crosslinked with 3%FA-DSG and then lysed with nuclei isolated. DNA was then lightly sonicated and DNAse digested to an average size of approximately 150-1000 bp in length. Crosslinked protein-DNA complexes were isolated on NHS beads, DNA ends were repaired, dA-tailed to generate a protruding 3’ A-base for ligation of barcodes, and were then split-pool tagged with a series of barcodes over multiple rounds of split-and-pool tagging. After split-and-pool tagging, crosslinks were reversed, the DNA was isolated, was amplified 8-12 cycles using standard Illumina library prep (single index), and purified using SPRI beads. Libraries were sequenced on the NextSeq 500 following the manufacturer's protocols.

treatment_protocol: 100ng/mL of LPS for 0, 4 or 24 hours

value: mouse bone marrow derived dendritic cells

tag: antibody

tag: treatment

value: LPS


title: BMDC SIP-H3K4me3 3

tag: cell type


title: PSPPH_3297_cycle2_Rep2


title: BMDC SIP-H3K4me3 2


title: Input for ssDRIP of human embryonic stem cells (hESC)

source_name: human embryonic stem cells (hESC)

value: embryonic stem cells (hESC)


title: PSPPH_4020_cycle2_Rep1


title: PSPPH_4020_cycle3_Rep1


title: PSPPH_3297_cycle1_Rep2


title: BMDC SIP-H3K4me3 1


title: mESC SIP-H3K4me3

source_name: mESC

growth_protocol: V6.5 mESCs, DGCR8 knockout mESCs, and Dicer knockout mESCs were cultured in Dulbecco’s Modified Eagle’s Medium (Thermo Scientific) supplemented with HEPES pH 7.0, 15% fetal bovine serum (FBS), 1000 U/ml leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM l-glutamine, penicillin and streptomycin, and 0.11 mM β-mercaptoethanol.

value: mouse embryonic stem cells

value: untreated


title: PSPPH_3294_cycle4_Rep1


title: PSPPH_4020_cycle1_Rep1


title: PSPPH_3911_cycle4_Rep1


title: PSPPH_3294_cycle3_Rep1


title: PSPPH_3294_cycle2_Rep1


title: PSPPH_3911_cycle2_Rep1


title: PSPPH_3911_cycle3_Rep1


title: PSPPH_3294_cycle1_Rep1


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T06

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T06


title: PSPPH_3911_cycle1_Rep1


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T06

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T06


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T05

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T05


title: PSPPH_3257_cycle3_Rep1


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T01

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T01


title: muscly biopsy, overweight T2DM male, before cold acclimation, subject T03

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T03


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T01

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T01


title: PSPPH_3611_cycle4_Rep1


title: Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 3

data_processing:
FastQC v0.11.9 is used to check the quality of the samples
Sequenced reads were then mapped to mm10 transcriptome using HiSat2 v2.2.0 with default parameters and --max-intronlen 1000000
The mapping files were converted into bam files using samtools v1.10 with parameters -l 9
Reads were counted using FeatureCounts v2.0.0 with parameters -s 0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output FeatureCounts, only column 1 and 7) for each sample

source_name: Liver

tag: diet

value: western diet

value: 24 weeks


title: Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 2


title: Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 4


title: Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 6


title: Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 1


title: PSPPH_3257_cycle2_Rep1


title: Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 5


title: PSPPH_3257_cycle4_Rep1


title: PSPPH_3611_cycle2_Rep1


title: PSPPH_3611_cycle3_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject BE50

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject BE50

growth_protocol: Experimental procedures of the 12 week combined exercise training intervention study have been previously published (PMID: 20028948)  Eighteen healthy middle-aged male subjects (mean age 59.0 ± 0.8, mean BMI 29.7 ± 0.8 kg/m2; average ± SD) participated in this study.

treatment_protocol: Eighteen healthy middle-aged male subjects performed 12 weeks of combined exercise training. Combined exercise training consisted of 2 endurance exercise sessions and 1 resistance exercise session per week. See Meex et al. (Diabetes. 2010;59(3):572-9. doi: 10.2337/db09-1322 , PMID:  20028948) for more details.

value: healthy

value: after training intervention period


title: PSPPH_3257_cycle1_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject HM67

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject HM67

value: before training intervention period


title: muscly biopsy, overweight T2DM male, after 10 day cold acclimation, subject T05

source_name: biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, after 10 day cold acclimation intervention period, subject T05


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject BE50

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject BE50


title: moKCs derived from mice fed a western diet for 24 weeks, 5


title: PSPPH_3220_cycle4_Rep1


title: moKCs derived from mice fed a western diet for 24 weeks, 3


title: moKCs derived from mice fed a western diet for 24 weeks, 2


title: PSPPH_3220_cycle3_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject RS59

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject RS59


title: PSPPH_3220_cycle2_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject PP58

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject PP58


title: PSPPH_3577_cycle4_Rep1


title: PSPPH_3577_cycle2_Rep1


title: PSPPH_3577_cycle3_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject HM67

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject HM67


title: moKCs derived from mice fed a western diet for 24 weeks, 1


title: Kupffer cells derived from mice fed a western diet for 24 weeks, 6


title: PSPPH_3577_cycle1_Rep1


title: Kupffer cells derived from mice fed a western diet for 24 weeks, 5


title: PSPPH_3220_cycle1_Rep1


title: PSPPH_2022_cycle3_Rep1


title: PSPPH_2022_cycle4_Rep1


title: PSPPH_3611_cycle1_Rep1


title: PSPPH_3385_cycle3_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject RN38

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject RN38


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject RS59

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject RS59


title: moKCs derived from mice fed a western diet for 24 weeks, 4


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject DG51

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject DG51


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject PP58

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject PP58


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject RN38

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject RN38


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject RT1

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject RT1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject RT1

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject RT1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject DG51

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject DG51


title: PSPPH_2022_cycle2_Rep1


title: Kupffer cells derived from mice fed a western diet for 24 weeks, 4


title: PSPPH_3385_cycle2_Rep1


title: PSPPH_2022_cycle1_Rep1


title: PSPPH_3385_cycle1_Rep1


title: Kupffer cells derived from mice fed a western diet for 24 weeks, 2


title: Kupffer cells derived from mice fed a western diet for 24 weeks, 3


title: PSPPH_3385_cycle4_Rep1


title: PSPPH_3285_cycle4_Rep1


title: PSPPH_2004_cycle3_Rep2


title: PSPPH_3285_cycle3_Rep1


title: PSPPH_2004_cycle2_Rep2


title: PSPPH_3285_cycle1_Rep1


title: PSPPH_2004_cycle1_Rep2


title: PSPPH_3285_cycle2_Rep1


title: PSPPH_1651_cycle4_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject FL37

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject FL37


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject FL37

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject FL37


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject LC26

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject LC26


title: Kupffer cells derived from mice fed a standard diet for 24 weeks, 5

source_name: Liver

value: standard diet


title: PSPPH_3233_cycle4_Rep1

value: wide type


title: Kupffer cells derived from mice fed a standard diet for 24 weeks, 3


title: Kupffer cells derived from mice fed a standard diet for 24 weeks, 4


title: PSPPH_3233_cycle3_Rep1


title: PSPPH_2004_cycle4_Rep2


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject JS22

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject JS22


title: PSPPH_1651_cycle3_Rep1


title: Kupffer cells derived from mice fed a standard diet for 24 weeks, 2


title: PSPPH_3233_cycle2_Rep1


title: PSPPH_1651_cycle1_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject JS22

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject JS22


title: Kupffer cells derived from mice fed a standard diet for 24 weeks, 6


title: Kupffer cells derived from mice fed a standard diet for 24 weeks, 1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject LB36

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject LB36


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject GS25

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject GS25


title: PSPPH_1580_cycle4_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject LC26

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject LC26


title: Kupffer cells derived from mice fed a western diet for 12 weeks, 5

value: 12 weeks


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject LB36

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject LB36