title: HMW_SeV_cGAMP_rep1


title: Patient 24 week0

status: Public on Jul 01 2020

type: SRA

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ files were aligned to the GRCh37 human reference genome assembly using STAR. After alignment, we performed deduplication of the PCR duplicates using UMItools  to mark and after removing with samtools.
Gene-level read counts of the deduplicated bam files were obtained with featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
Whole blood samples were obtained at the start of the therapy with abatacept and at week 12. Blood was collected using RNA-stabilizing PaxGene tubes (PreAnalytiX, Switzerland), which preserve total RNA from the time of venipuncture. Total RNA was extracted using the PaxGene blood isolation kit (Qiagen). All samples had a RIN index > 7 and were included for RNA-seq analysis
RNA-seq libraries were performed using with the KAPA RNA HyperPrep Kit, with RiboErase (HMR) Globin (globin and rRNA depletion protocol) for Illumina sequencing platforms and with the addition of Unique Molecule Identifiers (UMIs). Sequencing was performed using the NovaSeq platform (Illumina) at average of 250 paired-end reads

tag: age

tag: gender

value: M

tag: treatment

value: control

tag: time

value: 0 week

tag: individual id

tag: tissue

value: Whole Blood


title: TTC_SC_233

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

data_processing:
Single-cell RNA sequence reads were evaluated by AfterQC. Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than.
The reads were mapped to the mouse genome(mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts. Gene expression was represented by CPM (tags per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

organism: Mus musculus

source_name: KO

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: Tail tendons from 4-wk-old wild-type or Mkx-/- mice  was minced into desired pieces and digested in 0.2% collagenase I diluted in low-glucose Dulbecco’s modified Eagle’s medium solution at 37°C for 2 hours. Then the cell suspension was filtered using 40 μm strainer to remove the incompletely digested clumps and adjusted to a concentration of 4×10^5 cells/ml.

tag: strain

value: tail tendon

tag: genotype

value: Mkx-/-


title: 8iH3_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 3, iCRT14 treated

city: Davis

first: Jack

last: Cazet

state: CA

address: 1 Shields Ave.

department: MCB

country: USA

institute: University of California, Davis

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: SE -threads 16  -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were then mapped to the Hydra vulgaris 2.0 genome and read counts were calculated using rsem (V. 1.2.31) using the following settings: --no-bam-output --bowtie2.
processed data files format and content: Read count matrix for gene models from the Hydra vulgaris 2.0 genome for all RNA-seq samples. Generated using rsem.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

molecule: polyA RNA

organism: Hydra vulgaris

source_name: Mid-Body Column Tissue

growth_protocol: Hydra vulgaris strain 105 polyps were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C and fed 1-2 times weekly with Artemia nauplii.

extract_protocol:
Total RNA was extracted from 30 regenerating tissue pieces using a standard trizol extraction. DNA was then removed using a DNaseI digest. A final purification step was then performed using a Zymogen RNA Clean & Concentrator kit.
KAPA Biosystems Stranded RNA-seq

treatment_protocol: For iCRT14 treatment, Hydra were pre-incubated in 5uM iCRT14 for two hours prior to amputation. Following amputation, iCRT14 treatment continued until tissue was collected for library preparation.

value: Mid-Body Column

tag: timepoint

value: 8 hours post amputation

tag: regeneration type

value: Head Regeneration

value: treated with  5uM iCRT14 for 10 hours


title: Patient 15 week12

value: F

value: abatacept

value: 12 weeks


title: HMW_rep2

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

data_processing:
Reads were aligned with BWA aln version 0.7.15 with -l 24
Alignments were demultiplexed with a custom script
UMIs were used to collapse reads and make a count table using a custom script
Genome_build: mm10

source_name: Bone marrow

growth_protocol: Bone marrow-derived dendritic cells (BMDCs) were generated from 6- to 8-week old female C57BL/6J mice. Bone marrow cells were collected from femora and tibiae and plated at 2X10^6 cells in 10-cm non-tissue culture treated petri dishes (Corning 351029) in 10 mL of complete RPMI medium containing RPMI-1640 medium (ThermoFisher Scientific 11875119) supplemented with 10% volume/volume (v/v) heat-inactivated fetal bovine serum (Seradigm 1400-500), L-glutamine (2 mM, Corning 25005CI), penicillin/streptomycin (100 U/mL/100g/mL, Lonza Biowhittaker 17602E), MEM non-essential amino acids (0.5X, Corning 25025CI), HEPES (10 mM, Corning 25-060-CI), sodium pyruvate (1 mM, Corning 25000CI), -mercaptoethanol (55M, Fisher Scientific 21-985-023), and recombinant murine GM-CSF (15 ng/mL; Peprotech 315-03-100g). Cells were fed at day 2, 5 and 7 with 3 mL of complete RPMI medium supplemented with GM-CSF as described.

extract_protocol:
Stimulated BMDCs were lysed with 30 µL of RLT buffer (Qiagen 79216) containing 1% (v/v) b-mercaptoethanol (VWR 97604-848). Total RNA was isolated using Dynabeads MyOne Silane (Thermo Fisher Scientific 37002D) and RLT buffer. Remaining genomic DNA was removed by on-bead DNase I (Thermo Fisher Scientific AM2239) treatment at 37oC for 20 min. After washing two times with 80% ethanol, total RNA was eluted from beads in nuclease-free water.
Total RNA samples obtained from 1x10^5 mouse BMDCs were reverse transcribed to cDNA by denaturing 10-µL RNA samples with 1 µL containing 2 pmoles of a custom RT primer at 72oC for 2 min and snap cooled on ice. A 9-µL RT mix containing 4 µL of 5X RT buffer, 1 µL of 10 mM dNTPs, 2 pmoles of template switching oligo, 0.5 µL Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific EP0753) and 3.5 µL of nuclease-free water was added to the denatured RNA samples, and plates were incubated at 42oC for 120 min. Double-stranded cDNA samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research D4013), and residual RT primers were removed using exonuclease I (New England Biolabs M0293).  Pooled full-length cDNA was amplified with 4-6 cycles of single-primer PCR with the Advantage 2 PCR Kit (Clontech 639206) in a 50-µL reaction volume. Amplified cDNAs were cleaned up with magnetic beads Agencourt AMPure XP (Beckman Coulter A63880) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851). 1 ng of cDNA was tagmented and amplified by PCR using Nextera XT Kit (Illumina). Libraries were gel purified using E-Gel EX Agarose Gels, 2% (ThermoFisher Scientific G402002), quantified with the Qubit dsDNA High Sensitivity Assay Kit, and sequenced on the NextSeq550 platform (Illumina).

treatment_protocol: 100,000 BMDCs were plated in 100 µL of medium in non-tissue culture treated 96-well flat bottom plates (ThermoFisher Scientific 260860) and incubated overnight prior to stimulations as indicated. Cells were stimulated with ligands and their combinations for 6 hours.

tag: cell type

value: Bone marrow derived dendritic cells

tag: ligands

value: HMW


title: TTC_SC_232


title: 12iH1_RNA: Head regeneration RNA-seq, 12 hours post amputation, replicate 1, iCRT14 treated

value: 12 hours post amputation

value: treated with  5uM iCRT14 for 14 hours


title: HMW_rep1


title: HMW_CpGB_rep3

value: HMW, CpGB


title: Patient 2 week12


title: 8iH2_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 2, iCRT14 treated


title: TTC_SC_230


title: TTC_SC_231


title: HMW_CpGB_rep2


title: 0iF3_RNA: Foot regeneration RNA-seq, 0 hours post amputation, replicate 3, iCRT14 treated

value: 0 hours post amputation

value: Foot Regeneration

value: treated with  5uM iCRT14 for 2 hours


title: Patient 2 week0

value: control

value: 0 week

value: Whole Blood


title: 8iH1_RNA: Head regeneration RNA-seq, 8 hours post amputation, replicate 1, iCRT14 treated

value: Mid-Body Column

value: 8 hours post amputation


title: TTC_SC_229

value: tail tendon

value: Mkx-/-


title: TTC_SC_228


title: HMW_CpGB_rep1


title: 0iF2_RNA: Foot regeneration RNA-seq, 0 hours post amputation, replicate 2, iCRT14 treated


title: HMW_cGAMP_rep3

value: HMW, 3',3'-cGAMP


title: HMW_rep3


title: TTC_SC_227

source_name: WT

value: WT


title: 0iH3_RNA: Head regeneration RNA-seq, 0 hours post amputation, replicate 3, iCRT14 treated

value: Head Regeneration


title: 0iF1_RNA: Foot regeneration RNA-seq, 0 hours post amputation, replicate 1, iCRT14 treated


title: HMW_cGAMP_rep2

value: Bone marrow derived dendritic cells


title: TTC_SC_226


title: Patient 15 week0

value: F


title: ipf_H03

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

data_processing:
base-calling done by Real-Time Analysis software v3.3.3
fastq file demultiplexing done by bcl2fastq2 Conversion Software v2.20.0.422
genome indexing, pseudoalignments, and counts quantification done by kallisto v0.45.0
Genome_build: GENCODE GRCh38 v27
Supplementary_files_format_and_content: CSV matrix containing all quantified counts

source_name: Human lung

extract_protocol:
Lung tissue was collected from all participants as either a surgical lung biopsy or at the time of lung transplantation. RNA and DNA were isolated from tissues using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA), according to manufacturer’ s protocol.
To establish RNA library, we used  TruSeq Stranded mRNA Library Prep Kit (San Diego, CA) accoridng to maunfacture`s protocol

value: lung tissue

tag: Sex

value: male

tag: diagnosis

value: ipf

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: UNKNOWN

value: GG

tag: sample type

value: explant

tag: psl

tag: is

value: NO

tag: batch

value: other

tag: lane

tag: plate

tag: institution

value: LTRC


title: Patient 1 week12

tag: age

tag: gender

tag: treatment

value: abatacept

tag: time

value: 12 weeks

tag: individual id

tag: tissue

value: Whole Blood


title: 0iH2_RNA: Head regeneration RNA-seq, 0 hours post amputation, replicate 2, iCRT14 treated

tag: strain

value: Mid-Body Column

tag: timepoint

value: 0 hours post amputation

tag: regeneration type

value: treated with  5uM iCRT14 for 2 hours


title: HMW_cGAMP_rep1

tag: cell type

value: Bone marrow derived dendritic cells

tag: ligands

value: HMW, 3',3'-cGAMP


title: TTC_SC_225

value: tail tendon

tag: genotype

value: WT


title: 0iH1_RNA: Head regeneration RNA-seq, 0 hours post amputation, replicate 1, iCRT14 treated

value: Head Regeneration

value: treated with 5uM iCRT14 for 2 hours


title: ipf_1176

value: lung tissue

tag: Sex

value: female

tag: diagnosis

value: ipf

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

tag: sample type

value: biopsy

tag: psl

value: UNKNOWN

tag: is


title: HMW_cGAMP_CpGB_rep3

value: HMW, 3',3'-cGAMP, CpGB


title: ipf_1172

tag: age

value: no

value: NO

tag: batch

tag: lane

tag: plate

tag: institution

value: LTRC


title: TTC_SC_224

tag: strain

tag: tissue


title: 12F2_RNA: Foot regeneration RNA-seq, 12 hours post amputation, replicate 2

value: Mid-Body Column

tag: timepoint

value: 12 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: Untreated


title: TTC_SC_222

value: tail tendon

tag: genotype

value: WT


title: Patient 1 week0

tag: gender

value: F

value: control

tag: time

value: 0 week

tag: individual id

value: Whole Blood


title: Ctrl_rep3

tag: cell type

value: Bone marrow derived dendritic cells

tag: ligands

value: Ctrl


title: TTC_SC_221


title: 12H3_RNA: Head regeneration RNA-seq, 12 hours post amputation, replicate 3

value: Head Regeneration


title: ipf_1168

value: lung tissue

tag: Sex

value: female

tag: diagnosis

value: ipf

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: explant

tag: psl

value: UNKNOWN

tag: is

value: UCSF


title: HMW_cGAMP_CpGB_rep1

value: HMW, 3',3'-cGAMP, CpGB


title: ipf_1169

value: male

tag: age

value: GT

value: NO

tag: batch

tag: lane

tag: plate

tag: institution


title: ipf_1164

tag: tissue


title: 12H2_RNA: Head regeneration RNA-seq, 12 hours post amputation, replicate 2

tag: strain

value: Mid-Body Column

tag: timepoint

value: 12 hours post amputation

tag: regeneration type

tag: treatment

value: Untreated


title: Ctrl_rep1

tag: cell type

value: Bone marrow derived dendritic cells

tag: ligands

value: Ctrl


title: ipf_1181

value: lung tissue

tag: Sex

tag: diagnosis

value: biopsy

value: LTRC


title: TTC_SC_219

value: tail tendon

tag: genotype

value: WT


title: 12H1_RNA: Head regeneration RNA-seq, 12 hours post amputation, replicate 1

value: Head Regeneration


title: ipf_1130

value: ipf

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: explant

tag: psl

value: UNKNOWN

value: VU


title: 12F3_RNA: Foot regeneration RNA-seq, 12 hours post amputation, replicate 3

value: Foot Regeneration


title: HMW_cGAMP_CpGB_rep2

value: HMW, 3',3'-cGAMP, CpGB


title: TTC_SC_218

tag: age


title: ipf_1170

value: male

value: GT

tag: is

value: NO

tag: batch

tag: lane

value: UCSF


title: CpGB_rep3

value: Bone marrow derived dendritic cells

value: CpGB


title: ipf_1125

tag: tissue

value: lung tissue

value: female

value: GG

tag: plate

tag: institution


title: TTC_SC_217

tag: strain

value: tail tendon

value: WT


title: control_1113

value: control

value: no


title: Biofilm cells_Treated_rep4

city: Jefferson

first: Kidon

last: Sung

state: AR

address: 3900 NCTR Road

institute: National Center for Toxicological Research

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic version 0.39 (leading and tailing threshold: 32, minimum length remains: 50 bps).
The remained high-quality reads were fed to Bowtie2 for the mapping against P. aeruginosa PAO1 reference genome NC_002516.2 released by NCBI. Default parameters of Bowtie2 were applied.
Then, the reads were mapped to Pseudomonas aeruginosa PAO1, complete genome (NCBI Reference Sequence: NC_002516.2) using bowtie2 with default parameters.
After the algined reads were sorted and the duplicates were marked, the raw read counts were calculated using htseq-count version 0.11.2 with PATRIC annotation 208964.12.
Transcripts per million (TPM) was measured by Kallisto (v0.46.0)
Genome_build: NC_002516.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa biofilm cells

growth_protocol: Overnight-grown P. aeruginosa PAO1 strain was inoculated into a fresh tryptic soy broth (TSB) (Thermo Fisher Scientific, Waltham, MA) and grown at 37oC for 7 hr. The bacterial culture was centrifuged at 10,000 rpm at 4oC for 10 min and washed three times with PBS. Then the pellet was resuspended with TSB and used for inoculation in a CDC biofilm reactor.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s procedure. RNA quantity and integrity was analyzed using a NanoDrop 2000/2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples with an Ribosomal Integrity Number (RIN) value greater than 9.0 were considered acceptable in the RNA sequencing.
RNA sequencing libraries were prepared with a ScriptSeq Complete Kit from Illumina (San Diego, CA) and validated with the Agilent Bioanalyzer 2100. The library from each sample was sequenced on Illumina NextSeq 550 sequencer (San Diego, CA) with SE-75.

treatment_protocol: 1.3 × 10^7 CFU/ml of P. aeruginosa PAO1 cells were inoculated in a CDC biofilm bioreactor (BioSurface Technologies, Bozeman, MT) containing control (without antibiotic-impregnation) or clindamycin/rifampicin-impregnated (CR-IC, Integra LifeSciences, Plainsboro NJ) catheters. The culture was stirred at 150 rpm at 37oC for 6 days and the fresh media was continuously flowed through the reactor at a flow rate of 15 ml/min.

tag: growth condition

value: Biofilm cells

tag: treated

value: Treated


title: Biofilm cells_Treated_rep3


title: CpGB_rep2

tag: cell type

tag: ligands


title: TTC_SC_223


title: TTC_SC_216


title: CpGB_rep1


title: 12F1_RNA: Foot regeneration RNA-seq, 12 hours post amputation, replicate 1

value: Mid-Body Column

tag: timepoint

value: 12 hours post amputation

tag: regeneration type

value: Foot Regeneration

tag: treatment

value: Untreated


title: Ctrl_rep2

value: Ctrl


title: cGAMP_rep3


title: control_1112

tag: Sex

tag: diagnosis

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: explant

value: UNKNOWN

value: NO

value: UCSF


title: Biofilm cells_Treated_rep2


title: TTC_SC_215

tag: genotype

tag: age


title: Biofilm cells_Treated_rep1


title: control_1111

tag: tissue

value: lung tissue

value: female

value: GG

tag: psl

tag: is

tag: batch

tag: lane


title: TTC_SC_214

tag: strain

value: tail tendon

value: WT


title: cGAMP_rep2

tag: cell type

value: Bone marrow derived dendritic cells


title: TTC_SC_220


title: Planktonic cells_Treated_rep4

source_name: Pseudomonas aeruginosa planktonic cells

tag: growth condition

value: Planktonic cells

tag: treated

value: Treated


title: cGAMP_rep1

tag: ligands


title: control_1102

value: control

tag: plate

tag: institution


title: control_1109

tag: Sex

tag: diagnosis


title: Planktonic cells_Treated_rep3


title: TTC_SC_212


title: cGAMP_CpGB_rep3

value: 3',3'-cGAMP, CpGB


title: control_1097

value: male

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

tag: sample type


title: TTC_SC_213

tag: genotype

tag: age


title: TTC_SC_211

tag: tissue


title: control_1096

value: explant

tag: psl

tag: is


title: cGAMP_CpGB_rep2


title: cGAMP_CpGB_rep1


title: Planktonic cells_Treated_rep2


title: Biofilm cells_Control_rep4

value: Biofilm cells

value: Control


title: Planktonic cells_Treated_rep1


title: ZScG_2

library_source: genomic

data_processing:
Sequences were aligned using bowtie2 version 2.2.9 with -X 2000
Peaks were called with MACS2 version 1.4 with -q .01 –nolambda
Peaks were merged with bedtools merge version 2.26
Reads were counted using the featureCounts() function from Rsubread in R
Genome_build: mm10

molecule: genomic DNA

source_name: Mouse bone marrow

extract_protocol:
To extract nuclei 50,000 mouse BMDCs were lysed in lysis buffer containing 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630
Extracted nuclei is processed for tagmentation by adding 2.5 µL transposase in 25 µL of TD buffer and incubating the mixture at 37oC for 30 min using the Nextera DNA library prepare kit (Illumina FC-121-1030). Tagmented genomic DNA was purified using DNA clean and concentrator-25 columns (Zymo research D4033). Sequencing libraries were generated using the following forward (5’-aatgatacggcgaccaccgagatctacactcgtcggcagcgtcagatgtg-3’) and barcoded reverse (5’- caagcagaagacggcatacgagat[8-bp barcode]gtctcgtgggctcggagatgt-3’) primers, and by performing 12 cycles of amplification with the Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs M0494) using the following cycling conditions: 1 cycle of 72oC for 5 min, 1 cycle of 98oC for 30 sec, 12 cycles of 98oC for 10 sec, 63oC for 30 sec, 72oC for 1 min, hold at 4oC. Libraries were purified using DNA clean and concentrator-25 columns (Zymo research D4033) to remove remaining primers, and amplicon size distributions measured using high sensitivity D5000 screentape (Agilent Technologies 5067-5592). Libraries were then quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and sequenced on the NextSeq550 platform (Illumina) using the NextSeq 500/550 high output kit v2 and following sequencing conditions: 42 cycles of Read 1,  8 cycles of Index 1, 42 cycles of Read 2.

treatment_protocol: 2.5X10^6 BMDCs were plated in2.5 mL of medium in non-tissue culture treated 6cm plate and incubated overnight prior to ligand stimulations as indicated.

value: Zymosan depleted, SeV_3',3'-cGAMP


title: TTC_SC_209


title: Biofilm cells_Control_rep2


title: ZScG_1


title: ZS_2

value: Zymosan depleted, SeV


title: control_1092

value: lung tissue

value: female

value: UNKNOWN

value: NO

tag: batch

tag: lane

value: UCSF


title: ipf_1074

value: ipf

value: GG


title: Biofilm cells_Control_rep1

tag: strain


title: TTC_SC_207

value: tail tendon

value: WT


title: control_1089

value: control

value: yes


title: Biofilm cells_Control_rep3

tag: growth condition


title: TTC_SC_206


title: ipf_1071


title: ZS_1

tag: cell type

value: Bone marrow derived dendritic cells


title: ZcG_2

tag: ligands

value: Zymosan depleted, 3',3'-cGAMP


title: ipf_1067

value: male

value: no

value: explant

tag: plate


title: TTC_SC_210


title: TTC_SC_205


title: Planktonic cells_Control_rep3

value: Planktonic cells

tag: treated

value: Control


title: ZcG_1


title: ipf_1063

value: lung tissue

tag: Sex

value: female

value: GT

tag: institution


title: Z_2

value: Zymosan depleted


title: Planktonic cells_Control_rep4


title: TTC_SC_203


title: TTC_SC_204


title: ipf_1061

tag: diagnosis

value: ipf

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: UNKNOWN

value: NO

value: UCSF


title: Planktonic cells_Control_rep2


title: Planktonic cells_Control_rep1


title: TTC_SC_208

value: tail tendon

tag: genotype

value: WT


title: TTC_SC_202

tag: age


title: ipf_1084

tag: tissue

value: yes

tag: sample type


title: ZScG_45_3

source_name: Whole blood

growth_protocol: Human whole peripheral blood from three healthy donors was obtained from Stemcell Technologies (catalog number 70504.5). Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation. 15 mL lymphocyte separation medium (LSM) (Corning 25072CV) was carefully underlaid beneath 35 ml of diluted blood in a 50 ml tube and centrifuged at 400 g for 30 minutes at 20C without break. The upper layer was aspirated leaving the white buffy coat interphase containing PBMCs (lymphocytes, monocytes) undisturbed. The interphase was transferred to a new 50 mL tube containing 10 mL 1XPBS, mixed and centrifuged at 400 g for 10 minutes at 20C. Following the washing step, supernatant was removed and PBMC pellet was resuspended in PBS.  CD14+ Monocytes were then purified from the PBMCs by positive selection with the Monocyte Isolation kit II (Miltenyi Biotec 130-091-153). CD14+ monocytes were plated at 10^6 cells/mL in 10-cm non-tissue culture treated petri in 10 mL of complete RPMI medium supplemented with everything detailed above except sodium pyruvate and MEM non-essential amino acids and containing recombinant human IL-4 (40 ng/ml; Peprotech 200-04µg) and human GM-CSF (100 ng/ml; Peprotech 300-03µg).  Cells were fed at day 3 and 5 with 5 ml of complete RPMI medium supplemented with GM-CSF and IL-4 as described above. At day 7, non-adherent cells were collected by pipetting, centrifuged and resuspended in fresh complete RPMI medium without GM-CSF and IL-4.

extract_protocol:
Stimulated DCs were lysed with 30 µL of RLT buffer (Qiagen 79216) containing 1% (v/v) b-mercaptoethanol (VWR 97604-848). Total RNA was isolated using Dynabeads MyOne Silane (Thermo Fisher Scientific 37002D) and RLT buffer. Remaining genomic DNA was removed by on-bead DNase I (Thermo Fisher Scientific AM2239) treatment at 37oC for 20 min. After washing two times with 80% ethanol, total RNA was eluted from beads in nuclease-free water.
Total RNA samples obtained from 1x10^4 mouse BMDCs were reverse transcribed to cDNA by denaturing 10-µL RNA samples with 1 µL containing 2 pmoles of a custom RT primer at 72C for 2 min and snap cooled on ice. A 9-µL RT mix containing 4 µL of 5X RT buffer, 1 µL of 10 mM dNTPs, 2 pmoles of template switching oligo, 0.5 µL Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific EP0753) and 3.5 µL of nuclease-free water was added to the denatured RNA samples, and plates were incubated at 42C for 120 min. Double-stranded cDNA samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research D4013), and residual RT primers were removed using exonuclease I (New England Biolabs M0293).  Pooled full-length cDNA was amplified with 4-6 cycles of single-primer PCR with the Advantage 2 PCR Kit (Clontech 639206) in a 50-µL reaction volume. Amplified cDNAs were cleaned up with magnetic beads Agencourt AMPure XP (Beckman Coulter A63880) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851). 1 ng of cDNA was tagmented and amplified by PCR using Nextera XT Kit (Illumina). Libraries were gel purified using E-Gel EX Agarose Gels, 2% (ThermoFisher Scientific G402002), quantified with the Qubit dsDNA High Sensitivity Assay Kit, and sequenced on the NextSeq550 platform (Illumina).

treatment_protocol: 10,000 DCs were plated in 100 µL of medium in non-tissue culture treated 96-well flat bottom plates (ThermoFisher Scientific 260860) and incubated overnight prior to stimulations as indicated. Cells were stimulated with ligands and their combinations for 6 hours.

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

tag: prr ligands

value: Zymosan depleted, SeV, 2',3'-cGAMP


title: ipf_1060

value: male

value: no

value: explant

tag: psl

tag: is

tag: batch

tag: lane


title: ipf_1057

value: lung tissue


title: TTC_SC_201

tag: strain


title: ScG_1

tag: cell type

value: Bone marrow derived dendritic cells

tag: ligands

value: SeV, 3',3'-cGAMP


title: ZScG_45_2


title: ScG_2


title: TTC_SC_200


title: ZScG_45_1


title: ipf_1056

tag: Sex

value: GG

tag: plate


title: S_2

value: SeV


title: S_1


title: TTC_SC_199


title: ZScG_39_3

value: Donor 39


title: PScG_1

value: PAM, SeV_3',3'-cGAMP


title: ipf_1048

value: female

tag: diagnosis

value: ipf

value: GT

value: UNKNOWN

value: NO

tag: institution

value: UCSF


title: ipf_1049

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)


title: Z_1

value: Zymosan depleted


title: TTC_SC_196

value: tail tendon

tag: genotype

value: WT

tag: age


title: ZScG_39_1

value: Monocyte derived dendritic cells

value: Zymosan depleted, SeV, 2',3'-cGAMP


title: PS_1

value: Bone marrow derived dendritic cells

value: PAM, SeV


title: ZScG_27_3

value: Donor 27


title: ipf_1043

tag: tissue

value: lung tissue

value: male

value: yes

value: GG

tag: sample type

value: explant


title: PLH_2

value: PAM, LPS_HMW


title: TTC_SC_193


title: ipf_1038

value: female

value: ipf

value: no

value: UNKNOWN


title: PLH_1


title: TTC_SC_195

value: tail tendon


title: PS_2


title: ZScG_27_2

tag: donor

tag: prr ligands


title: TTC_SC_194

value: WT


title: ZScG_27_1

value: Monocyte derived dendritic cells


title: ZS_45_2

value: Donor 45

value: Zymosan depleted, SeV


title: ipf_1041

value: TT

tag: psl

tag: is

value: NO

value: UCSF


title: ipf_1042

value: lung tissue

tag: batch

tag: lane


title: ipf_1034


title: PL_1

tag: cell type

value: Bone marrow derived dendritic cells

tag: strain

value: PAM, LPS


title: ipf_1053

tag: Sex

value: male

value: yes

value: GT

value: explant


title: ZS_45_3


title: TTC_SC_190


title: TTC_SC_198


title: PScG_2

tag: ligands

value: PAM, SeV_3',3'-cGAMP


title: TTC_SC_197


title: TTC_SC_189


title: ipf_1031

tag: diagnosis

value: ipf

value: GG

value: UNKNOWN

tag: plate


title: ipf_1036

value: female

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: institution


title: PH_2

value: PAM, HMW


title: ZScG_39_2

value: Monocyte derived dendritic cells

value: Donor 39

value: Zymosan depleted, SeV, 2',3'-cGAMP


title: TTC_SC_192

value: tail tendon

tag: genotype

value: WT

tag: age


title: PL_2

value: Bone marrow derived dendritic cells

value: PAM, LPS


title: TTC_SC_191

tag: tissue


title: ZS_39_2

tag: donor

value: Zymosan depleted, SeV


title: PH_1


title: ZS_45_1

value: Donor 45

tag: prr ligands


title: ZS_39_3


title: ZS_39_1


title: TTC_SC_188


title: ipf_1029

value: lung tissue

value: male

tag: sample type

value: explant

tag: psl

value: NO

value: UCSF


title: PcG_2

value: PAM, 3',3'-cGAMP


title: ZS_27_3

value: Donor 27


title: TTC_SC_187


title: PcG_1


title: ZS_27_2


title: ipf_1024

value: female

value: ipf

value: no

value: TT

value: UNKNOWN

tag: is

tag: batch


title: TTC_SC_186

value: tail tendon

value: WT


title: ipf_1022

value: GG

tag: lane


title: P_2

tag: cell type

value: Bone marrow derived dendritic cells

tag: strain

value: PAM


title: ipf_1030

value: lung tissue

tag: Sex

value: yes

value: GT


title: ZS_27_1

value: Monocyte derived dendritic cells

value: Zymosan depleted, SeV


title: TTC_SC_185


title: ipf_1017

tag: diagnosis

value: explant

value: NO

value: UCSF


title: TTC_SC_184


title: LH_2

tag: ligands

value: LPS, HMW


title: P_1


title: ipf_998

value: female

value: ipf

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: plate


title: ZcG_45_2

value: Donor 45

value: Zymosan depleted, 2',3'-cGAMP


title: ZcG_45_3


title: ipf_997

value: male

value: UNKNOWN

tag: institution


title: TTC_SC_183

value: tail tendon

tag: genotype

value: WT

tag: age


title: TTC_SC_182

tag: tissue


title: ipf_994

value: lung tissue

value: no

value: GG

value: biopsy


title: L_2

value: Bone marrow derived dendritic cells

value: LPS


title: TTC_SC_181


title: ZcG_45_1

value: Monocyte derived dendritic cells

tag: donor

tag: prr ligands


title: LH_1


title: L_1


title: ZcG_39_3

value: Donor 39


title: ZcG_39_2


title: TTC_SC_180


title: TTC_SC_179


title: ZcG_39_1


title: control_982

value: control

value: yes

tag: sample type

value: explant

tag: psl

value: NO

value: PT


title: TTC_SC_178


title: H_1

value: HMW


title: ZcG_27_3

value: Donor 27

value: Zymosan depleted, 2',3'-cGAMP


title: Ctrl_2

value: Ctrl


title: ZcG_27_2


title: TTC_SC_177

value: tail tendon

value: WT


title: ZcG_27_1


title: control_980

value: lung tissue

value: female

value: no

value: GG

value: UNKNOWN

tag: is

tag: batch


title: TTC_SC_176


title: ipf_992

value: male

value: ipf

value: GT

tag: lane

value: UCSF


title: cG_2

tag: cell type

value: Bone marrow derived dendritic cells

tag: strain


title: Ctrl_1


title: control_978

tag: Sex

tag: diagnosis

value: control

value: TT

value: explant

value: NO

value: PT


title: control_975

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)


title: Z_45_3

value: Monocyte derived dendritic cells

value: Donor 45

value: Zymosan depleted


title: cG_1

tag: ligands


title: control_973

value: lung tissue

value: female

value: no

tag: plate

tag: institution


title: ipf_990

value: male

tag: age

value: GG

value: UNKNOWN


title: TTC_SC_174

tag: tissue

value: tail tendon

tag: genotype

value: WT


title: H_2

value: Bone marrow derived dendritic cells

value: HMW


title: TTC_SC_173


title: Z_45_2

tag: donor

tag: prr ligands


title: ipf_965

value: ipf

tag: sample type

value: explant

tag: psl


title: Z_45_1


title: control_964

value: control

value: GT

tag: is

value: NO

tag: batch

value: PT


title: TTC_SC_175


title: TTC_SC_172


title: control_961

value: yes

tag: lane


title: TTC_SC_171

tag: strain


title: control_956

value: lung tissue

tag: Sex


title: TTC_SC_170


title: control_955

value: female

tag: diagnosis


title: Z_39_2

tag: cell type

value: Monocyte derived dendritic cells

value: Donor 39

value: Zymosan depleted


title: Z_39_1


title: ipf_954

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

value: UNKNOWN


title: TTC_SC_169

value: tail tendon

value: WT


title: Z_27_3

value: Donor 27


title: Z_27_2


title: control_951

value: male

value: explant

tag: plate


title: control_947

value: control

tag: institution


title: Z_27_1


title: TTC_SC_167

tag: age


title: ipf_940

tag: tissue

value: ipf

value: NO


title: ScG_45_3

value: Donor 45

value: SeV, 2',3'-cGAMP


title: TTC_SC_166

tag: genotype


title: TTC_SC_165


title: ScG_45_1

tag: donor


title: control_932

value: lung tissue

value: female

value: PT


title: Z_39_3

value: Monocyte derived dendritic cells

value: Donor 39

tag: prr ligands

value: Zymosan depleted


title: ScG_45_2


title: ScG_39_3


title: TTC_SC_164


title: ipf_938

value: GG

tag: sample type

value: UNKNOWN


title: TTC_SC_162

value: tail tendon

value: WT


title: HRAS_E15_rep3

city: New York

first: Vincent

last: Fiore

state: NY

address: 1230 York St.

institute: Rockefeller University

data_processing:
Alignment: 50-bp sequences were aligned to mm10 using STAR and Gencode release M9 and counts generated from STAR output --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: NCBI Gene ID, Counts

source_name: Embyronic skin

extract_protocol:
Embyronic epidermal basal cells. Each sample was pooled from 3 embryos.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research). Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8.
TruSeq Stranded mRNA Library Preparation (Poly-A selection and Stranded RNA-Seq)

value: Mixed

value: HRAS

value: Skin

tag: sorting markers


title: TTC_SC_161


title: TTC_SC_163


title: ScG_39_2


title: control_929

value: control

value: yes

value: explant

tag: psl

tag: is


title: TTC_SC_168


title: ScG_39_1

value: SeV, 2',3'-cGAMP


title: control_927

value: lung tissue

value: GT

value: NO

tag: batch

tag: lane


title: HRAS_E15_rep2

tag: strain

tag: Sex


title: HRAS_E15_rep1


title: ipf_926

value: male

tag: diagnosis

value: ipf

value: PT


title: ScG_27_3

tag: cell type

value: Monocyte derived dendritic cells

value: Donor 27


title: ScG_27_2


title: TTC_SC_159

value: tail tendon


title: ipf_924

value: female

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: UNKNOWN

tag: plate


title: SmoM2_E15_rep3

value: Mixed

value: Skin

tag: age


title: control_933

tag: tissue

value: control

value: yes

value: GG

tag: institution


title: ScG_27_1

tag: donor

value: SeV, 2',3'-cGAMP


title: TTC_SC_158

tag: genotype

value: WT


title: SmoM2_E15_rep2


title: S_45_3

value: Donor 45

tag: prr ligands

value: SeV


title: TTC_SC_157


title: control_920

value: lung tissue

tag: sample type

value: explant

value: NO


title: SmoM2_E15_rep1

tag: sorting markers


title: TTC_SC_156


title: control_919

tag: psl

tag: is

value: PT


title: S_45_2

value: Monocyte derived dendritic cells


title: TTC_SC_160

value: tail tendon


title: ipf_917

value: male

value: ipf

value: no

value: GT

tag: batch

tag: lane


title: WT_E15_rep3

tag: strain

value: Mixed

value: Skin

tag: Sex


title: WT_E15_rep2


title: S_45_1

tag: cell type


title: TTC_SC_154


title: TTC_SC_155


title: ipf_916

value: female

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

value: UNKNOWN


title: WT_E15_rep1

value: WT

tag: age


title: S_39_2

value: Donor 39

value: SeV


title: ipf_914

tag: tissue

value: lung tissue

value: explant

tag: plate


title: S_39_3

tag: donor


title: control_923

value: control

value: NO

tag: institution

value: PT


title: S_39_1

value: Monocyte derived dendritic cells

tag: prr ligands


title: TTC_SC_152

value: tail tendon

tag: genotype


title: control_912

value: male

value: no

tag: sample type


title: TTC_SC_153


title: TTC_SC_151


title: Group_2_(RCas9)_12_week_post_injection

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
Group_2_(RCas9)_12_week_post_injection
Supplementary Table 4 - Gene Expression
G2-6-12w

data_processing:
RNA-seq data was aligned to the mouse mm10 genome build using Olego aligner, expression and alternative splicing were estimated using quantas as described below.
Quantas software as described in Charizanis et al, 2012, Neuron, was used to estimate gene expression and alternative splicing. Olego aligned alignment files were used to count observed junction reads (for splicing) for each exon or RPKMs for each gene expression. Weighted number of exon or exon-junction fragments uniquely supporting the inclusion or skipping isoform of each cassette exon and a probability score was assigned to each isoform. A Fisher’s exact test was used to evaluate the statistical significance of splicing changes using both exon and exon-junction fragments, followed by Benjamini multiple testing correction to estimate the false discovery rate (FDR). In addition, inclusion or exclusion junction reads were used to calculate the proportional change of exon inclusion (dI). Forcalculate  gene expression between various groups edgeR was used which is a part of the Quantas suite. See documentation at http://zhanglab.c2b2.columbia.edu/index.php/Quantas_Documentation.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: Mouse Tibialis Anterior

growth_protocol: HSALR mice are a model of myotonic dystrophy expression CTG250 repeats under the control of human skeletal actin (ACTA1) promoter.

extract_protocol:
Total RNA was isolated using TRIzol reagent using the manufacturer’s protocol (Life Technologies)
For RNA-seq, libraries were made using the Illumina polyA selection truseq library kit using different barcodes according to the manufacturer's protocol. Libraries were not strand specific.
Non-strand specific for Illumina Hiseq 4000. Each library was run in 2 lanes.

treatment_protocol: HSALR and WT tibialis anterior muscles were treated with either AAV9 containing either non-targeting (NT) or CTG-targeting (CTG) sgRNA and PIN-dCas9 (RNA targeting Cas9 or RCas9)  for 4 weeks  and harvested for RNA-seq library prep. Treatment with AAV9-MBNL1 in HSALR tibialis anterior was used as positive control for reversing splicing.

value: Tibialis Anterior muscle

tag: time point

value: 12 weeks post treatment

value: FVB/NJ


description:
Group_1_(guide_only)_12_week_post_injection
Supplementary Table 4 - Gene Expression
G1-2-12w


title: control_900

value: yes

value: GG

tag: psl

tag: is


title: S_27_2

value: Donor 27


title: ipf_899

value: ipf

value: TT

value: UNKNOWN

tag: batch

tag: lane


description:
Group_2_(RCas9-CTG)_6_week_post_injection
Supplementary Table 4 - Gene Expression
G2F1-6w

value: 6 weeks post treatment

value: WT

tag: strain


title: S_27_3

tag: cell type

value: SeV


title: TTC_SC_149


title: S_27_1


title: ipf_894

value: lung tissue

tag: Sex

value: female

tag: diagnosis

value: explant

value: NO

value: PT


description:
Group_5_(RCas9-CTG_+_immunosuppression)_12_weeks_post_injection
Supplementary Table 4 - Gene Expression
G518-12w

value: Tibialis Anterior muscle


title: LZS_45_3

value: Monocyte derived dendritic cells

value: Donor 45

value: LPS, Zymosan depleted, SeV


title: TTC_SC_148

value: tail tendon

tag: age


title: ipf_888

tag: tissue

value: male

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG


description:
Group_5_(RCas9-CTG_+_immunosuppression)_6_weeks_post_injection
Supplementary Table 4 - Gene Expression
G5F2-6w

value: FVB/NJ


title: TTC_SC_147


title: LZS_45_1

tag: donor


title: ipf_887

value: ipf

value: UNKNOWN

tag: plate

tag: institution


title: TTC_SC_146

tag: genotype

value: WT


title: LZS_45_2

tag: prr ligands


title: control_878

value: lung tissue

value: control

tag: sample type

value: other


description:
Group_2_(RCas9-CTG)_1_week_post_injection
Supplementary Table 4 - Gene Expression
G2F2-1w

tag: time point

value: 1 weeks post treatment


description:
Group_1_(guide_only)_1_week_post_injection
Supplementary Table 4 - Gene Expression
G1F2-1w


title: LZS_39_3

value: Donor 39


title: TTC_SC_144


title: TTC_SC_145


description:
Group_1_(guide_only)_6_week_post_injection
Supplementary Table 4 - Gene Expression
G1F1-6w

value: Tibialis Anterior muscle

value: 6 weeks post treatment


title: LZS_39_2

value: Monocyte derived dendritic cells


title: HSALR-PIN3 CTG-Targetting RCas9 -3

description:
Treatment with AAV9 RCas9-CTG Targeting
Supplementary Table 1 - Significant AS changes; Supplementary Table 2 - Gene Expression
PIN3-12

value: 4 weeks post treatment

value: HSALR (DM1)


title: ipf_856

value: female

value: GT

value: biopsy

tag: psl

tag: is

value: NO

value: LTRC


title: TTC_SC_150

value: tail tendon


title: TTC_SC_143

value: WT


title: LZS_39_1

value: LPS, Zymosan depleted, SeV


title: HSALR-PIN2 CTG-Targetting RCas9 -2

description:
Treatment with AAV9 RCas9-CTG Targeting
Supplementary Table 1 - Significant AS changes; Supplementary Table 2 - Gene Expression
PIN2-10


title: LZS_27_3

value: Donor 27


title: ipf_853

value: lung tissue

value: male

value: ipf

value: yes

value: GG

value: explant

value: UNKNOWN

tag: batch

value: other

tag: lane


title: HSALR-PIN1 CTG-Targetting RCas9 -1

description:
Treatment with AAV9 RCas9-CTG Targeting
Supplementary Table 1 - Significant AS changes; Supplementary Table 2 - Gene Expression
Rcas9-PIN1

value: Tibialis Anterior muscle

value: 4 weeks post treatment

value: HSALR (DM1)


title: LZS_27_2

tag: cell type

value: Monocyte derived dendritic cells


title: TTC_SC_141

tag: strain


title: ipf_852

tag: Sex

value: female

tag: diagnosis

value: no

value: NO

value: LTRC


title: HSALR-NT2 Non-Targeting RCas9 -2

description:
Treatment with AAV9 RCas9-Non targeting
Supplementary Table 1 - Significant AS changes; Supplementary Table 2 - Gene Expression
NT-F

tag: tissue


title: TTC_SC_140

value: tail tendon

value: WT

tag: age


title: ipf_877

value: lung tissue

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: NJH


title: control_851

value: control

value: GT

tag: plate


title: LZS_27_1

tag: donor

value: Donor 27

value: LPS, Zymosan depleted, SeV


title: HSALR-MBNL1

description:
Treatment with AAV9 MBNL1
Supplementary Table 1 - Significant AS changes; Supplementary Table 2 - Gene Expression
MBNL-10

tag: genotype


title: TTC_SC_139


title: control_849

value: male

value: yes

value: GG

value: explant

value: UNKNOWN

value: other

tag: institution


title: control_854

value: female

value: no

tag: sample type


title: LZcG_45_3

value: Monocyte derived dendritic cells

value: Donor 45

tag: prr ligands

value: LPS, Zymosan depleted, 2',3'-cGAMP


title: tdTAKO3 [A305R-TDT_S5_L003]

city: Stanford

first: Juyong

middle: Brian

last: Kim

address: 300 Pasteur Dr.

institute: Stanford University

description:
A305R-TDT_S5_L003
processed data file: scRNAseq_rawmatrix.txt, scRNAseq_metadata.txt

data_processing:
scRNA-seq: Fastq files from each experimental time point and mouse genotype were aligned to the reference genome individually using CellRanger Software (10X Genomics). Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization. The aggregated dataset was then analyzed using the R package Seurat.34 The dataset was trimmed of cells expressing fewer than 500 genes, and genes expressed in fewer than 5 cells. The number of genes, the number of unique molecular identifiers (UMIs) and the percentage of mitochondrial genes were examined to identify outliers. As an unusually high number of genes can result from a “doublet” event, in which two different cell types are captured together with the same barcoded bead, cells with > 4000 genes were discarded. Cells containing >10% mitochondrial genes were presumed to be of poor quality and were also discarded. The gene expression values then underwent library size normalization, using the published sctranform function in the Seurat R package.35 Principal component analysis was used for dimensionality reduction, followed by clustering in PCA space using a graph-based clustering approach.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts, bigwig, log_transformed counts matrix and metadata matrix of scRNAseq

source_name: single-cell library

extract_protocol: Cells were enzymatically dissociated from the aortic root and ascending aorta of experimental mice, sorted for live/dead cells and tdTomato signal by FACS, and captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using the V2 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

value: mouse aortic sinus

tag: genotype/treatment

value: AHR KO


title: HSALR-NT1 Non-Targeting RCas9 -1

description:
Treatment with AAV9 RCas9-Non targeting
Supplementary Table 1 - Significant AS changes; Supplementary Table 2 - Gene Expression
NT-11

value: Tibialis Anterior muscle

tag: time point

value: 4 weeks post treatment

value: HSALR (DM1)


title: tdTAKO2 [A305N-TDT_S6_L003]

description:
A305N-TDT_S6_L003
processed data file: scRNAseq_rawmatrix.txt, scRNAseq_metadata.txt


title: LZcG_45_2


title: TTC_SC_137

value: tail tendon

value: WT


title: control_842

value: lung tissue

value: control

tag: psl

tag: is

value: NO

tag: batch

value: LTRC


title: tdTAKO1 [TDT-A120RL_S4_L007]

description:
TDT-A120RL_S4_L007
processed data file: scRNAseq_rawmatrix.txt, scRNAseq_metadata.txt


title: TTC_SC_142

tag: strain


title: LZcG_39_3

tag: cell type

value: Donor 39


title: tdTAKO1 [TDT-A120RL_S4_L008]

description:
TDT-A120RL_S4_L008
processed data file: scRNAseq_rawmatrix.txt, scRNAseq_metadata.txt

value: AHR WT


title: TTC_SC_135


title: LZcG_39_2


title: TTC_SC_134


title: ipf_829

tag: Sex

value: male

tag: diagnosis

value: ipf

value: no

value: GG

value: biopsy

value: UNKNOWN

value: other

tag: lane


title: TTC_SC_133

tag: tissue

tag: age


title: tdTWT1 [SMC16-D10_S3_L001]

description:
SMC16-D10_S3_L001
processed data file: scRNAseq_rawmatrix.txt, scRNAseq_metadata.txt

value: mouse aortic sinus


title: TTC_SC_132


title: LZcG_39_1

value: Monocyte derived dendritic cells

tag: donor

value: LPS, Zymosan depleted, 2',3'-cGAMP


title: TTC_SC_138

value: tail tendon

tag: genotype

value: WT


title: LZcG_27_2

value: Donor 27


title: LZcG_27_3


title: LZcG_45_1

value: Donor 45


title: TTC_SC_136


title: TTC_SC_131


title: ipf_826

value: lung tissue

value: female

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

value: NO

tag: plate

tag: institution

value: LTRC


title: Sample 8_Hippocampal microglia 4 hours after PBS injection

city: San Francisco

first: Leah

last: Dorman

address: 499 Illinois St

department: Data Science

institute: CZBiohub

data_processing:
QC with FASTQC (all samples passed)
Alignment in STAR version 2.5.4b
Reads counted with HTSeq (version 0.9.0)
Reads normalization and DEGs calculation using DESeq2 version 1.24.0
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized counts for each sample
Supplementary_files_format_and_content: FPKM values for each sample

extract_protocol:
Mice were perfused with PBS and hippocampi were dissected out, mechanically homogenized in whole cell isolation medium, and microglia were isolated through FACS for CD45lo/CD11B+/Ly-6C- cells
QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: Microglia

value: hippocampus

tag: mouse strain

value: Male


title: LZcG_27_1

tag: prr ligands


title: control_825

value: control

value: no

tag: sample type

value: biopsy

tag: psl

value: UNKNOWN

value: other


title: Hippocampal Neuronal Nuclei: Control

data_processing:
Cell Ranger 2.1 (STAR aliger) with reference genome including pre-mRNA
Filter cells with fewer than 500 or more than 3000 genes/cell detected (Seurat V2.3.4)
Filter cells with >1% mitochondrial mRNA (Seurat V2.3.4)
Log normalization (Seurat V2.3.4)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Text files with normalized counts for all cells and genes which passed quality thresholds. "A1" = Wild type; "A3" = Il-33 high expressing cell.
Supplementary_files_format_and_content: Summary file: raw counts for all filtered cells

source_name: Hippocampal neurons

extract_protocol:
Mice were perfused with PBS and hippocampi were dissected out, mechanically homogenized in nuclear isolation medium, and neuronal nuclei were isolated through FACS.
10x Chromium V2

value: Neuronal nuclei

tag: number and sex

value: 1 Male + 1 Female

value: Wild Type

tag: rna fraction

value: Nuclear RNA


title: control_836

value: lung tissue

value: male

value: GG

tag: is

tag: batch


title: ipf_845

tag: Sex

tag: diagnosis

value: ipf

value: yes

value: NO


title: Hippocampal Neuronal Nuclei: IL-33 Enriched

description: Raw data file contains male and female (Xist+) cells. The female cells  express Il33-mCherry as confirmed by FACS.

tag: cell type

tag: tissue

value: hippocampus

value: 1 Female

value: Il33-H2B-mCherry heterozygous


title: LZ_45_3

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

value: LPS, Zymosan depleted


title: control_823

tag: age

value: control

value: no

value: biopsy

value: UNKNOWN

value: other

tag: lane

value: LTRC


title: tdTWT2 [SMC16-D11_S4_L001]

description:
SMC16-D11_S4_L001
processed data file: scRNAseq_rawmatrix.txt, scRNAseq_metadata.txt

value: mouse aortic sinus

tag: genotype/treatment

value: AHR WT


title: Sample 6_Hippocampal microglia 4 hours after PBS injection

value: Microglia

value: Female


title: Sample 7_Hippocampal microglia 4 hours after PBS injection

value: Male


title: TTC_SC_129

tag: strain

value: tail tendon

tag: genotype

value: WT


title: control_828

value: lung tissue

value: male

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

value: NO

tag: plate

tag: institution


title: LZ_45_1

value: Monocyte derived dendritic cells

value: Donor 45

tag: prr ligands

value: LPS, Zymosan depleted


title: ipf_813

value: ipf

value: no

tag: sample type

value: biopsy

tag: psl

value: UNKNOWN


title: ipf_827

value: yes

value: GT

tag: is

tag: batch

value: other

value: LTRC


title: TTC_SC_127

value: tail tendon


title: Sample 5_Hippocampal microglia 4 hours after PBS injection

value: Microglia

value: hippocampus

tag: mouse strain

tag: Sex

value: Female


title: ipf_812

tag: tissue

value: lung tissue

value: female

tag: diagnosis


title: TTC_SC_126

value: WT

tag: age


title: Sample 4_Hippocampal microglia 4 hours after IL-33 Injection

tag: cell type

value: Male


title: Sample 3_Hippocampal microglia 4 hours after IL-33 Injection


title: TTC_SC_125


title: LZ_39_2

value: Monocyte derived dendritic cells

tag: donor

value: Donor 39

value: LPS, Zymosan depleted


title: ipf_799

value: ipf

value: explant

value: NO

tag: lane


title: ipf_809

value: yes

value: GT

value: UNKNOWN


title: LZ_39_1


title: Sample 2_Hippocampal microglia 4 hours after IL-33 Injection


title: TTC_SC_124

tag: strain

value: tail tendon

tag: genotype


title: Sample 1_Hippocampal microglia 4 hours after IL-33 Injection

value: Microglia


title: TTC_SC_123


title: ipf_798

value: male

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

value: other

tag: plate

value: LTRC


title: LZ_27_3

value: Donor 27

tag: prr ligands


title: control_796

value: lung tissue

value: female

value: control

tag: sample type

tag: institution


title: TTC_SC_122

value: WT


title: LZ_27_1

value: Monocyte derived dendritic cells

value: LPS, Zymosan depleted


title: LZ_39_3

value: Donor 39


title: control_794

value: yes

value: GT

value: explant

tag: psl

tag: is

value: NO


title: TTC_SC_120

value: tail tendon


title: T119g_Ctrl_F_Liver_5mo

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

data_processing:
The sample quality was first assessed with FastQC (v0.11.3), then Trim Galore! (v0.4.5) was used for adapter and quality trimming. More specifically, low-quality bases (quality score lower than 20), adapter sequences (required overlap of 6bp), and end-repair bases from the 3’ end of reads were trimmed, and all reads shorter than 20bp after trimming were discarded.
Bismark was used for alignment and methylation calling, where reads were aligned to mm10 genome using Bowtie2 and methylation calls were reported for all nucleotides with a read depth of at least 5.
Genome_build: mm10
Supplementary_files_format_and_content: bismark coverage files including the percentage of methylation at each position, the number of C bases that are methylated and the number of C bases that are unmethylated

source_name: Liver

extract_protocol:
Upon euthanasia at both 3 weeks and 5 months of age, blood and liver samples were collected. Briefly, blood was collected by cardiac puncture, followed by liver and mesenteric fat. Blood was collected with EDTA anticoagulant, centrifuged, and plasma was removed. Liver was then separated into individual lobes, and the left lobe of the liver was cryo-pulverized and suspended in Buffer RLT (Qiagen, cat # 1053393). Blood and liver DNA extraction were performed using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen #80224).
A total of 50 ng of genomic DNA was digested using restriction enzyme Mspl, and the digested DNA was then purified using phenol:chloroform extraction and ethanol precipitation in the presence of glycogen, before blunt-ending and phosphorylation. A single adenine nucleotide was next added to the 3′ end of the fragments in preparation for the ligation of the adapter duplex with a thymine overhang. The ligated fragments were cleaned, then processed for size selection on agarose gel. Selected fragments were treated with sodium bisulfite to convert unmethylated cytosines to uracils, which are then replaced with thymines during PCR amplification. These libraries were next cleaned up with AMPure XP beads (Product #A63880; Beckman Coulter), quantified using the Agilent TapeStation genomic DNA kit (Catalog #G2991AA; Agilent) and Qubit High Sensitivity dsDNA (Catalog #Q32850; Invitrogen).

value: Female

tag: treatment

value: Ctrl

tag: time

value: 5 months


title: T119g_Ctrl_F_Blood_5mo

source_name: Blood

tag: Sex


title: T119e_Ctrl_F_Liver_5mo


title: control_788

tag: tissue

value: male

tag: diagnosis

value: no

value: GG

value: biopsy

value: UNKNOWN

tag: batch

value: other

value: LTRC


title: TTC_SC_121

value: WT

tag: age


title: LScG_45_2

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

value: LPS, SeV, 2',3'-cGAMP


title: LScG_45_3


title: LScG_45_1


title: TTC_SC_119

tag: strain

tag: genotype


title: ipf_787

value: lung tissue

value: ipf

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: explant

tag: lane

tag: plate


title: T119e_Ctrl_F_Blood_5mo

value: Female


title: T119c_Ctrl_F_Liver_PND21

value: Ctrl


title: TTC_SC_118

value: tail tendon


title: LScG_39_3

value: Donor 39

tag: prr ligands


title: TTC_SC_117


title: LScG_39_2


title: LZ_27_2

value: Donor 27

value: LPS, Zymosan depleted


title: control_784

value: male

value: control

value: yes

value: GG

tag: sample type

value: biopsy

tag: psl

value: NO

tag: institution


title: ipf_785

value: TT

value: UNKNOWN

tag: is

value: other

value: LTRC


title: T119c_Ctrl_F_Blood_PND21

tag: Sex

tag: treatment

tag: time


title: TTC_SC_116

tag: tissue

value: WT


title: T119b_Ctrl_M_Liver_PND21

value: Male


title: ipf_782

value: lung tissue

value: female

tag: age

tag: diagnosis

value: ipf

tag: batch


title: control_792

value: no


title: LScG_39_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 39

value: LPS, SeV, 2',3'-cGAMP


title: T119b_Ctrl_M_Blood_PND21

value: Ctrl


title: ipf_780

value: male

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT


title: LScG_27_2

value: Donor 27


title: LScG_27_3


title: TTC_SC_115

tag: strain

value: tail tendon

tag: genotype


title: T119a_Ctrl_F_Blood_PND21

value: Female


title: TTC_SC_113


title: LScG_27_1

tag: prr ligands


title: ipf_774

value: yes

value: GG

tag: sample type

value: biopsy

value: UNKNOWN

value: NO

value: other

tag: lane

tag: plate


title: control_772

value: lung tissue

value: control

tag: psl

tag: is

tag: institution

value: LTRC


title: T118j_Ctrl_M_Liver_PND21

tag: Sex

value: Male

tag: treatment

tag: time


title: TTC_SC_112

tag: tissue

value: WT

tag: age


title: LS_45_3

tag: cell type

value: Monocyte derived dendritic cells

value: Donor 45

value: LPS, SeV


title: TTC_SC_111


title: control_768

value: male

tag: diagnosis

tag: batch


title: T118j_Ctrl_M_Blood_PND21

value: Ctrl


title: T118h_Ctrl_M_Liver_5mo

value: 5 months


title: TTC_SC_110

tag: strain

value: tail tendon


title: control_766

value: female

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG


title: LS_45_1

tag: donor

tag: prr ligands


title: T118h_Ctrl_M_Blood_5mo


title: T119a_Ctrl_F_Liver_PND21

value: Female


title: ipf_779

value: ipf

tag: sample type

value: biopsy

value: UNKNOWN

value: NO

value: other

tag: lane


title: LS_45_2


title: ipf_765

value: lung tissue

tag: psl

tag: plate

value: LTRC


title: TTC_SC_114

tag: genotype

value: WT


title: TTC_SC_109


title: TTC_SC_108


title: ipf_763

tag: Sex

value: GT

tag: is

tag: institution


title: LS_39_3

value: Monocyte derived dendritic cells

value: Donor 39

value: LPS, SeV


title: LS_39_2


title: T118d_Ctrl_M_Blood_5mo

value: Male

tag: treatment

value: Ctrl

tag: time

value: 5 months


title: LS_39_1

tag: cell type


title: ipf_762

tag: tissue

value: female

tag: age

tag: diagnosis

value: yes


title: T118c_Ctrl_F_Liver_5mo

value: Female


title: TTC_SC_106

tag: strain

value: tail tendon


title: LS_27_3

tag: donor

value: Donor 27


title: ipf_757

value: ipf

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: biopsy

value: UNKNOWN

value: NO

tag: batch


title: TTC_SC_107

value: WT


title: LS_27_2

tag: prr ligands


title: TTC_SC_105


title: ipf_756

value: lung tissue

value: GT

tag: sample type

tag: psl

value: other

tag: lane

value: LTRC


title: T118c_Ctrl_F_Blood_5mo

tag: Sex


title: TTC_SC_104

tag: genotype


title: LS_27_1

value: Monocyte derived dendritic cells

value: LPS, SeV


title: TTC_SC_103


title: T118b_Ctrl_M_Liver_PND21

value: Male

value: Ctrl


title: T118d_Ctrl_M_Liver_5mo

value: 5 months


title: LHZ_45_3

value: Donor 45

value: LPS, HMW, Zymosan depleted


title: ipf_751

value: male

value: yes

tag: is

tag: plate

tag: institution


title: ipf_755

value: ipf

value: no

value: biopsy


title: T118a_Ctrl_F_Liver_PND21

value: Female

tag: treatment

tag: time


title: TTC_SC_102

tag: tissue

value: tail tendon

value: WT

tag: age


title: T118b_Ctrl_M_Blood_PND21


title: TTC_SC_101

tag: strain


title: control_750

value: lung tissue

value: female

tag: diagnosis

value: control

value: GT

value: UNKNOWN

value: NO

value: other


title: LHZ_45_2

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45


title: LHZ_45_1

tag: prr ligands

value: LPS, HMW, Zymosan depleted


title: ipf_747

value: male

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

tag: batch

value: LTRC


title: TTC_SC_100


title: LHZ_39_3

value: Donor 39


title: T117h_DEHP_M_Blood_5mo

tag: Sex

value: Male

value: DEHP

value: 5 months


title: T118a_Ctrl_F_Blood_PND21

value: Female

value: Ctrl


title: TTC_SC_99

value: tail tendon

tag: genotype

value: WT


title: control_744

value: lung tissue

value: female

value: control

value: biopsy

tag: psl

value: UNKNOWN

tag: is

value: NO

tag: lane


title: ipf_742

value: ipf

value: no

value: other

tag: plate

tag: institution


title: T117d_DEHP_M_Liver_5mo

tag: treatment

tag: time


title: TTC_SC_98

tag: strain

tag: tissue

tag: age


title: T117d_DEHP_M_Blood_5mo


title: TTC_SC_97


title: ipf_739

value: male

tag: diagnosis

value: yes

value: GT

value: LTRC


title: LHZ_27_3

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands

value: LPS, HMW, Zymosan depleted


title: TTC_SC_96

value: tail tendon

value: WT


title: LHZ_39_1

value: Donor 39


title: T117b_DEHP_M_Liver_PND21

value: Male

value: DEHP


title: T117b_DEHP_M_Blood_PND21


title: control_738

value: lung tissue

value: control

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: TT

tag: sample type

value: biopsy

value: UNKNOWN

tag: batch


title: TTC_SC_95

tag: genotype


title: ipf_735

tag: Sex

value: male

value: ipf

value: GG

value: explant

tag: psl

tag: is

value: NO

value: other


title: T117h_DEHP_M_Liver_5mo

value: 5 months


title: T117a_DEHP_F_Liver_PND21

value: Female


title: TTC_SC_94

value: tail tendon

value: WT


title: ipf_733

value: no

value: GT

tag: lane

tag: plate

tag: institution

value: LTRC


title: TTC_SC_93

tag: strain


title: LHZ_39_2

value: Monocyte derived dendritic cells

value: Donor 39

value: LPS, HMW, Zymosan depleted


title: ipf_732

tag: tissue

value: lung tissue

value: female

value: UNKNOWN


title: T116d_Lead_M_Liver_5mo

value: Male

tag: treatment

value: Lead

tag: time


title: TTC_SC_92

tag: age


title: LHS_45_2

tag: cell type

tag: donor

value: Donor 45

value: LPS, HMW, SeV


title: LHZ_27_1

value: Donor 27

tag: prr ligands


title: LHS_45_3


title: ipf_730

tag: diagnosis

value: ipf

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: explant

value: NO

value: other


title: T116d_Lead_M_Blood_5mo

tag: Sex

value: 5 months


title: ipf_731

value: male

value: no

tag: psl

tag: batch

value: LTRC


title: control_740

value: lung tissue

value: female

value: control

value: biopsy

tag: is

tag: lane


title: LHS_39_3

value: Monocyte derived dendritic cells

value: Donor 39


title: TTC_SC_130

value: tail tendon

tag: genotype

value: WT


title: T116c_Lead_F_Liver_5mo

value: Female

value: Lead


title: TTC_SC_90

tag: strain


title: LHS_45_1

value: Donor 45

value: LPS, HMW, SeV


title: T116c_Lead_F_Blood_5mo


title: TTC_SC_91

tag: tissue


title: ipf_729

value: ipf

value: GG

value: explant

value: UNKNOWN

value: NO

value: other

tag: plate

tag: institution


title: LHS_39_2


title: LHS_39_1


title: TTC_SC_89

tag: age


title: ipf_726

value: lung tissue

value: female

value: no

value: TT

value: LTRC


title: TTC_SC_88

value: tail tendon


title: T116b_Lead_M_Liver_PND21

value: Male

tag: treatment

tag: time


title: ipf_724

value: male

value: yes


title: T116b_Lead_M_Blood_PND21

value: Lead


title: TTC_SC_87

value: WT


title: LZ_45_2

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

tag: prr ligands

value: LPS, Zymosan depleted


title: control_714

tag: diagnosis

value: control

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: explant

value: UNKNOWN

value: PT


title: control_710

value: lung tissue

tag: Sex

tag: psl

value: NO

tag: batch


title: TTC_SC_86

tag: genotype


title: TTC_SC_85

tag: strain


title: control_709

tag: tissue

tag: is

tag: lane


title: T116a_Lead_F_Liver_PND21

value: Female


title: T115d_DEHP_M_Liver_5mo

value: DEHP

value: 5 months


title: TTC_SC_84

value: tail tendon

tag: age


title: TTC_SC_128


title: T116a_Lead_F_Blood_PND21

tag: treatment


title: LHcG_45_3

value: LPS, HMW, 2',3'-cGAMP


title: LHS_27_1

value: Donor 27

value: LPS, HMW, SeV


title: LHcG_45_2

value: Monocyte derived dendritic cells


title: control_699

value: female

value: yes

tag: plate

tag: institution


title: T115c_DEHP_F_Liver_5mo

tag: time


title: T115d_DEHP_M_Blood_5mo

value: Male


title: TTC_SC_83

value: WT


title: LHcG_45_1

tag: cell type

tag: donor

value: Donor 45

tag: prr ligands


title: LHS_27_3


title: TTC_SC_82


title: control_698

tag: diagnosis

value: control

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: explant

value: UNKNOWN


title: T115c_DEHP_F_Blood_5mo

tag: Sex

value: Female

value: DEHP


title: LHS_27_2


title: control_695

value: lung tissue

tag: psl

value: NO

tag: batch

value: PT


title: TTC_SC_81

tag: strain

tag: tissue

value: tail tendon

tag: genotype


title: LHcG_39_2

value: Monocyte derived dendritic cells

value: Donor 39

value: LPS, HMW, 2',3'-cGAMP


title: T115b_DEHP_M_Liver_PND21

value: Male


title: TTC_SC_80

value: WT

tag: age


title: control_703

value: male

value: yes

tag: is

tag: lane


title: control_691

value: control

value: GT

tag: plate

tag: institution


title: control_687

value: explant


title: control_671

value: no

value: GG

value: UNKNOWN


title: TTC_SC_78


title: LHcG_39_3

tag: cell type


title: T115b_DEHP_M_Blood_PND21

tag: treatment

value: DEHP

tag: time


title: TTC_SC_79


title: T115a_DEHP_F_Blood_PND21

value: Female


title: control_666

value: lung tissue

tag: diagnosis

value: NO

value: PT


title: TTC_SC_76

value: tail tendon


title: LH_45_3

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

tag: prr ligands

value: LPS, HMW


title: LHcG_39_1

value: Donor 39

value: LPS, HMW, 2',3'-cGAMP


title: TTC_SC_77

value: WT


title: T114d_DEHP_M_Liver_5mo

tag: Sex

value: Male

value: 5 months


title: LHcG_27_3

value: Donor 27


title: LHcG_27_2


title: control_661

value: female

value: control

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: explant

tag: psl


title: LHcG_27_1


title: TTC_SC_75

tag: strain

tag: tissue


title: LH_45_2


title: control_657

value: lung tissue

value: male

tag: age

value: UNKNOWN

value: NO

tag: batch


title: T114c_DEHP_F_Liver_5mo

value: Female

value: DEHP


title: T115a_DEHP_F_Liver_PND21


title: TTC_SC_74

value: tail tendon

tag: genotype


title: LH_45_1

value: Monocyte derived dendritic cells

value: Donor 45

value: LPS, HMW


title: T114d_DEHP_M_Blood_5mo

value: Male

value: 5 months


title: control_646

tag: is

tag: lane

tag: plate

value: PT


title: T114c_DEHP_F_Blood_5mo

tag: treatment


title: TTC_SC_73

value: WT


title: control_576

value: control

value: yes

tag: institution


title: TTC_SC_72


title: T114b_DEHP_M_Liver_PND21

tag: time


title: control_574

value: female

tag: diagnosis

value: no

value: GG

value: explant


title: LH_39_3

tag: cell type

tag: donor

value: Donor 39

tag: prr ligands


title: TTC_SC_71


title: ipf_410

value: lung tissue

tag: Sex

value: ipf

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

tag: sample type

value: UNKNOWN

value: NO

value: LTRC


title: ipf_403

tag: tissue

value: male

value: biopsy

tag: psl


title: LH_39_1

value: Monocyte derived dendritic cells

value: LPS, HMW


title: T114a_DEHP_F_Blood_PND21

value: Female

value: DEHP


title: TTC_SC_69

tag: strain

value: tail tendon

value: WT

tag: age


title: T114b_DEHP_M_Blood_PND21

value: Male


title: LH_27_3

value: Donor 27


title: T113d_Ctrl_M_Blood_5mo

value: Ctrl

value: 5 months


title: TTC_SC_68

tag: genotype


title: control_342

value: lung tissue

value: control

value: no

value: GG

value: explant

tag: is

tag: batch

tag: lane


title: ipf_341

value: male

value: ipf

value: yes

value: UNKNOWN

value: NO

tag: plate

tag: institution

value: LTRC


title: T113c_Ctrl_F_Liver_5mo

value: Female

tag: treatment

tag: time


title: LH_27_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: LPS, HMW


title: TTC_SC_67

value: tail tendon

value: WT


title: LcG_45_3

value: Donor 45

tag: prr ligands

value: LPS, 2',3'-cGAMP


title: T113c_Ctrl_F_Blood_5mo

tag: Sex

value: Ctrl

value: 5 months


title: LH_39_2

value: Donor 39


title: LcG_45_2


title: control_339

value: lung tissue

tag: diagnosis

value: control

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: explant


title: T113b_Ctrl_M_Liver_PND21

value: Male


title: TTC_SC_66

tag: strain

tag: tissue


title: TTC_SC_65

tag: genotype

tag: age


title: T114a_DEHP_F_Liver_PND21

value: DEHP


title: LH_27_2

value: Donor 27


title: LcG_45_1


title: TTC_SC_64


title: T113b_Ctrl_M_Blood_PND21


title: control_337

value: male

value: yes

value: GT

value: biopsy

tag: psl

value: UNKNOWN

tag: is

value: NO

tag: batch

value: LTRC


title: ipf_336

value: ipf

tag: lane

tag: plate

tag: institution


title: LcG_39_3

tag: cell type

value: Monocyte derived dendritic cells

value: LPS, 2',3'-cGAMP


title: TTC_SC_63

value: tail tendon

value: WT


title: LcG_39_2

tag: donor

value: Donor 39


title: T113a_Ctrl_F_Liver_PND21

value: Female

tag: treatment

value: Ctrl

tag: time


title: T113a_Ctrl_F_Blood_PND21

tag: Sex


title: TTC_SC_62


title: control_340

value: lung tissue

value: female

tag: diagnosis

value: control

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG


title: control_332

value: yes

tag: sample type

value: biopsy


title: LcG_39_1

tag: prr ligands


title: control_330

tag: tissue

value: GT

value: UNKNOWN

value: NO


title: LcG_27_3

value: Monocyte derived dendritic cells

value: Donor 27


title: LcG_27_2

value: LPS, 2',3'-cGAMP


title: ipf_328

value: male

tag: age

value: ipf

value: LTRC


title: T112d_Lead_M_Blood_5mo

value: Male

value: Lead

value: 5 months


title: control_327

value: lung tissue

value: control

value: explant

tag: psl


title: TTC_SC_60

tag: strain

value: tail tendon

tag: genotype

value: WT


title: LcG_27_1


title: control_324

value: GG

value: biopsy

tag: is

tag: batch

tag: lane


title: control_319

value: yes

value: UNKNOWN

value: NO

tag: plate

tag: institution


title: TTC_SC_57


title: T112b_Lead_M_Liver_PND21

tag: treatment


title: control_331

value: female

value: no


title: L_45_3

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

value: LPS


title: TTC_SC_61


title: ipf_318

tag: Sex

value: male

tag: diagnosis

value: ipf

value: LTRC


title: TTC_SC_55


title: T112d_Lead_M_Liver_5mo

value: Male

value: Lead

tag: time

value: 5 months


title: L_45_1

tag: prr ligands


title: T112a_Lead_F_Liver_PND21

value: Female


title: control_315

tag: tissue

value: lung tissue

value: control

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

tag: sample type


title: T112c_Lead_F_Liver_5mo


title: L_39_3

value: Donor 39


title: TTC_SC_59

tag: strain

value: tail tendon

value: WT

tag: age


title: T112c_Lead_F_Blood_5mo


title: TTC_SC_54

tag: genotype


title: T112a_Lead_F_Blood_PND21


title: L_39_2


title: TTC_SC_58


title: T117a_DEHP_F_Blood_PND21

value: DEHP


title: ipf_309

value: no

value: GG

value: biopsy

tag: psl

value: UNKNOWN

tag: is

value: NO

tag: batch


title: L_45_2

value: Monocyte derived dendritic cells

value: Donor 45

value: LPS


title: LHZ_27_2

value: Donor 27

value: LPS, HMW, Zymosan depleted


title: T112b_Lead_M_Blood_PND21

value: Male

value: Lead


title: TTC_SC_53


title: TTC_SC_56


title: T111g_DEHP_F_Blood_5mo

value: Female

value: 5 months


title: L_27_3


title: TTC_SC_52

value: tail tendon


title: ipf_307

value: lung tissue

value: male

value: ipf

value: yes

value: GT

tag: lane

tag: plate

tag: institution

value: LTRC


title: TTC_SC_51

value: WT


title: L_39_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 39


title: control_306

tag: Sex

value: female

tag: diagnosis

value: control

value: no

value: biopsy

value: UNKNOWN

value: NO


title: L_27_2

value: Donor 27

tag: prr ligands

value: LPS


title: T111d_DEHP_M_Liver_5mo

value: Male

tag: treatment

value: DEHP

tag: time

value: 5 months


title: ipf_301

tag: tissue

value: lung tissue

value: ipf

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: explant


title: T111d_DEHP_M_Blood_5mo


title: TTC_SC_50

tag: strain

value: tail tendon

tag: genotype

value: WT

tag: age


title: T111g_DEHP_F_Liver_5mo

value: Female


title: TTC_SC_70


title: L_27_1

value: Monocyte derived dendritic cells


title: T111b_DEHP_M_Liver_PND21


title: control_300

value: male

value: control

value: GT

tag: psl

tag: is

tag: batch

value: LTRC


title: TTC_SC_49


title: HZS_45_3

value: Donor 45

value: HMW, Zymosan depleted, SeV


title: control_299

value: UNKNOWN

value: NO

tag: lane

tag: plate

tag: institution


title: TTC_SC_48


title: T111b_DEHP_M_Blood_PND21

tag: Sex

value: Male

value: DEHP


title: TTC_SC_47


title: HZS_45_2

tag: cell type

tag: donor


title: HZS_45_1

tag: prr ligands


title: control_296

value: lung tissue

value: female

tag: diagnosis

value: no

value: GG


title: TTC_SC_46

tag: tissue

value: tail tendon

value: WT


title: T111a_DEHP_F_Liver_PND21

value: Female

tag: treatment

tag: time


title: control_295

value: male

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: explant


title: control_293

tag: age

value: control

value: biopsy

value: LTRC


title: TTC_SC_44

tag: strain

tag: genotype


title: T110c_DEHP_F_Blood_5mo

value: 5 months


title: T111a_DEHP_F_Blood_PND21


title: T110c_DEHP_F_Liver_5mo


title: T110b_DEHP_M_Liver_PND21


title: HZS_39_3

value: Monocyte derived dendritic cells

value: Donor 39

value: HMW, Zymosan depleted, SeV


title: TTC_SC_43


title: HZS_39_1


title: HZS_39_2


title: HZS_27_3

value: Donor 27


title: control_292

value: lung tissue

value: female

tag: psl

value: UNKNOWN

tag: is

value: NO

tag: batch


title: T110b_DEHP_M_Blood_PND21

value: Male

value: DEHP


title: TTC_SC_42

value: tail tendon

value: WT


title: control_291

value: no

value: GG

tag: lane

tag: plate

tag: institution


title: control_298

tag: Sex

value: male

value: control

value: yes

value: biopsy


title: HZS_27_2

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

tag: prr ligands


title: control_289

tag: tissue

tag: diagnosis

value: LTRC


title: HZS_27_1

value: Donor 27

value: HMW, Zymosan depleted, SeV


title: T110a_DEHP_F_Liver_PND21

value: Female

tag: treatment

tag: time


title: T110a_DEHP_F_Blood_PND21


title: control_294

value: lung tissue

tag: age

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GT

tag: sample type

value: explant

value: UNKNOWN


title: control_288

tag: psl

value: NO


title: T109d_Ctrl_M_Liver_5mo

value: Male

value: Ctrl

value: 5 months


title: TTC_SC_40

tag: strain

value: tail tendon

tag: genotype

value: WT


title: TTC_SC_45


title: HZcG_45_2

value: Donor 45

value: HMW, Zymosan depleted, 2',3'-cGAMP


title: T109d_Ctrl_M_Blood_5mo


title: TTC_SC_39


title: control_286

value: female

value: control

value: yes

value: GG

value: biopsy

tag: is

tag: batch

tag: lane


title: TTC_SC_38


title: ipf_285

value: lung tissue

tag: Sex

value: male

value: ipf

tag: plate

tag: institution

value: LTRC


title: HZcG_45_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

tag: prr ligands


title: T109c_Ctrl_F_Liver_5mo

value: Female

tag: treatment


title: HZcG_39_3

value: Donor 39


title: ipf_282

tag: tissue

tag: diagnosis

value: no

value: GT

value: UNKNOWN

value: NO


title: control_283

tag: age

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)


title: HZcG_39_2

value: HMW, Zymosan depleted, 2',3'-cGAMP


title: TTC_SC_36

value: tail tendon

value: WT


title: TTC_SC_41


title: TTC_SC_35


title: T109c_Ctrl_F_Blood_5mo

value: Ctrl

tag: time

value: 5 months


title: control_281

value: female

value: control

value: GG

tag: sample type

value: biopsy

tag: psl


title: HZcG_39_1


title: T109b_Ctrl_M_Blood_PND21

value: Male


title: control_280

value: lung tissue

value: male

value: yes

tag: is

value: LTRC


title: TTC_SC_34

tag: strain

tag: genotype


title: HZcG_27_3

value: Monocyte derived dendritic cells

value: Donor 27


title: T109a_Ctrl_F_Liver_PND21

tag: Sex

value: Female


title: TTC_SC_33


title: HZcG_27_2

value: HMW, Zymosan depleted, 2',3'-cGAMP


title: HZcG_45_3

value: Donor 45


title: control_279

value: no

value: UNKNOWN

value: NO

tag: batch

tag: lane

tag: plate


title: TTC_SC_32

value: tail tendon

value: WT


title: TTC_SC_37


title: T109a_Ctrl_F_Blood_PND21

value: Ctrl


title: control_273

value: female

value: control

value: GT

value: biopsy

tag: institution


title: TTC_SC_31


title: T108d_Ctrl_M_Liver_5mo

value: Male

value: 5 months


title: T108d_Ctrl_M_Blood_5mo


title: ipf_270

value: lung tissue

value: male

value: ipf

value: yes

value: LTRC


title: HZcG_27_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands

value: HMW, Zymosan depleted, 2',3'-cGAMP


title: T109b_Ctrl_M_Liver_PND21

tag: treatment


title: TTC_SC_30

tag: tissue

value: tail tendon

tag: age


title: T108b_Ctrl_M_Liver_PND21

tag: time


title: TTC_SC_29

value: WT


title: control_267

tag: diagnosis

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: sample type

value: UNKNOWN

value: NO


title: HZ_45_2

value: Donor 45

value: HMW, Zymosan depleted


title: HZ_45_1


title: TTC_SC_28

tag: strain


title: control_264

value: female

value: control

value: biopsy

tag: psl

tag: is


title: T108a_Ctrl_F_Liver_PND21

tag: Sex

value: Female

value: Ctrl


title: TTC_SC_27

tag: genotype


title: TTC_SC_26


title: ipf_261

value: lung tissue

value: ipf

value: yes

tag: batch

tag: lane

tag: plate


title: T108a_Ctrl_F_Blood_PND21


title: T108b_Ctrl_M_Blood_PND21

value: Male


title: HZ_45_3

tag: cell type

value: Monocyte derived dendritic cells

tag: donor


title: HZ_39_2

value: Donor 39

tag: prr ligands


title: TTC_SC_25

tag: tissue

value: tail tendon

value: WT


title: HZ_39_3


title: HZ_39_1


title: control_258

tag: age

value: GG

value: UNKNOWN

tag: institution

value: LTRC


title: T107d_Lead_M_Liver_5mo

tag: treatment

value: Lead

tag: time

value: 5 months


title: T107d_Lead_M_Blood_5mo


title: HZ_27_3

value: Donor 27

value: HMW, Zymosan depleted


title: TTC_SC_24


title: TTC_SC_23


title: control_257

value: female

tag: diagnosis

value: control

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: sample type

value: biopsy

value: NO


title: control_256

value: lung tissue

value: male

value: yes

value: explant

tag: psl

tag: is


title: HZ_27_1

value: Monocyte derived dendritic cells


title: HScG_45_3

value: Donor 45

value: HMW, SeV, 2',3'-cGAMP


title: ipf_244

tag: Sex

value: ipf

value: GG

value: UNKNOWN

value: LTRC


title: T107b_Lead_M_Blood_PND21

value: Male

value: Lead


title: TTC_SC_22

tag: strain

value: tail tendon

tag: genotype

value: WT


title: TTC_SC_19


title: chp_138

value: chp

value: GT

tag: batch

tag: lane

tag: plate

value: UCSF


title: chp_143

value: lung tissue

value: female

value: YES


title: TTC_SC_20


title: HScG_39_2

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 39

tag: prr ligands


title: HScG_45_1

value: Donor 45

value: HMW, SeV, 2',3'-cGAMP


title: TTC_SC_21

tag: tissue

tag: age


title: TTC_SC_17


title: chp_142

value: male

value: yes

value: explant

value: NO

tag: institution


title: chp_144

tag: diagnosis

value: no


title: chp_141

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG


title: T106d_Lead_M_Blood_5mo

value: Male

tag: treatment

value: Lead

tag: time

value: 5 months


title: TTC_SC_18

value: tail tendon

value: WT


title: T107a_Lead_F_Liver_PND21

value: Female


title: T106d_Lead_M_Liver_5mo


title: HZ_27_2

value: Donor 27

value: HMW, Zymosan depleted


title: TTC_SC_16


title: HScG_39_3

value: Monocyte derived dendritic cells

value: Donor 39


title: chp_137

value: lung tissue

value: chp

tag: sample type

tag: psl

value: YES

tag: is

value: UCSF


title: HScG_27_3

value: HMW, SeV, 2',3'-cGAMP


title: HScG_39_1


title: T106c_Lead_F_Blood_5mo

tag: Sex


title: HScG_45_2

value: Donor 45


title: TTC_SC_15

tag: strain

tag: genotype


title: T106c_Lead_F_Liver_5mo


title: T106b_Lead_M_Liver_PND21


title: T107a_Lead_F_Blood_PND21


title: HScG_27_2


title: chp_136

value: male

value: yes

value: GT

value: explant

value: NO

tag: batch

tag: lane

tag: plate


title: T107b_Lead_M_Liver_PND21

value: Male

value: Lead


title: TTC_SC_14

value: tail tendon

value: WT


title: HScG_27_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 27

tag: prr ligands


title: HS_45_3

value: HMW, SeV


title: TTC_SC_13

tag: tissue

tag: age


title: HS_45_2


title: T106a_Lead_F_Blood_PND21

value: Female


title: chp_132

value: lung tissue

value: female

tag: diagnosis

value: chp

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: GG

tag: institution


title: chp_135

value: male

value: yes

tag: sample type

value: YES

value: UCSF


title: TTC_SC_12


title: HS_39_3

value: Donor 39


title: T106b_Lead_M_Blood_PND21

value: Male

tag: treatment

value: Lead

tag: time


title: chp_131

tag: Sex

value: GT

value: explant

tag: psl

tag: is

value: NO


title: T105d_Lead_M_Blood_5mo

value: 5 months


title: HS_39_2

value: Monocyte derived dendritic cells

value: HMW, SeV


title: HS_45_1

value: Donor 45


title: chp_130

value: lung tissue

value: chp

tag: batch


title: TTC_SC_10

tag: strain

value: tail tendon

tag: genotype

value: WT


title: chp_134

value: male

value: no

value: GG

tag: lane

tag: plate


title: T105d_Lead_M_Liver_5mo


title: chp_133

value: YES

value: UCSF


title: TTC_SC_11


title: T106a_Lead_F_Liver_PND21

value: Female

value: Lead


title: HS_39_1

tag: cell type

tag: donor

value: Donor 39

tag: prr ligands


title: TTC_SC_9

tag: tissue

tag: age


title: T105c_Lead_F_Liver_5mo


title: T105b_Lead_M_Liver_PND21

value: Male


title: T105c_Lead_F_Blood_5mo

value: 5 months


title: TTC_SC_7


title: TTC_SC_8


title: HS_27_3

value: Monocyte derived dendritic cells

value: Donor 27


title: chp_128

value: female

tag: diagnosis

value: yes

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: explant

value: NO

tag: institution


title: TTC_SC_6

value: tail tendon

value: WT


title: T105b_Lead_M_Blood_PND21

tag: treatment

tag: time


title: chp_127

value: lung tissue

tag: Sex

value: male

value: chp

value: no

tag: sample type

tag: psl


title: HS_27_2

value: HMW, SeV


title: HS_27_1


title: T105a_Lead_F_Blood_PND21

value: Female

value: Lead


title: chp_129

value: GG

tag: is

tag: batch

value: UCSF


title: TTC_SC_3

tag: strain

tag: genotype


title: TTC_SC_5


title: chp_122

value: GT

value: YES

tag: lane

tag: plate


title: chp_121

value: female


title: HcG_45_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

tag: prr ligands

value: HMW, 2',3'-cGAMP


title: T104j_DEHP_M_Liver_5mo

value: Male

value: DEHP

value: 5 months


title: chp_125

tag: tissue

value: lung tissue

value: male

tag: age

tag: diagnosis

value: explant

value: NO


title: HcG_45_3


title: T104j_DEHP_M_Blood_5mo

tag: treatment


title: TTC_SC_2

value: tail tendon

value: WT


title: TTC_SC_1


title: chp_120

value: chp

value: no

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: institution


title: HcG_45_2


title: HcG_39_3

value: Donor 39


title: T104d_DEHP_M_Blood_5mo

tag: Sex

tag: time


title: T104c_DEHP_F_Liver_5mo

value: Female


title: T105a_Lead_F_Liver_PND21

value: Lead


title: chp_119

value: female

value: yes

value: GT

tag: sample type

tag: psl

tag: is

value: UCSF


title: TTC_SC_4

tag: strain

tag: genotype


title: chp_117

value: GG

value: YES

tag: batch

tag: lane

tag: plate


title: HcG_39_1

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

tag: prr ligands

value: HMW, 2',3'-cGAMP


title: chp_126

tag: tissue

value: lung tissue

tag: age

tag: diagnosis

value: explant


title: T104c_DEHP_F_Blood_5mo

tag: treatment

value: DEHP

value: 5 months


title: chp_115

tag: Sex

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: NO

tag: institution


title: HcG_27_2

value: Donor 27


title: HcG_27_1


title: HcG_27_3


title: T104d_DEHP_M_Liver_5mo

value: Male

tag: time


title: chp_113

value: male

value: no

tag: sample type

tag: psl

tag: is


title: T104b_DEHP_M_Liver_PND21


title: T104a_DEHP_F_Liver_PND21

value: Female


title: H_45_3

value: Donor 45

value: HMW


title: chp_114

value: GG

tag: batch

value: UCSF


title: chp_112

value: female

value: YES

tag: lane


title: H_45_2

value: Monocyte derived dendritic cells


title: T104a_DEHP_F_Blood_PND21


title: T103d_Lead_M_Blood_5mo

value: Lead


title: T104b_DEHP_M_Blood_PND21

value: DEHP


title: HcG_39_2

value: Donor 39

value: HMW, 2',3'-cGAMP


title: chp_111

value: lung tissue

value: chp

value: yes

value: GT

value: explant

value: NO

tag: plate


title: A549 cells, 2D-cultured, gefitinib-treated

type: RNA

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.2.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

label: biotin

label_protocol: 100ng of total RNA were amplified and labeled with the IVT PLUS Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: For 3D conditions, 100.000 cells per cell line were seeded onto a collagen scaffold and cultured for 14 days under static conditions at 37°C with 5% CO2 and 95% humidity. Under 2D conditions, 200.000 cells were seeded onto 21cm² culture dishes and cultured for 7 days at 37°C with 5% CO2 and 95% humidity.

extract_protocol: Collagen matrices with cells were harvested and frozen at -80°C. Frozen samples were cut into small pieces and lysed using metal beads and the Qiagen TissueLyser at 50Hz for 5min. RNA extraction was carried out according to the Qiagen RNeasy micro kit (3D samples) or RNeasy mini kit (2D samples) protocols.

treatment_protocol: Control samples were cultured without inhibitor treatment as described above for both culture conditions. The EGFR-Inhibitor gefitinib was applied after 11 days of static culture at a concentration of 1µM for the following 3 days under 3D culture conditions. Under 3D conditions gefitinib was applied after 4 days of culture at a concentration of 1µM.

tag: cell line

tag: activating egfr mutation

value: no

value: gefitinib

tag: cell culture


title: T103d_Lead_M_Liver_5mo

value: Male

value: 5 months


title: HCC827 cells, 2D-cultured, gefitinib-treated


title: H_45_1

tag: cell type

tag: donor

value: Donor 45

tag: prr ligands

value: HMW


title: HCC827 cells, 2D-cultured, control-treated

tag: treatment

value: control


title: A549 cells, 2D-cultured, control-treated


title: HCC827 cells, 3D-cultured, gefitinib-treated


title: HCC827 cells, 3D-cultured, control-treated


title: armadillo_uterus_NP_1

city: West Haven

first: Arun

middle: Rajendra

last: Chavan

state: CT

address: 850 West Campus Drive

department: Ecology and Evolutionary Biology

institute: Yale University

data_processing:
BaseCalls performed using CASAVA
Reads were aligned to the Dasypus novemcinctus genome Dasnov3.0 using Tophat2 v2.0.6
Aligned reads mapping to each gene were counted using HTSeq-count. GTF file for Ensembl genebuild Dasnov3.0.77 was used.
Genome_build: Dasnov3.0
Supplementary_files_format_and_content: tab delimited file with Ensembl Gene ID and the number of reads mapping to each Ensembl Gene ID

organism: Dasypus novemcinctus

source_name: Uterus

extract_protocol:
RNA was extracted with Qiagen RNeasy kit
Standard Illumina protocol

tag: tissue

value: Uterus

tag: Stage

value: non-pregnant

tag: tissue preparation

value: The area of whole uterus was collected into RNA extraction buffer by microdissection from tissue frozen in OCT block.


title: H_39_1

value: Monocyte derived dendritic cells

value: Donor 39


title: H_39_2


title: chp_108

value: lung tissue

tag: Sex

value: female

tag: age

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

tag: institution

value: UCSF


title: A549 cells, 3D-cultured, gefitinib-treated


title: armadillo_uterus_imp_1

description: Two raw and processed files are for two sequencing runs of the same sample. Means of TPM normalized gene expression were used for analysis.

value: peri-implantation

value: Uterine tissue was collected and stored in RNAlater


title: chp_109

value: no

value: GG

tag: sample type

value: explant

tag: psl

value: YES

tag: is

value: NO

tag: batch

tag: lane


title: T103b_Lead_M_Liver_PND21

value: Male

value: Lead

tag: time


title: H_39_3

tag: cell type

tag: donor

value: HMW


title: H_27_3

value: Donor 27

tag: prr ligands


title: chp_110

tag: tissue

value: yes

value: GT

tag: plate


title: chp_105

value: lung tissue


title: DN-SM2

city: Beijing

first: Gaoyan

last: La

address: Huayuan North Road NO.49

department: The Department of Rehabilitation Medicine

institute: Peking University Third Hospital

data_processing:
base-calling using GATK
Data Filtering using SOAPnuke
alignment using HISAT2 to map clean reads to reference genome
Gene quantification using RSEM
Screening of differentially expressed genes using NOISeq
Genome_build: ucsc,rn6
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: gastrocnemius muscle

growth_protocol: 8 weeks old male rats, the specific pathogen free rats were housed in at 20℃,with alternating 12:12 of light/darkness cycles, and consumed a standard chow diet and water ad libitum.

extract_protocol:
Total RNA was harvested using Trizol reagent. BGISEQ-500 was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA library was prepared following DNase I digest, mRNA isolation, mRNA fragment, cDNA synthesis, repair and validated on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: The animals in the group of DN-SM accepted daily electrical stimulation for 4 weeks immediately after the surgery day. 15 minutes after anesthesia by sodium pentobarbital, the left leg skin above the gastrocnemius muscle region were shaved and wetted by warm saline, and two surface electrodes were put on the skin. The stimulator (ZS Dichuang, China) connected to the electrodes were set as: voltage 25 V , current 1mA, square pulse 2 Hz, pulse width 300 ms. Apparent heel lifting movement could be observed while being stimulated. The animals in SHAM and DN groups were also anesthetized, shaved, wetted and placed with the two electrodes for 10 minutes, which was in the same way with the DN-SM group, but no electricity was provided.

value: 8 weeks

value: male

value: gastrocnemius muscle

tag: operation

value: sciatic nerve injury

tag: treatmant

value: electrical stimulation


title: DN-SM3

tag: age

tag: Sex


title: T103c_Lead_F_Blood_5mo

value: Female

tag: treatment

value: 5 months


title: H_27_1

value: Monocyte derived dendritic cells


title: H_27_2


title: T103b_Lead_M_Blood_PND21


title: T103c_Lead_F_Liver_5mo


title: DN-SM1


title: chp_106

value: female

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: explant

value: YES

tag: institution

value: UCSF


title: T103a_Lead_F_Liver_PND21

value: Lead


title: DN2

value: no treatment


title: chp_101

value: no

value: GG

tag: sample type

value: biopsy

tag: psl

value: NO

tag: is


title: T103a_Lead_F_Blood_PND21

tag: time


title: DN3

value: 8 weeks

value: male

value: gastrocnemius muscle


title: chp_50

value: lung tissue

value: UNKNOWN

value: GT

tag: batch

tag: lane

value: NJH


title: Ctrl_45_6

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

tag: prr ligands

value: Ctrl


title: chp_103

tag: tissue

value: chp

value: yes

value: YES

tag: plate

value: UCSF


title: Ctrl_45_5


title: chp_49

value: female

tag: age

value: explant


title: DN1

tag: Sex

tag: operation

value: sciatic nerve injury

tag: treatmant

value: no treatment


title: T102b_Lead_M_Liver_PND21

value: Male

tag: treatment

value: Lead


title: SHAM3

value: 8 weeks

value: male

value: gastrocnemius muscle

value: sham operation


title: T102c_Lead_F_Blood_5mo

value: Female

value: 5 months


title: A549 cells, 3D-cultured, control-treated

tag: cell line

tag: activating egfr mutation

value: no

value: control

tag: cell culture


title: chp_48

value: lung tissue

tag: diagnosis

value: chp

tag: race (hispanic;1, black;3,asian;4, white;5, other;6)

value: UNKNOWN

value: GT

tag: sample type

tag: psl

tag: is

value: NO

tag: institution

value: NJH


title: Ctrl_45_4

tag: cell type

value: Monocyte derived dendritic cells

tag: donor

value: Donor 45

tag: prr ligands

value: Ctrl


title: Ctrl_45_3


title: SHAM1

tag: age

value: 8 weeks

tag: tissue

value: no treatment


title: T102c_Lead_F_Liver_5mo

tag: Sex

value: Lead

tag: time


title: chp_47

value: male

value: GG

value: explant

tag: batch

tag: lane

tag: plate


title: Ctrl_45_1


title: chp_45


title: T102a_Lead_F_Liver_PND21

value: Female

tag: treatment


title: T102a_Lead_F_Blood_PND21