title: Invitro-E1

description:
tpm_invitro.txt
Invitro-E1_S13
24476 protein-coding and 16648 non-coding RNA genes


title: BRBS248

status: Public on Jul 07 2020

type: SRA

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to mouse genome GRCm38 using STAR version 2.2.1 with default parameters except --sjdbOverhang 49 --outSAMstrandField intronMotif --outFilterMultimapNmax 1 (The max number of multiple alignments allowed for a read is 1. if exceeded, the read is considered unmapped).
Read counting was performed using HTSeq-Count (version 0.9.1) with parameters --stranded=no -m union, and using the annotations of mouse genome GRCm38 release 94 downloaded from the ENSembl website. In short, our RNA-Seq data has not been made with a strand-specific protocol. When a read was mapped to more than one gene, it was considered as ambiguous and assigned to none of them.
Genome_build: GRCm38 with an additional artificial chromosome for the YFP sequence
Supplementary_files_format_and_content: Text files with tab delimiters including raw gene counts and metadata (including index sorting information) for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: splenic plasmacytoid dendritic cells

extract_protocol:
Single cells were FACS sorted into 96-well PCR plates (Eppendorf), each well containing 10 µl of TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol. Plates were spun down at 800g for 1 min, flash frozen on dry ice and stored at -80°C until further processing (Villani and Shekhar, 2017).
Single cell RNA-sequencing libraries were generated using an adaptation of Smart-Seq2 (Villani and Shekhar, 2017).
Full-length RNA-sequencing was performed.

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: BRBS113

value: UN


title: Invitro-E2

city: Pittsburgh

first: Samira

last: Kiani

state: Pennsylvania

address: A809-B Scaife Hall 3550 Terrace Street Pittsburgh

department: Division of Experimental Pathology

country: USA

institute: University of Pittsburgh

description:
tpm_invitro.txt
Invitro-E2_S14
24476 protein-coding and 16648 non-coding RNA genes

data_processing:
FASTQ files for samples were aligned to genome GRCm38 (Ensembl 96) respectively, by STAR (ver 2.6.0.a) with paraters of --outSAMmultNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.2 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000'
TPM (Transcripts Per Kilobase Million) values were calculated based on the formula  〖RPK〗_i=  (Reads mapped to 〖gene〗_i  ×10^3)/(Longest 〖gene〗_i  transcript in bp)  〖TPM〗_i=〖RPK〗_i×  1/(∑_i▒〖RPK〗_i )×10^6
Longest gene transcripts in bp were obtained from GRCm38 (Ensembl 96).  Customized GRCm38 (Ensembl 96), where gene sequence was added into the reference genome, and been annotated as ‘ENSG0000’ in gene id.
Genome_build: GRCm38
Supplementary_files_format_and_content: A text file with abundance measurement matrix in TPM

molecule: total RNA

source_name: Neuro-2A cells

growth_protocol: For the invitro data, Neuro-2a cell lines (purchased from ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM - Life Technologies) with 10% fetal bovine serum (FBS - Life Technologies), 2mM glutamine, 1.0 mM sodium pyruvate (Life Technologies) and 1% streptomycin– penicillin mix (Gibco) in incubators at 37 °C and 5% CO2.

extract_protocol:
For the invitro data, Cells were lysed, and RNA was extracted using RNeasy Plus mini kit (Qiagen) 72 hrs post transfection and sent to UCLA TCGB core on dry ice. For the invivo data, RNA was extracted from mice bone marrow samples using RNeasy Plus Mini Kit (Qiagen) followed by globin mRNA depletion using GLOBINclear™ Kit, mouse/rat kit (Thermofisher).
For the invitro data,, Ribosomal RNA depletion and paired end read library preparation were performed at UCLA core followed by RNA sequencing using NextSeq500.  Coverage was 20 million reads per sample.  FASTQ files with pair-ended 75bp reads were then aligned to the mouse GRCm38 reference genome sequence (Ensembl release 90) with STAR, and uniquely-mapped read counts (an average of 14.8  million reads per sample) were obtained with Cufflink.  The read counts for each sample were then normalized for the library size to CPM (counts per million reads) with edgeR .  Custom R scripts were then used to generate plots. For the invivo data, None-directional library preparation was performed at Novogene Corporation Inc. followed by RNA sequencing using Illumina Nova Platform with paired-end 150 run (2×150 bases). Coverage was minimum 25 million reads per sample. FASTQ files were then aligned to mouse genome sequence using STAR software and uniquely mapped read counts were visualized with Integrative Genomics Viewer (IGV). Gene expression level was calculated by the number of mapped reads. According to all gene expression level (RPKM or FPKM) of each sample, correlation coefficient of sample between groups was calculated. Read counts obtained from Gene Expression Analysis were used for differential expression analysis and differential expression analysis of different groups was performed using the DESeq2 R package51. Hierarchical clustering analysis was carried out of log10 (FPKM+1) of union differential expression genes, within all comparison groups. ClusterProfiler52 software was used for enrichment analysis, including GO Enrichment, DO Enrichment, KEGG Enrichment and Reactome Enrichment.

treatment_protocol: For the invitro data, Neuro-2a cells were co-transfected with 10ng gRNA targeting Myd88 loci, respectively. 200ng dCas9 constructs, 100ng MS2-HP1aKRAB, 50ng puromycin resistant gene, and 25ng transfection control. Cells were treated with 0.5ug/ml puromycin (Gibco-life tech) at 24 hours post-transfection.

tag: cell line

value: Neuro 2A

tag: treatment

value: Transfected with Cas9, full length gRNA targeting Myd88 locus and repressor domains


title: PTID3_Visit2_PBMC

type: RNA

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

hyb_protocol: standard as recommended by illumina

scan_protocol: standard Illumina protocol using Illumina iScan system

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 7 samples were included in the analysis.

organism: Homo sapiens

source_name: PBMC from PTID3 at Visit2

label_protocol: Labeling was performed using 275 ng total RNA and the Life Technologies/Ambion Illumina TotalPrep RNA Amplification kit

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit

tag: ptid

tag: visit

value: PBMC

tag: rin


title: PTID4_Visit2_PBMC

source_name: PBMC from PTID4 at Visit2


title: PTID2_Visit2_PBMC

source_name: PBMC from PTID2 at Visit2


title: BRBS251


title: BRBS247


title: Invitro-D3

description:
tpm_invitro.txt
Invitro-D3_S12
24476 protein-coding and 16648 non-coding RNA genes

value: Transfected with Cas9, truncated gRNA targeting Myd88 locus and repressor domains


title: PTID8_Enrollment_Duodenal

source_name: Duodenal from PTID8 at Enrollment

extract_protocol: Total RNA was extracted using the Qiagen Fibrous Tissue RNeasy mini kit

value: Enrollment

value: Duodenal


title: PTID1_Enrollment_PBMC

source_name: PBMC from PTID1 at Enrollment


title: PTID2_Enrollment_PBMC

source_name: PBMC from PTID2 at Enrollment


title: PTID6_Enrollment_Duodenal

source_name: Duodenal from PTID6 at Enrollment


title: PTID7_Visit2_Duodenal

source_name: Duodenal from PTID7 at Visit2


title: PTID7_Enrollment_Duodenal

source_name: Duodenal from PTID7 at Enrollment


title: PTID5_Enrollment_Duodenal

source_name: Duodenal from PTID5 at Enrollment


title: PTID4_Visit2_Duodenal

source_name: Duodenal from PTID4 at Visit2


title: PTID5_Visit2_Duodenal

source_name: Duodenal from PTID5 at Visit2


title: PTID6_Visit2_Duodenal

source_name: Duodenal from PTID6 at Visit2


title: BRBS245


title: BRBS246


title: Invitro-D2

description:
tpm_invitro.txt
Invitro-D2_S11
24476 protein-coding and 16648 non-coding RNA genes


title: Invitro-D1

description:
tpm_invitro.txt
Invitro-D1_S10
24476 protein-coding and 16648 non-coding RNA genes


title: BRBS242


title: BRBS240

value: MCMV YFPpos


title: BRBS243


title: BRBS241


title: BRBS244


title: CREpos_m2037_div8neg

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 using TopHat2 and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to fragments per kilobase per million (FPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 3 reads per million in all samples for at least one group.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing FPKM normalized read counts for all detected genes.

source_name: B cell

extract_protocol:
Cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: B cells were harvested from the spleen 72 hours following LPS innoculation.

tag: Sex

value: Female

tag: mouse id

tag: sorting markers

value: Spleen

tag: cell division

tag: cd138 status

value: Negative

tag: cd19-cre status

value: Positive

tag: b cell genotype

value: CD19-CRE;Blimp1 fl/fl


title: BRBS238

tag: mouse genotype

tag: cell type


title: BRBS239

tag: tissue

tag: infection time


title: PTID2_Enrollment_Duodenal

source_name: Duodenal from PTID2 at Enrollment


title: PTID6_Visit2_PAXgene

source_name: PAXgene from PTID6 at Visit2

extract_protocol: Total RNA was extracted using the Preanalytix PAXgene Blood RNA Kit

value: whole blood


title: PTID1_Enrollment_Duodenal

source_name: Duodenal from PTID1 at Enrollment


title: PTID5_Enrollment_PAXgene

source_name: PAXgene from PTID5 at Enrollment


title: CREpos_m2037_div5


title: PTID5_Visit2_PAXgene

source_name: PAXgene from PTID5 at Visit2


title: PTID3_Visit2_PAXgene

source_name: PAXgene from PTID3 at Visit2


title: PTID3_Visit2_Duodenal

source_name: Duodenal from PTID3 at Visit2


title: PTID3_Enrollment_Duodenal

source_name: Duodenal from PTID3 at Enrollment


title: PTID2_Visit2_Duodenal

source_name: Duodenal from PTID2 at Visit2


title: PTID4_Enrollment_Duodenal

source_name: Duodenal from PTID4 at Enrollment


title: PTID8_Visit2_PAXgene

source_name: PAXgene from PTID8 at Visit2


title: CREpos_m2037_div3


title: PTID1_Visit2_Duodenal

source_name: Duodenal from PTID1 at Visit2


title: PTID7_Enrollment_PAXgene

source_name: PAXgene from PTID7 at Enrollment


title: PTID7_Visit2_PAXgene

source_name: PAXgene from PTID7 at Visit2


title: CREpos_m2037_div1


title: BRBS237

source_name: splenic plasmacytoid dendritic cells

value: pDC

tag: eyfp status

tag: plate


title: PTID8_Enrollment_PAXgene

source_name: PAXgene from PTID8 at Enrollment


title: BRBS112

value: spleen


title: PTID4_Enrollment_PAXgene

source_name: PAXgene from PTID4 at Enrollment


title: PTID2_Enrollment_PAXgene

source_name: PAXgene from PTID2 at Enrollment


title: PTID3_Enrollment_PAXgene

source_name: PAXgene from PTID3 at Enrollment


title: PTID6_Enrollment_PAXgene

source_name: PAXgene from PTID6 at Enrollment


title: PTID2_Visit2_PAXgene

source_name: PAXgene from PTID2 at Visit2


title: CREneg_m2016_div8pos

source_name: B cell

value: Blimp1 fl/fl


title: PTID4_Visit2_PAXgene

source_name: PAXgene from PTID4 at Visit2


title: PTID1_Enrollment_PAXgene

source_name: PAXgene from PTID1 at Enrollment


title: CREneg_m2016_div8neg


title: MTN017_036_RectalBiopsy_TFV_RectalPericoital_Visit10

first: Florian

last: Hladik

address: 850 Republican Street

department: Obstetrics and Gynecology

data_processing:
The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.
Matrix normalized data: This table contains detection p-values and signal intensity data that were transformed with a variance stabilizing transformation and normalized with a robust spline normalization using the Bioconductor lumi package (version 2.34.0). The normalized data was filtered to only include probes with a detection threshold p value <0.05 in at least 10 samples. Non-normalized data: This table contains raw signal intensity values and detection p-values for each sample.

source_name: Rectal tissue from participant MTN017 036 during Rectal pericoital treatment

label_protocol: Labeling was performed using 500 ng total RNA and the Life Technologies/Ambion Illumina TotalPrep RNA Amplification kit

value: rectal

tag: site

value: Thailand - Bangkok


title: BRBS234

value: MCMV YFPneg


title: BRBS236


title: CREneg_m2016_div5


title: CREneg_m2016_div3


title: BRBS232


title: BRBS233


title: CREneg_m2015_div8pos


title: CREneg_m2015_div5


title: PTID1_Visit2_PAXgene

source_name: PAXgene from PTID1 at Visit2

tag: ptid


title: BRBS230


title: BRBS231


title: BRBS235


title: BRBS229


title: CREneg_m2015_div3


title: MTN017_035_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 035 during Rectal daily treatment


title: MTN017_036_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 036 at Baseline


title: CREneg_m2015_div1


title: MTN017_036_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 036 during Oral treatment


title: MTN017_035_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 035 at Baseline


title: BRBS228


title: MTN017_035_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 035 during Oral treatment


title: MTN017_034_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 034 during Oral treatment


title: MTN017_034_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 034 during Rectal daily treatment


title: MTN017_033_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 033 during Rectal pericoital treatment


title: CREneg_m2015_div0


title: CREpos_m2014_div8neg


title: MTN017_033_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 033 during Rectal daily treatment


title: MTN017_036_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 036 during Rectal daily treatment


title: MTN017_035_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 035 during Rectal pericoital treatment


title: MTN017_034_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 034 during Rectal pericoital treatment


title: MTN017_033_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 033 during Oral treatment


title: MTN017_034_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 034 at Baseline


title: BRBS111

source_name: splenic plasmacytoid dendritic cells

value: UN


title: CREpos_m2014_div3

source_name: B cell


title: CREpos_m2014_div5


title: BRBS227


title: BRBS226


title: MTN017_032_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 032 during Rectal daily treatment


title: MTN017_033_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 033 at Baseline


title: MTN017_031_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 031 during Rectal pericoital treatment


title: MTN017_032_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 032 during Oral treatment


title: MTN017_031_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 031 during Rectal daily treatment


title: CREpos_m2014_div0


title: MTN017_032_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 032 during Rectal pericoital treatment


title: MTN017_032_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 032 at Baseline


title: MTN017_031_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 031 during Oral treatment


title: BRBS224


title: BRBS223


title: CREpos_m2012_div8neg

value: Male


title: MTN017_031_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 031 at Baseline


title: MTN017_030_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 030 during Oral treatment


title: CREpos_m2014_div1


title: BRBS221


title: MTN017_030_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 030 during Rectal daily treatment


title: MTN017_030_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 030 during Rectal pericoital treatment


title: MTN017_029_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 029 during Rectal pericoital treatment


title: BRBS225


title: MTN017_029_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 029 during Rectal daily treatment


title: MTN017_030_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 030 at Baseline


title: CREpos_m2012_div3


title: MTN017_029_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 029 during Oral treatment


title: BRBS220

source_name: splenic plasmacytoid dendritic cells


title: BRBS222


title: MTN017_028_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 028 during Rectal pericoital treatment


title: CREpos_m2012_div1

source_name: B cell


title: CREpos_m2012_div0


title: BRBS219


title: CREpos_m2012_div5


title: CREpos_m2011_div8neg


title: BRBS218


title: CREpos_m2011_div5


title: BRBS110


title: BRBS217


title: CREpos_m2011_div3


title: BRBS216


title: CREpos_m2011_div1


title: CREpos_m2011_div0


title: BRBS214


title: BRBS213


title: CREneg_m2010_div8neg


title: CREneg_m2010_div8pos


title: MTN017_028_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 028 during Rectal daily treatment


title: BRBS215


title: CREneg_m2010_div5


title: CREneg_m2010_div3


title: CREneg_m2010_div1


title: MTN017_028_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 028 during Oral treatment


title: MTN017_025_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 025 during Rectal daily treatment


title: MTN017_029_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 029 at Baseline


title: MTN017_024_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 024 during Rectal pericoital treatment


title: MTN017_027_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 027 during Rectal daily treatment


title: BRBS210


title: BRBS209


title: BRBS212


title: MTN017_026_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 026 during Rectal daily treatment


title: BRBS208


title: MTN017_025_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 025 at Baseline


title: MTN017_024_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 024 during Oral treatment


title: MTN017_027_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 027 at Baseline


title: MTN017_026_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 026 during Oral treatment


title: MTN017_026_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 026 at Baseline


title: MTN017_024_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 024 at Baseline


title: CREneg_m2010_div0


title: MTN017_027_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 027 during Rectal pericoital treatment


title: MTN017_025_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 025 during Oral treatment


title: MTN017_024_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 024 during Rectal daily treatment


title: MTN017_026_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 026 during Rectal pericoital treatment


title: MTN017_028_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 028 at Baseline


title: MTN017_023_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 023 during Oral treatment


title: MTN017_023_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 023 during Rectal daily treatment


title: BRBS109

source_name: splenic plasmacytoid dendritic cells


title: BRBS207


title: shHMGB1 Bliss Untreated Replicate 1

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

data_processing:
trimming with Trimmomatic (v0.32)
extract UMI with umi_tools extract (v0.5.3)
alignment with bwa mem (v0.7.5-r404)
filtering for quality (samtools view -q 5)
deduplicate UMI with umi_tools dedup (--edit-distance-threshold 2 )
aggregation with bedtools (samtools view -b -f 67 ; bamToBed ; bedtools sort ; bedtools merge -o collapse,count -d 8 -c 2,2)
Genome_build: mm10
Supplementary_files_format_and_content: clean.umi_dedup.aggregated.bed = BED file with aggregated Double Strand Breaks with number of different UMIs in column 3 and count in column 4

source_name: AB22 cells plus shHMGB1

growth_protocol: Murine malignant mesothelioma (MM) AB22 cells were obtained from Cell Bank Australia and cultured in RPMI 1640 supplemented with 10% v/v FBS, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin.

extract_protocol:
the BLISS protocol described in Yan et al, 2017 was followed. Paraformaldehyde fixed cells on coverslips were permeabilised and DNA free ends were blunted prior to ligation in situ of oligonucleotides adapters. Genomic DNA is isolated from cells by phenol:chloroform purification protocol and sonicated to achieve a mean fragment size of 300-500bp. Genomic DNA purified with AMPure beads is used as template in In Vitro Transcription reaction. RNA is isolated from IVT reaction using agencourt RNAClean XP beads after DNAseI treatment.
libraries were prepared from RNA with TruSeq smallRNA Library Prep Kit (Illumina)

treatment_protocol: For the silencing of HMGB1, shCTRL-MM and shHMGB1-MM were obtained by infection with pTRIPZ-shCTRL or pTRIPZ-shHMGB1 viral particles at a multiplicity of infection of 20; transduced cells were selected with 4 μg/mL puromycin. Cells were then cultured in RPMI1640, as above, using tetracycline-free FBS (Euroclone).  All cells were cultured in humidified incubator at 37°C with 5% oxygen.shRNA expression was induced by adding 1 μM doxycycline (Sigma) to the culture medium. All experiments were performed after 7-10 days from doxycycline addition.  For the DSB irradiation treatment, G1-synchronised shCTRL and shHMGB1 MM cells and irradiated them with 0, 3, 5 and 10 Grays from a Caesium137 source.

tag: cell line

tag: silencing

tag: dose (gy)


title: MTN017_023_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 023 during Rectal pericoital treatment

tag: rin


title: BRBS204


title: BRBS206


title: shHMGB1 Bliss 5 Gy Replicate 2


title: shHMGB1 Bliss Untreated Replicate 2


title: BRBS205


title: BRBS202


title: MTN017_022_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 022 during Oral treatment


title: MTN017_027_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 027 during Oral treatment


title: BRBS200


title: MTN017_025_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 025 during Rectal pericoital treatment


title: BRBS201


title: shHMGB1 Bliss 5 Gy Replicate 1


title: shHMGB1 Bliss 3 Gy Replicate 1


title: shHMGB1 Bliss 3 Gy Replicate 2


title: shHMGB1 Bliss 10 Gy Replicate 2


title: BRBS198


title: MTN017_022_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 022 during Rectal pericoital treatment


title: MTN017_021_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 021 during Oral treatment


title: MTN017_020_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 020 at Baseline


title: BRBS199


title: BRBS108


title: shCTRL Bliss Untreated Replicate 1

source_name: AB22 cells plus shCTRL

value: shCTRL


title: MTN017_021_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 021 at Baseline


title: shHMGB1 Bliss 10 Gy Replicate 1


title: MTN017_019_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 019 during Oral treatment


title: MTN017_019_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 019 at Baseline


title: MTN017_020_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 020 during Oral treatment


title: MTN017_021_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 021 during Rectal pericoital treatment


title: MTN017_022_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 022 during Rectal daily treatment


title: shCTRL Bliss 5 Gy Replicate 2


title: MTN017_020_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 020 during Rectal daily treatment


title: MTN017_018_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 018 during Oral treatment

value: USA - Pittsburgh


title: MTN017_021_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 021 during Rectal daily treatment


title: MTN017_019_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 019 during Rectal daily treatment


title: shCTRL Bliss Untreated Replicate 2


title: MTN017_018_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 018 during Rectal pericoital treatment


title: BRBS99

source_name: splenic plasmacytoid dendritic cells


title: MTN017_020_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 020 during Rectal pericoital treatment


title: MTN017_023_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 023 at Baseline


title: MTN017_022_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 022 at Baseline


title: MTN017_018_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 018 during Rectal daily treatment


title: MTN017_018_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 018 at Baseline


title: shCTRL Bliss 3 Gy Replicate 2

source_name: AB22 cells plus shCTRL


title: KLBtdTomHyp_Rep3_Panel1

city: Iowa City

first: Kyle

middle: Harrington

last: Flippo

state: IA

address: 169 Newton Road, 3320 PBDB

department: Neuroscience and Pharmacology

institute: University of Iowa

description: UMI counts per cell

data_processing:
BD Rhapsody Analysis Pipeline:
Filter by read quality
Annotate R1 reads. R1 contains the cell barcode and UMI according to the structure shown in read1_structure_image.png, available on the series record.
Annotate R2 reads
Combine R1 and R2 reads
Annotate molecules
Determine putative cells: The number of reads associated with each cell ID were on a log10 transformed cumulative curve with reads associated with a cell ID plotted in descending order. Using second derivative analysis we identify the inflection point in the curve and anything cell ID with a number of reads greater than that defined at the inflection point is considered a putative cell (cell ID set A). Any cell ID with a number of reads less than that defined by the inflection point is considered noise and not counted as a cell. We then remove potential false positively identified cells through identifying the most variable genes (using a method similar to that previously described, PMID: 26000488) and performing second derivative analysis on the most variable genes. Specifically, a second derivative analysis is applied on variable gene sets defined by a different cutoff value for the normalized dispersion to derive the filtered cell ID set (cell ID set B). For each dispersion cutoff, the noise cell labels are determined as A   B. For instance, for three cutoff values, noise cell labels are N1 = A   B1, N2 = A   B2, and N3 = A   B3, where the minus sign represents the set difference. The common noise cell IDs detected among N1, N2, and N3 are subtracted from cell ID set A.
Generate expression matrices
Annotate SAM
Genome_build: mm9
Supplementary_files_format_and_content: .csv with UMI counts per cell

source_name: Hypothalamus

extract_protocol:
The method used here for generating single cell suspensions for FACs sorting was modified from a previously published protocol (Chung et. al, 2017, Nature). Brains were dissected from mice immediately following decapitation and placed in ice cold artificial cerebrospinal fluid (ACSF) containing 126 mM NaCl, 20 mM NAHCO3, 20 mM dextrose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM MgCl2 which was bubbled with carbogen gas (95% O2 and 5% CO2) for at least 15 minutes prior to dissection. The hypothalamus was then dissected from each brain, and three hypothalami were pooled for each capture. The tissue was then minced and placed in 2mg/ml Pronase in ACSF and incubated at 37°C for 30 minutes. Following incubation, the supernatant was removed and tissue was resuspended in HBSS w/ 10% FBS. The tissue was then titrurated using fire polished Pasteur pipets and strained through a 70 µM cell strainer. Hoechst cell viability dye (Hoechst 33258) was added to the cell suspension at a final dilution of 4ug/ml just prior to sorting to allow for selection of living cells during FACs sorting. Cells were then FACs sorted for tdTomato fluorescence and viability via Hoechst staining. Sorting was performed on a BD FACSAriaII using a 130 µM nozzle, a sheath pressure of 10 p.s.i., and in the single cell sorting mode at the University of Iowa Flow Cytometry Facility.
FACS isolated cells were then loaded on the BD Rhapsody where capture of the single cells was performed per manufacturer instructions. Following lysis of the cells and capture of mRNA on oligonucleotide barcoded beads the cDNA synthesis was performed per manufacturer instructions. cDNA libraries were then generated using two custom primer panels (with one primer panel containing lowly expressed genes and the other containing highly expressed genes with overlapping genes incorporated into each panel (Table S1 and S2) designed by BD and generated by Integrated DNA Technologies (IDT) targeted against cell type specific markers for cell types previously identified in the hypothalamus based on previous publications (Romanov et. al, Chen et. al).

tag: strain

tag: genotype

value: KLB-CRE; Ai14

value: Hypothalamus

tag: cell population

value: KLB expressing cells

tag: sequenced molecule

value: cDNA transcript library


title: MTN017_017_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 017 during Oral treatment


title: shCTRL Bliss 3 Gy Replicate 1


title: MTN017_017_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 017 during Rectal daily treatment


title: KLBtdTomHyp_Rep2_Panel2

description: UMI counts per cell


title: shCTRL Bliss 5 Gy Replicate 1


title: shCTRL Bliss 10 Gy Replicate 2


title: MTN017_017_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 017 at Baseline


title: KLBtdTomHyp_Rep3_Panel2

description: UMI counts per cell


title: MTN017_019_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 019 during Rectal pericoital treatment


title: MTN017_016_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 016 at Baseline


title: shCTRL Bliss 10 Gy Replicate 1


title: MTN017_016_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 016 during Oral treatment


title: shHMGB1 ATAC-Seq

library_source: genomic

data_processing:
trimming with Trimmomatic (v0.32)
alignment with bwa mem (v0.7.5-r404)
remove duplicates with MarkDuplicates
filtering for Paired Unique, quality, autosomic plus sex chromosome (samtools view -F 3844 -f 2 -q 15)
filtering out blacklist (From Encode with intersectBed -v)
peak calling (MACS2 callpeak -q 0.05 --extsize 73 --nomodel --shift 73 --nolamda)
Nucleosome calling with NucleoATAC (v0.3.4)
Genome_build: mm10 GRCm38
Supplementary_files_format_and_content: narrowPeak called by MACS on sorted filtered bam files
Supplementary_files_format_and_content: occ, nfr and nuc positioning bed and bedgraph calculated by NucleoATAC

molecule: genomic DNA

source_name: AB22 cells plus shHMGB1

extract_protocol:
ATACseq protocol is described in Buenrostro et al, 2015. Permeabilised cells are incubated with Tn5 from Illumina to tagment chromatin. Genomic DNA is purified using Quiagen MinElute PCR Purification kit.
Libraries are prepared from tagmented genomic DNA following the protocol described in Buenrostro et al, 2015.


title: MTN017_015_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 015 during Rectal pericoital treatment


title: KLBtdTomHyp_Rep2_Panel1

description: UMI counts per cell


title: KLBtdTomHyp_Rep1_Panel2

description: UMI counts per cell


title: Non_targeting_462_replicate_F

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Non targeting sgRNA control for CRISPRa

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.6.1, default parameters) and mapped to the mouse mm10 genome assembly using Hisat2 v2.0.5, as guided by known splice sites taken from Ensembl v68. Hits were filtered to remove mappings with MAPQ scores <20. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) with strand specific quantification using mRNA probes. Quantified data are reported in log2 reads per million.
Genome_build: GRCm38
Supplementary_files_format_and_content:  Quantified data for each sample are reported in log2 reads per million.

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESCs) were grown under serum/LIF conditions: DMEM (Gibco, 11995-040), 15% fetal bovine serum, 1 U/ml penicillin - 1 mg/ml streptomycin (Gibco, 15140-122), 0.1 mM nonessential amino acids (Gibco, 11140-050), 4 mM GlutaMAX (Gibco, 35050-061), 50 mM β-mercaptoethanol (Gibco, 31350-010), and 103 U/ml LIF (Stem Cell Institute, Cambridge), and cultured at 37 ̊C in 5% CO2 on gelatinized tissue-culture plates. The media was refreshed every day and the cells passaged every other day with Trypsin EDTA (Thermo Fisher Scientific, 25200056).

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen, 74104) and treated with DNaseI (Thermo Fisher Scientific, EN0521) following manufacturer’s instructions.
Opposite strand-specific polyA RNA libraries were made using 1 μg DNase-treated RNA using the Sanger Institute Illumina bespoke pipeline.
50 bp single-end, Illumina HiSeq4000

treatment_protocol: For CRISPRa, individual lentiviral transductions were performed into SAM mESCs with the specified sgRNA targeting the promoter of the gene of interest, by direct supplementation of lentivirus into the cells for 24 hours; 48 hours after transduction, cells were selected with 1ug/ul puromycin for sgRNA expression and RNA was harvested 8 days later. For cDNA overexpression, GFP fusion constructs with the gene of interest were transfected into E14 mESCs using Lipofectamine 2000 Reagent Opti-MEM (GIBCO, 31985) (Thermo Fisher Scientific, 11668019), following manufacturer’s instructions; cells were grown for 48 hours before GFP+ FACS sorting on BD Influx High-Speed Cell Sorter and RNA extraction.

value: 129/Ola ES-E14

value: SAM mESCs (E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1)


title: MTN017_016_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 016 during Rectal pericoital treatment


title: shHMGB1 RNA-Seq Replicate C

data_processing:
trimming with Trimmomatic (v0.32)
alignment with STAR_2.5.3a
counting reads with featureCounts (Gencode M13 annotation)
normalization (Table with log2RPKM Normalized values, with edgeR rpkm() function on TMM normalized)
Genome_build: mm10 GRCm38

extract_protocol:
Total RNA from G1-synchronized cells was isolated using the NucleoSpin RNA II kit (Macherey-Nagel). Ribosomal RNA was subtracted using RiboMinus Gold TM Technology (ThermoFisher)
Libraries of cDNA were prepared with TruSeq RNA Library Prep Kit (Illumina)


title: MTN017_015_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 015 at Baseline


title: MTN017_016_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 016 during Rectal daily treatment


title: MTN017_014_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 014 during Rectal pericoital treatment


title: MTN017_017_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 017 during Rectal pericoital treatment


title: MTN017_015_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 015 during Oral treatment


title: MTN017_014_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 014 during Rectal daily treatment


title: MTN017_015_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 015 during Rectal daily treatment


title: shHMGB1 RNA-Seq Replicate B


title: Non_targeting_462_replicate_E

description: Non targeting sgRNA control for CRISPRa


title: MTN017_014_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 014 at Baseline


title: MTN017_013_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 013 during Oral treatment


title: shHMGB1 RNA-Seq Replicate A


title: MTN017_014_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 014 during Oral treatment


title: MTN017_013_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 013 during Rectal daily treatment


title: shCTRL RNA-Seq Replicate C

source_name: AB22 cells plus shCTRL


title: MTN017_013_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 013 at Baseline


title: MTN017_012_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 012 during Rectal daily treatment


title: shCTRL RNA-Seq Replicate B


title: MTN017_012_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 012 during Rectal pericoital treatment


title: MTN017_012_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 012 during Oral treatment


title: Non_targeting_461_replicate_E

description: Non targeting sgRNA control for CRISPRa

source_name: Embryonic stem cells


title: Non_targeting_461_replicate_D

description: Non targeting sgRNA control for CRISPRa


title: Non_targeting_461_replicate_F

description: Non targeting sgRNA control for CRISPRa


title: Non_targeting_462_replicate_D

description: Non targeting sgRNA control for CRISPRa


title: shCTRL RNA-Seq Replicate A


title: Sirt1_sgRNA_74_replicate_C

description: CRISPRa of Sirt1


title: MTN017_012_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 012 at Baseline


title: MTN017_011_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 011 during Rectal daily treatment


title: MTN017_011_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 011 during Rectal pericoital treatment


title: Sirt1_sgRNA_74_replicate_B

description: CRISPRa of Sirt1


title: Sirt1_sgRNA_74_replicate_A

description: CRISPRa of Sirt1


title: MTN017_013_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 013 during Rectal pericoital treatment


title: MTN017_010_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 010 during Rectal daily treatment


title: MTN017_011_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 011 at Baseline


title: Arnt_sgRNA_17_replicate_C

description: CRISPRa of Arnt


title: MTN017_011_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 011 during Oral treatment


title: MTN017_010_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 010 during Oral treatment


title: Arnt_sgRNA_17_replicate_B

description: CRISPRa of Arnt


title: MTN017_009_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 009 during Rectal daily treatment


title: Arnt_sgRNA_17_replicate_A

description: CRISPRa of Arnt


title: MTN017_010_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 010 during Rectal pericoital treatment


title: Tsc22d4_sgRNA_338_replicate_C

description: CRISPRa of Tsc22d4


title: MTN017_009_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 009 at Baseline


title: MTN017_009_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 009 during Oral treatment


title: MTN017_009_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 009 during Rectal pericoital treatment


title: MTN017_008_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 008 during Oral treatment


title: MTN017_010_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 010 at Baseline


title: MTN017_008_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 008 during Rectal pericoital treatment


title: Tsc22d4_sgRNA_338_replicate_B

description: CRISPRa of Tsc22d4

source_name: Embryonic stem cells


title: MTN017_008_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 008 during Rectal daily treatment


title: MTN017_008_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 008 at Baseline


title: Tsc22d4_sgRNA_338_replicate_A

description: CRISPRa of Tsc22d4


title: MTN017_007_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 007 during Rectal pericoital treatment


title: Pou2f2_sgRNA_75_replicate_C

description: CRISPRa of Pou2f2


title: Pou2f2_sgRNA_75_replicate_B

description: CRISPRa of Pou2f2


title: MTN017_007_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 007 during Oral treatment


title: Pou2f2_sgRNA_75_replicate_A

description: CRISPRa of Pou2f2


title: MTN017_006_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 006 during Rectal daily treatment


title: MTN017_006_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 006 during Oral treatment


title: MTN017_007_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 007 at Baseline


title: MTN017_005_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 005 during Oral treatment


title: Smad1_sgRNA_164_replicate_C

description: CRISPRa of Smad1


title: MTN017_005_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 005 during Rectal pericoital treatment


title: MTN017_006_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 006 at Baseline


title: Smad1_sgRNA_164_replicate_B

description: CRISPRa of Smad1


title: MTN017_005_RectalBiopsy_TFV_RectalDaily_Visit4

source_name: Rectal tissue from participant MTN017 005 during Rectal daily treatment


title: Smad1_sgRNA_164_replicate_A

description: CRISPRa of Smad1


title: Dppa4_sgRNA_321_replicate_C

description: CRISPRa of Dppa4


title: shCTRL ATAC-Seq

source_name: AB22 cells plus shCTRL


title: MTN017_006_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 006 during Rectal pericoital treatment


title: MTN017_004_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 004 during Oral treatment


title: MTN017_004_RectalBiopsy_TFV_RectalPericoital_Visit10

source_name: Rectal tissue from participant MTN017 004 during Rectal pericoital treatment


title: MTN017_004_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 004 during Rectal daily treatment


title: MTN017_003_RectalBiopsy_TFV_RectalPericoital_Visit7

source_name: Rectal tissue from participant MTN017 003 during Rectal pericoital treatment


title: MTN017_003_RectalBiopsy_TDF/FTC_Oral_Visit4

source_name: Rectal tissue from participant MTN017 003 during Oral treatment


title: MTN017_004_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 004 at Baseline


title: Dppa4_sgRNA_321_replicate_B

description: CRISPRa of Dppa4

source_name: Embryonic stem cells


title: MTN017_002_RectalBiopsy_TDF/FTC_Oral_Visit7

source_name: Rectal tissue from participant MTN017 002 during Oral treatment


title: MTN017_003_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 003 during Rectal daily treatment


title: MTN017_005_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 005 at Baseline


title: MTN017_003_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 003 at Baseline


title: Dppa4_sgRNA_321_replicate_A

description: CRISPRa of Dppa4


title: CARD14E138A 1 month 6

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

institute: University College London

data_processing:
Then sequencing reads were aligned to the mouse genome and transcriptome (Ensembl GRCm38 release-89) using RSEM version 1.3.0 in conjunction with the STAR aligner version 2.5.2
Differential gene expression was determined using the R-bioconductor package DESeq2 version 1.14.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file containing TMM normalized data. Rows represent ensembl gene identifiers and columns represent individual samples.

source_name: CARD14E138A 1 month

extract_protocol:
RNA was isolated using PureLink RNAeasy Mini kit (Qiagen #74106) according to the manufacturer’s instructions.
RNA-sequencing was performed by the Crick  advanced sequencing facility using the polyA KAPA mRNA Hyper Prep kit (Roche) and coding mRNA as starting material. Sequencing was performed on an Illumina HiSeq4000 instrument with single end reads of at least 75 bp.

treatment_protocol: C57BL/6 mice were injected intraperitoneally with Tamoxifen once a day for three consecutive days. We took samples counting from the first injection of Tamoxifen

value: Whole Ear

tag: treatment

value: Tamoxifen

tag: time

value: 1 month after Tamoxifen injection


title: CARD14E138A 1 month 3


title: MTN017_002_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 002 during Rectal pericoital treatment


title: MTN017_002_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 002 at Baseline


title: MTN017_001_RectalBiopsy_TFV_RectalDaily_Visit7

source_name: Rectal tissue from participant MTN017 001 during Rectal daily treatment


title: CARD14E138A 1 month 2


title: Wt 1 month 6

source_name: Wt 1 month

value: Wt


title: CARD14E138A 1 month 1


title: MTN017_001_RectalBiopsy_TFV_RectalPericoital_Visit4

source_name: Rectal tissue from participant MTN017 001 during Rectal pericoital treatment

value: rectal


title: GMSB_115_PBMC_TDF

hyb_protocol: Standard as recommended by Illumina, except that the temperature was 48C

scan_protocol: Standard Illumina protocol using Illumina iScan system

data_processing:
The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.
Matrix non-normalized table: This table contains raw signal intensity values and detection p-values for each sample.

source_name: PBMC from GMSB_115 treated with TDF

label_protocol: 50 ng of total RNA was labeled using the Ovation PicoSL WTA System V2 kit and the Encore BiotinIL kit (both NuGEN)

value: PBMC

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: valid

value: Excluded:after PrEP discontinuation


title: GMSB_116_PBMC_TDF

source_name: PBMC from GMSB_116 treated with TDF

tag: tissue

tag: ptid

tag: visit

value: prep

value: Yes

value: NoHC

tag: rin

value: Included


title: MTN017_001_RectalBiopsy_TDF/FTC_Oral_Visit10

source_name: Rectal tissue from participant MTN017 001 during Oral treatment

tag: site

value: USA - Pittsburgh


title: MTN017_001_RectalBiopsy_NoDrug_Baseline_Visit2

source_name: Rectal tissue from participant MTN017 001 at Baseline


title: MTN017_002_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 002 during Rectal daily treatment


title: CARD14E138A 1 month 4

tag: strain

tag: genotype

value: Whole Ear

tag: treatment

value: Tamoxifen

tag: time


title: CARD14E138A 1 month 5

value: 1 month after Tamoxifen injection


title: GMSB_117_PBMC_TDF

source_name: PBMC from GMSB_117 treated with TDF

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: Excluded:undetectable TDF


title: GMSB_119_PBMC_Placebo

source_name: PBMC from GMSB_119 treated with Placebo

tag: tissue

value: PBMC

tag: ptid

value: C

value: Placebo

value: placebo

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: valid


title: KLBtdTomHyp_Rep1_Panel1

description: UMI counts per cell

source_name: Hypothalamus

tag: strain

tag: genotype

value: KLB-CRE; Ai14

value: Hypothalamus

tag: cell population

value: KLB expressing cells

tag: sequenced molecule

value: cDNA transcript library


title: GMSB_114_PBMC_Placebo

source_name: PBMC from GMSB_114 treated with Placebo

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

value: Nohist

value: Positive

tag: rin


title: Wt 1 month 5

value: Wt

tag: tissue

tag: treatment

tag: time


title: GMSB_112_PBMC_TDF

source_name: PBMC from GMSB_112 treated with TDF

tag: ptid

value: A

value: TDF

value: prep

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Indeterminate

value: unknown

value: Included


title: GMSB_111_PBMC_TDF

source_name: PBMC from GMSB_111 treated with TDF

value: PBMC

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: drug

value: No

value: Negative

tag: valid

value: Excluded:undetectable TDF


title: Wt 1 month 4

tag: strain

tag: genotype

tag: tissue

value: Whole Ear

tag: treatment

value: Tamoxifen

tag: time

value: 1 month after Tamoxifen injection


title: GMSB_118_PBMC_FTC/TDF

source_name: PBMC from GMSB_118 treated with FTC/TDF

tag: ptid

value: B

value: FTC/TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

value: Positive

tag: rin


title: GMSB_109_PBMC_TDF

source_name: PBMC from GMSB_109 treated with TDF

tag: visit

tag: collectiondate

tag: age

value: A

value: TDF

value: prep

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent


title: GMSB_113_PBMC_TDF

source_name: PBMC from GMSB_113 treated with TDF

tag: tissue

tag: arm

tag: drug

value: Yes

value: unknown

tag: valid


title: GMSB_110_PBMC_TDF

source_name: PBMC from GMSB_110 treated with TDF

value: PBMC

tag: ptid

tag: prep

tag: tdfngperml

tag: tdfdetected

value: implant


title: GMSB_107_PBMC_TDF

source_name: PBMC from GMSB_107 treated with TDF

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: birthcontrollab

tag: rin

value: Included


title: Wt 1 month 2

source_name: Wt 1 month

tag: strain

tag: genotype

value: Wt

value: Whole Ear

tag: treatment

tag: time


title: Wt 1 month 1

value: Tamoxifen

value: 1 month after Tamoxifen injection


title: Wt 1 month 3


title: CARD14E138A day 5 6

source_name: CARD14E138A day 5

value: 5 days after Tamoxifen injection


title: Bliss 10 Gy 0 Nac Replciate 3

data_processing:
Library strategy: BLISS-Seq
trimming with Trimmomatic (v0.32)
extract UMI with umi_tools extract (v0.5.3)
alignment with bwa mem (v0.7.5-r404)
filtering for quality (samtools view -q 5)
deduplicate UMI with umi_tools dedup (--edit-distance-threshold 2 )
aggregation with bedtools (samtools view -b -f 67 ; bamToBed ; bedtools sort ; bedtools merge -o collapse,count -d 8 -c 2,2)
Genome_build: hg38
Supplementary_files_format_and_content: clean.umi_dedup.aggregated.bed = BED file with aggregated Double Strand Breaks with number of different UMIs in column 3 and count in column 4

source_name: MCF7 cells

growth_protocol: MCF7 cells were cultured in DMEM (Dulbecco's Modified Eagle Medium, Gibco) supplemented with 10% v/v FBS, 2 mM L-glutamine and 100 U/mL penicillin/streptomycin. Cells were maintained subconfluent in humidified incubator at 37°C with 5% CO2

treatment_protocol: 5x10^4 MCF7 cells were seeded on coverslips, pretreated 1 hour with 10mM of N-Acetyl-L-cysteine (10 NAC) or vehicle (0 NAC) in culture medium, then irradiated with 0 or 10 Gy of gamma rays from a Caesium137 source.

tag: dose (gy)

value: 10 Gy

tag: agent

value: untreated

tag: cell line


title: GMSB_108_PBMC_Placebo

source_name: PBMC from GMSB_108 treated with Placebo

tag: tissue

tag: visit

tag: collectiondate

tag: age

tag: arm

value: C

tag: drug

value: Placebo

value: placebo

value: Nohist

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive


title: GMSB_105_PBMC_FTC/TDF

source_name: PBMC from GMSB_105 treated with FTC/TDF

tag: ptid

value: B

value: FTC/TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NoHC

tag: rin

tag: valid


title: GMSB_104_PBMC_Placebo

source_name: PBMC from GMSB_104 treated with Placebo

tag: tissue

value: PBMC

tag: visit

tag: collectiondate

tag: age

value: Included


title: CARD14E138A day 5 5

tag: strain

tag: genotype

value: Whole Ear

tag: treatment

value: Tamoxifen

tag: time


title: GMSB_106_PBMC_FTC/TDF

source_name: PBMC from GMSB_106 treated with FTC/TDF

tag: ptid

tag: arm

tag: drug

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

value: unknown


title: MTN017_007_RectalBiopsy_TFV_RectalDaily_Visit10

source_name: Rectal tissue from participant MTN017 007 during Rectal daily treatment

value: rectal

tag: site

value: USA - Pittsburgh

tag: rin


title: GMSB_102_PBMC_TDF

source_name: PBMC from GMSB_102 treated with TDF

tag: tissue

tag: visit

value: A

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: injectable

tag: valid


title: GMSB_099_PBMC_FTC/TDF

source_name: PBMC from GMSB_099 treated with FTC/TDF

tag: ptid

tag: collectiondate

tag: age

tag: arm

tag: drug

value: Nohist

value: Positive


title: GMSB_103_PBMC_TDF

source_name: PBMC from GMSB_103 treated with TDF

value: No

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Excluded:undetectable TDF


title: GMSB_101_PBMC_TDF

source_name: PBMC from GMSB_101 treated with TDF

tag: tissue

tag: visit

tag: prep

value: prep

value: Yes

tag: rin


title: Bliss 0 Gy 0 Nac Replicate 3

tag: dose (gy)

value: untreated

tag: agent

tag: cell line


title: CARD14E138A day 5 4

tag: strain

tag: genotype

tag: treatment

tag: time

value: 5 days after Tamoxifen injection


title: GMSB_097_PBMC_FTC/TDF

source_name: PBMC from GMSB_097 treated with FTC/TDF

value: PBMC

tag: ptid

tag: collectiondate

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: valid

value: Included


title: Bliss 10 Gy 10 Nac Replicate 2

tag: dose (gy)

value: 10 Gy

tag: agent

value: NAC (10 mM)


title: CARD14E138A day 5 3

tag: strain

tag: tissue

value: Whole Ear

value: Tamoxifen


title: GMSB_098_PBMC_FTC/TDF

source_name: PBMC from GMSB_098 treated with FTC/TDF

tag: visit

tag: prep

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin


title: GMSB_100_PBMC_TDF

source_name: PBMC from GMSB_100 treated with TDF

tag: ptid

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: tdfngperml

tag: tdfdetected

value: Nohist


title: Bliss 0 Gy 10 Nac Replicate 2

tag: dose (gy)

tag: agent

tag: cell line


title: CARD14E138A day 5 2

tag: strain

tag: genotype

tag: tissue

tag: treatment

tag: time


title: GMSB_093_PBMC_Placebo

source_name: PBMC from GMSB_093 treated with Placebo

tag: visit

value: C

value: Placebo

tag: prep

value: placebo

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: valid


title: GMSB_095_PBMC_FTC/TDF

source_name: PBMC from GMSB_095 treated with FTC/TDF

tag: ptid

tag: collectiondate

tag: age

tag: arm

tag: drug

value: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: rin

value: Excluded:undetectable TDF


title: GMSB_094_PBMC_TDF

source_name: PBMC from GMSB_094 treated with TDF

tag: tissue

value: PBMC

tag: visit

tag: prep

tag: tdfresultdate


title: GMSB_096_PBMC_TDF

source_name: PBMC from GMSB_096 treated with TDF

value: Yes

tag: birthcontrolepi

tag: birthcontrollab

value: NoHC

tag: mpa

tag: lng

value: Negative

value: unknown

value: Included


title: GMSB_092_PBMC_TDF

source_name: PBMC from GMSB_092 treated with TDF

value: injectable

tag: eng

tag: net

tag: nugent

tag: valid


title: CARD14E138A day 5 1

source_name: CARD14E138A day 5

tag: strain

tag: genotype

value: Whole Ear

tag: treatment

value: Tamoxifen

tag: time

value: 5 days after Tamoxifen injection


title: Bliss 0 Gy 0 Nac Replicate 2

source_name: MCF7 cells

tag: dose (gy)

value: untreated

tag: agent

tag: cell line


title: Bliss 10 Gy 0 Nac Replicate 2

value: 10 Gy


title: Wt day 5 6

source_name: Wt day 5

value: Wt

tag: tissue


title: Bliss 0 Gy 10 Nac Replicate 1

value: NAC (10 mM)


title: Bliss 10 Gy 10 Nac Replicate 1


title: Wt day 5 5


title: GMSB_090_PBMC_TDF

source_name: PBMC from GMSB_090 treated with TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

value: implant

value: Positive

tag: rin


title: GMSB_086_PBMC_Placebo

source_name: PBMC from GMSB_086 treated with Placebo

value: PBMC

value: C

value: Placebo

value: placebo

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: valid


title: Wt day 5 4

tag: strain

tag: genotype

tag: tissue

tag: treatment

tag: time


title: Wt day 5 3


title: GMSB_088_PBMC_FTC/TDF

source_name: PBMC from GMSB_088 treated with FTC/TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

value: Yes

value: Nohist

value: NoHC

value: Included


title: Bliss 10 Gy 0 Nac Replicate 1

tag: dose (gy)

value: 10 Gy

tag: agent

value: untreated

tag: cell line


title: Bliss 0 Gy 0 Nac Replicate 1


title: GMSB_085_PBMC_TDF

source_name: PBMC from GMSB_085 treated with TDF

value: A

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

tag: rin

tag: valid


title: GMSB_083_PBMC_FTC/TDF

source_name: PBMC from GMSB_083 treated with FTC/TDF

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: drug

value: prep

value: No

value: Excluded:undetectable TDF


title: GMSB_087_PBMC_TDF

source_name: PBMC from GMSB_087 treated with TDF

value: PBMC

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

value: Positive

value: Excluded:MDS outlier and undetectable TDF


title: Wt day 5 1

tag: strain

tag: genotype

value: Wt

value: Whole Ear

tag: treatment

value: Tamoxifen

tag: time

value: 5 days after Tamoxifen injection


title: GMSB_084_PBMC_TDF

source_name: PBMC from GMSB_084 treated with TDF

value: Yes

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

value: Included


title: GMSB_089_PBMC_FTC/TDF

source_name: PBMC from GMSB_089 treated with FTC/TDF

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: valid


title: GMSB_081_PBMC_TDF

source_name: PBMC from GMSB_081 treated with TDF

value: A

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

value: Nohist

value: NoHC


title: Wt day 5 2

tag: strain

tag: genotype

tag: treatment

tag: time


title: GMSB_078_PBMC_Placebo

source_name: PBMC from GMSB_078 treated with Placebo

value: C

value: Placebo

value: placebo

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin


title: 8-D0-Neg

city: NEWCASTLE UPON TYNE

first: John

last: Loughlin

address: Centre For Life

institute: Newcastle University

data_processing:
Quality control of reads was performed using FastQC. Reads were mapped to the hg38 transcriptome using Salmon. Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Normalised gene counts in tab-delimited text

source_name: AD-hMSC

growth_protocol: The cells (SCRC-4000 ATCC, transduced with lentiCRISPR v2 plasmid 52961) were expanded in complete growth medium consisting of serum free media (PCS-500-030, ATCC) supplemented with Mesenchymal Stem Cell Growth Kit containing L-Alanyl-L-Glutamine (PCS-500-040, ATCC), G418 disulphate salt solution (G8168, Sigma Aldrich) and penicillin-streptomycin (30-2300, ATCC). Selection of Cas9 expressing cells was achieved by addition of 0.35ug/l of puromycin to the complete growth media. Constitutive expression of Cas9 was confirmed by immunoblot with a Cas9 antibody (7A9-3A3, Cell Signalling Technology).Cells were plated at sub-confluence (45,000 cells/well) in 6-well plates (VWR) and allowed to adhere for 24 hours prior to transfection with gRNAs

extract_protocol:
Cells were released by trypsinization, washed in phosphate-buffered saline (PBS), spun and the cell pellets frozen. DNA, RNA and protein were simultaneously extracted from pellets using the NucleoSpin TriPrep Kit (Macherey-Nagel, supplied by ThermoFisher). Deletion of the target region was confirmed by end-point PCR of DNA using primers flanking the guides (primers 5'-GAGGGGTTGAGCTGGATTCC-3' and 5'-CCAGCACCCACTCTGTAGAT-3') and by Sanger sequencing.
TruSeq Stranded mRNA Sequencing NextSeq High-Output 2 x 75 bp reads (total of 7 samples)

treatment_protocol: CHOPCHOP (https://chopchop.cbu.uib.no/) was used to design guide RNA (gRNA) sequences that would generate a 26bp frame-shift deletion of exon 3 of PLEC (primers 5'-CTGTATGAAGACCTCCGCGA-3' and 5'-CCCCGAGAGGACCTCCAGCA-3'). This exon is present in all isoforms of the gene. The gRNAs were then purchased as synthetic Alt-R® CRISPR-Cas9 crRNAs alongside Alt-R® CRISPR-Cas9 tracrRNA (Integrated DNA Technologies). For deletions (4 replicates), paired crRNAs were annealed to tracrRNA in a 1:1:2 ratio at 95oC for 5 minutes, whilst for controls (4 replicates), tracrRNA alone was used

tag: tissue

value: mesenchymal stem cell line

tag: condition

value: Control


title: 7-D0-Neg


title: GMSB_080_PBMC_TDF

source_name: PBMC from GMSB_080 treated with TDF

value: PBMC

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: drug

value: TDF

tag: prep

value: prep

tag: tdfngperml

value: injectable

value: Positive

tag: valid


title: Female_CTCFchip_Repl3_G133_M15

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: ChIP-seq Library

data_processing:
READ MAPPING: ChIP-seq reads were aligned using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using Macs2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9
Supplementary_files_format_and_content: Replicate merged peak lists for CTCF (Female_CTCF_merged.bed) and cohesin/Rad21 (Female_Rad21_merged.bed). Samples were combined at the fastq level and processed through a standard ChIP-seq pipeline as described. Columns are in BED6+4 format from MACS2 narrowPeak defaults. Specifically, columns 1-3 represent genomic coordinates of the indicated peak; column 4 is the peak name (unique identifier); column 5 is an integer score for display calculated as -10*log10(qvalue); column 6 indicates the strand; column 7 indicates the fold-change over background; column 8 indicates -(log10pvalue); column 9 indicates -log10(qvalue); and column 10 indicates the summit position relative to the 5' end of the peak.

source_name: Liver

growth_protocol: Male and female CD1 mice, 8-9 weeks of age, were purchased from Charles River Laboratories (Crl:CD1(ICR)).

extract_protocol:
Nuclei were isolated by ultracentrifugation in a high sucrose buffer then crosslinked with 0.8% formaldehyde for 9 minutes. Samples were sonicated with a Bioruptor Twin (Diagenode, UCD-400) until the majority of DNA fragments were between 100-400bp (60-70 cycles total, 30 sec ON 30 sec OFF). Chromatin was quantified and 70 ug of chromatinized DNA was incubated with the indicated ChIP antibody.
Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: chip antibody

value: Millipore anti CTCF (cat# 07-779)

tag: Sex

value: Female

value: 8 weeks


title: Female_CTCFchip_Repl4_G100_M1

description: ChIP-seq Library


title: 6-D0-Neg


title: GMSB_082_PBMC_FTC/TDF

source_name: PBMC from GMSB_082 treated with FTC/TDF

value: B

value: FTC/TDF

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

value: Included


title: Female_CTCFchip_Repl2_G133_M12

description: ChIP-seq Library

tag: age


title: GMSB_075_PBMC_FTC/TDF

source_name: PBMC from GMSB_075 treated with FTC/TDF

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: arm

value: No

tag: nugent

value: Negative

tag: rin

value: Excluded:undetectable TDF


title: GMSB_079_PBMC_TDF

source_name: PBMC from GMSB_079 treated with TDF

value: A

tag: drug

tag: prep

tag: tdfngperml

value: Unavailable

value: unknown

tag: valid


title: Female_CTCFchip_Repl1_G133_M11

description: ChIP-seq Library

tag: strain

tag: chip antibody

tag: Sex


title: GMSB_076_PBMC_FTC/TDF

source_name: PBMC from GMSB_076 treated with FTC/TDF

value: PBMC

value: prep

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

value: NoHC

tag: mpa

tag: lng

tag: eng


title: GMSB_074_PBMC_FTC/TDF

source_name: PBMC from GMSB_074 treated with FTC/TDF

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: net

value: Positive


title: GMSB_071_PBMC_TDF

source_name: PBMC from GMSB_071 treated with TDF

tag: drug

value: TDF

tag: prep

tag: tdfngperml

value: injectable

tag: nugent

tag: rin

tag: valid


title: GMSB_073_PBMC_Placebo

source_name: PBMC from GMSB_073 treated with Placebo

value: C

value: Placebo

value: placebo

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab


title: 2-D0-Del

tag: tissue

value: mesenchymal stem cell line

tag: condition

value: Deletion


title: Female_Rad21chip_Repl3_G100_M3

description: ChIP-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: chip antibody

value: Abcam anti Rad21 (cat# Ab992)

tag: Sex

value: Female

value: 8 weeks


title: GMSB_077_PBMC_TDF

source_name: PBMC from GMSB_077 treated with TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

value: Yes

tag: mpa

tag: lng

tag: eng

value: Included


title: 4-D0-Del


title: 1-D0-Del


title: Huh7 cells, matrigel_(6.0_mg/ml)_rep3

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
counts.txt.gz
tpms.txt.gz
mg_6_mg_ml_rep3

data_processing:
RNA-seq reads were subjected to 3’ adapter (5’-AGATCGGAAGAGCACACGTC-3’) and poly(T) trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011.
Reads shorter than 30 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--single”, “-l”, “-s”, “--rf-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference human transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCh38 (release 96) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample

source_name: Huh7 cells

growth_protocol: Huh-7 cells cultured on polystyrene coated flasks were subsequetly grown on a matrix of collagen and matrigel at the indicated concentrations for a duration of 7 days.

extract_protocol:
RNA was extracted with Trizol and subsequently purified with a RNA extraction kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols. 1μg total RNA was used for library preparation with the TruSeq Stranded mRNA Library Prep Kit High Throughput (Cat# RS-122-2103, Illumina, San Diego, CA, USA). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical).

treatment_protocol: No separate treatment was given to the cells except changing of media every alternate day.

tag: cell type

value: Huh7 human liver cell line

tag: passages

tag: matrix for cell growth

value: Matrigel (6.0 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: GMSB_068_PBMC_FTC/TDF

source_name: PBMC from GMSB_068 treated with FTC/TDF

tag: tissue

value: PBMC

value: B

tag: drug

value: FTC/TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: net

tag: nugent

value: Negative

tag: rin

tag: valid


title: GMSB_072_PBMC_TDF

source_name: PBMC from GMSB_072 treated with TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: TDF

value: injectable

tag: mpa

tag: lng

tag: eng

value: Positive


title: Female_Rad21chip_Repl1_G133_M4

description: ChIP-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: chip antibody

value: Abcam anti Rad21 (cat# Ab992)

tag: Sex


title: Female_Rad21chip_Repl2_G133_M5

description: ChIP-seq Library

value: Female

value: 8 weeks


title: 3-D0-Del

tag: tissue

value: mesenchymal stem cell line

tag: condition

value: Deletion


title: GMSB_067_PBMC_TDF

source_name: PBMC from GMSB_067 treated with TDF

value: A

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

value: NoHC

tag: net

value: Excluded:undetectable TDF


title: GMSB_065_PBMC_TDF

source_name: PBMC from GMSB_065 treated with TDF

value: PBMC

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: nugent

tag: rin

tag: valid


title: GMSB_066_PBMC_TDF

source_name: PBMC from GMSB_066 treated with TDF

tag: tissue

value: prep

value: Yes

tag: mpa

tag: lng

tag: eng

value: Included


title: GMSB_069_PBMC_FTC/TDF

source_name: PBMC from GMSB_069 treated with FTC/TDF

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: injectable


title: GMSB_070_PBMC_TDF

source_name: PBMC from GMSB_070 treated with TDF

value: TDF

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: net

value: Positive


title: Huh7 cells, matrigel_(6.0_mg/ml)_rep2

description:
counts.txt.gz
tpms.txt.gz
mg_6_mg_ml_rep2

tag: cell type

value: Huh7 human liver cell line

tag: passages

tag: matrix for cell growth

value: Matrigel (6.0 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: GMSB_060_PBMC_FTC/TDF

source_name: PBMC from GMSB_060 treated with FTC/TDF

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: mpa

tag: nugent

value: Negative

value: unknown

tag: rin

tag: valid


title: GMSB_061_PBMC_TDF

source_name: PBMC from GMSB_061 treated with TDF

value: A

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: lng

tag: eng

tag: net


title: GMSB_062_PBMC_Placebo

source_name: PBMC from GMSB_062 treated with Placebo

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

value: C

value: Placebo

value: placebo


title: Huh7 cells, matrigel_(3.0_mg/ml)_rep3

description:
counts.txt.gz
tpms.txt.gz
mg_3_mg_ml_rep3

tag: cell type

tag: passages

tag: matrix for cell growth

value: Matrigel (3.0 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality


title: GMSB_064_PBMC_FTC/TDF

source_name: PBMC from GMSB_064 treated with FTC/TDF

value: PBMC

tag: age

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: mpa

tag: nugent

tag: rin

tag: valid

value: Included


title: Huh7 cells, matrigel_(3.0_mg/ml)_rep2

description:
counts.txt.gz
tpms.txt.gz
mg_3_mg_ml_rep2


title: Huh7 cells, matrigel_(3.0_mg/ml)_rep1

description:
counts.txt.gz
tpms.txt.gz
mg_3_mg_ml_rep1


title: Huh7 cells, matrigel_(6.0_mg/ml)_rep1

description:
counts.txt.gz
tpms.txt.gz
mg_6_mg_ml_rep1


title: Huh7 cells, matrigel_(1.5_mg/ml)_rep3

description:
counts.txt.gz
tpms.txt.gz
mg_1.5_mg_ml_rep3

value: Matrigel (1.5 mg/ml)


title: GMSB_063_PBMC_Placebo

source_name: PBMC from GMSB_063 treated with Placebo

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: tdfresultdate

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

value: NoHC

tag: lng

tag: eng

tag: net

value: Positive


title: GMSB_058_PBMC_Placebo

source_name: PBMC from GMSB_058 treated with Placebo

tag: age

tag: arm

tag: drug

tag: prep


title: GMSB_055_PBMC_FTC/TDF

source_name: PBMC from GMSB_055 treated with FTC/TDF

value: B

value: FTC/TDF

tag: tdfngperml

tag: tdfdetected

value: injectable

tag: mpa

tag: nugent


title: GMSB_053_PBMC_FTC/TDF

source_name: PBMC from GMSB_053 treated with FTC/TDF

tag: tissue

tag: ptid

value: oral

tag: rin

tag: valid

value: Excluded:undetectable TDF


title: GMSB_057_PBMC_Placebo

source_name: PBMC from GMSB_057 treated with Placebo

tag: visit

tag: collectiondate

value: C

tag: tdfresultdate

tag: birthcontrolepi


title: GMSB_054_PBMC_Placebo

source_name: PBMC from GMSB_054 treated with Placebo

value: Placebo

tag: birthcontrollab

tag: lng

tag: eng

tag: net


title: GMSB_056_PBMC_FTC/TDF

source_name: PBMC from GMSB_056 treated with FTC/TDF

tag: age

tag: arm

tag: drug

tag: prep


title: Huh7 cells, matrigel_(1.5_mg/ml)_rep2

description:
counts.txt.gz
tpms.txt.gz
mg_1.5_mg_ml_rep2

source_name: Huh7 cells

tag: cell type

value: Huh7 human liver cell line

tag: passages

tag: matrix for cell growth

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: Huh7 cells, matrigel_(1.5_mg/ml)_rep1

description:
counts.txt.gz
tpms.txt.gz
mg_1.5_mg_ml_rep1


title: GMSB_059_PBMC_TDF

source_name: PBMC from GMSB_059 treated with TDF

tag: tissue

value: PBMC

tag: ptid

tag: visit

tag: collectiondate

value: A

value: TDF

tag: tdfngperml

tag: tdfdetected

tag: mpa

tag: nugent

tag: rin

tag: valid


title: GMSB_091_PBMC_FTC/TDF

source_name: PBMC from GMSB_091 treated with FTC/TDF

tag: age

tag: arm

tag: drug

tag: prep

value: prep

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NonDecided

tag: lng

tag: eng

tag: net

value: Included


title: GMSB_050_PBMC_TDF

source_name: PBMC from GMSB_050 treated with TDF

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

value: Positive


title: GMSB_051_PBMC_TDF

source_name: PBMC from GMSB_051 treated with TDF

tag: tdfngperml

tag: tdfdetected

value: Nohist

tag: mpa

tag: nugent


title: 25_S3_PBMC_monocytes_Run2

first: Klas

last: Hatje

state: Basel

address: Grenzacherstrasse 124

institute: Roche Pharma Research and Early Development

description:
processed data file: iPSCderived_myeloid_cells_counts.gct
processed data file: iPSCderived_myeloid_cells_rpkms.gct

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq v2.17.1.14 from Illumina (https://support.illumina.com/downloads.html).
In order to estimate gene expression levels, paired-end RNASeq reads were mapped to the human genome (hg38) with STAR aligner version 2.5.2a using default mapping parameters (Dobin et al. 2013).
Aligned reads were quality checked with FastQC and MultiQC version 1.7 (Andrews 2010, Ewels 2016).
Numbers of mapped reads for all RefSeq transcript variants of a gene (counts) were combined into a single value by using SAMTOOLS software (Li et al. 2009) and normalized as RPKMs (number of mapped reads per kilobase transcript per million sequenced reads, Mortazavi et al. 2008).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: iPSCderived_myeloid_cells_counts.gct: Read counts in GCT gene expression matrix format.
Supplementary_files_format_and_content: iPSCderived_myeloid_cells_counts.gct: RPKMs in GCT gene expression matrix format.

source_name: PBMC

growth_protocol:
Generation of macrophage progenitors from iPSC: The main elements were previously published by Wilgenburg et al. Briefly, to obtain uniformed EBs, iPSCs were plated into Aggrewell 800 (StemCell Technologies) plates. 2 ml mTesR1, supplemented with 10 μM ROCK inhibitor (Y27632, Callbiochem) and containing a single cell suspension of 4*10e6 single iPSCs, was added to each Aggrewell and centrifuged for 3 minutes at 100 g to assure an even and fast distribution of the iPSCs to the aggrewell microwells. The next day mesoderm induction and subsequent hemogenic endothelium induction was started by exchange of 75% (replacing twice 1 ml of the 2 ml in each well) of the mTeSR1 media with fresh mTeSR1 media supplemented with 50ng/ml hBMP4, 50ng/ml hVEGF and 20ng/ml hSCF, and repeated the following 2 days. At day 4 of differentiation EBs were harvested by gently dislodging the EBs by rinsing the aggrewells with PBS. EBs were collected in a 40µm strainer and transferred to factory media, consisting of XVIVO15 media (Lonza) supplemented with 2mM Glutamax, 1% Penicillin/Streptomycin, 50 ug/ml Mercaptoethanol, M-CSF (100 ng/ml) and IL3 (25 ng/ml). EBs were plated with a density of 1 EBs/cm2 on cell culture vessels (2-1000 cm2/ 6 well to cell disk). In contrast to the description of Wilgenburg et al., the EBs were plated on dishes pre-coated for 1 h at RT with growth factor reduced Matrigel (Corning) diluted in cold DMEM F12 1:1 1x Glutamax (Gibco). In order to allow adherence of EBs, EBs were evenly distributed by slow movements and culture vessels were placed immediately at 37°C with 5% CO2 without any further disturbance for the first week of differentiation. The following two weeks of differentiation 50 % of the starting volume of fresh factory media was added once per week. From the third week of differentiation half-media changes were done, until the production and release of (CD14+) macrophage progenitors (iPSC monocyte) in the supernatant was observed. From this point on, complete media change with fresh factory media was performed twice a week.
Macrophage progenitor harvesting and macrophage differentiation: Macrophage progenitors were collected from the supernatant by centrifugation (4 minutes, 300 g), cells were re-suspended, counted and quality control (CD68, Ki67, CD11b and CD14) of marker expressions by flow cytometry was performed weekly. Macrophage progenitors were transferred into differentiation media and differentiated to macrophages. According to application requirements, macrophages were either directly differentiated in the required plate format or pre-differentiated for 6 days and then re-plated, to the final plate format one day prior to assay start. For differentiation, cells were cultured in XVIVO 15 (supplemented with 2 mM Glutamax, 1 % Penstrep and 100 ng/ml M-CSF) at a density of 150.000 cells per cm2. Media was changed 3 days after plating; cells were differentiated for 7 days. Macrophage progenitors or CD14 positive cells from Lonza were either differentiated into unpolarized (M0) Macrophages using XIVIVO15 media supplemented with 2 mM Glutamax, 1 % Pen/Strep and 100 ng/ml M-CSF or polarized into pro-inflammatory (M1) or regulatory phenotype (M2). M1 polarization was induced by the addition of GM-CSF and 50 ng/ml IFNγ instead of M-CSF. M2 polarization was induced by addition of 100 ng/ml M-CSF and 50 ng/ml IL-4. If not stated otherwise cells were differentiated for 7 days prior to the experiments.

extract_protocol:
After the polarization period, the cells were lyzed and RNA was extracted using RNeasy Mini Kit from Qiagen. RNA content and purity were determined using Nanodrop. RNA integrity was assessed using Agilent Bioanalyzer. RNA sequencing was performed using the HiSeq4000 sequencing system.
mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina) according to manufacturer's instructions.

tag: cell type

value: PBMC monocyte


title: MSC_healthy donor 2_rep1

city: Shenzhen

first: Zhaopeng

last: Cai

address: No. 3025, Shennan Middle Road, Futian District

country: China

institute: Sun Yat-sen University

description:
Gene expression after culture in osteogenic differentiation medium for 10 days.
s9

hyb_protocol: Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent).

data_processing: The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: bone marrow-derived MSCs from healthy people (2)

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: MSCs were isolated from bone marrow and cultured in DMEM medium containing 10% fetal bovine serum.All cells were cultured in 5% CO2 at 37 °C, and the culture medium was changed every 3 days.

extract_protocol: Total RNA containing small RNA was extracted from MSCs by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: To induce osteogenic differentiation, MSCs were cultured for 10 days in osteogenic differentiation medium containing DMEM with 10% FBS, 100 IU/ml penicillin, 100 IU/ml streptomycin, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate and 50 μM ascorbic acid. All cells were cultured in 5% CO2 at 37 °C, and the culture medium was changed every 3 days.

value: mesenchymal stem cells

tag: disease state

value: healthy

value: bone marrow

tag: gender

value: female


title: GMSB_046_PBMC_FTC/TDF

source_name: PBMC from GMSB_046 treated with FTC/TDF

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfresultdate

value: injectable

tag: rin

tag: valid


title: 24_S2_PBMC_monocytes_Run2


title: MSC_healthy donor 3_rep1

description:
Gene expression after culture in osteogenic differentiation medium for 10 days.
s12

source_name: bone marrow-derived MSCs from healthy people (3)

tag: tissue

value: male


title: GMSB_048_PBMC_TDF

source_name: PBMC from GMSB_048 treated with TDF

value: PBMC

tag: ptid

tag: visit

value: A

value: No

tag: birthcontrolepi

tag: birthcontrollab

value: NoHC

tag: lng

tag: eng

tag: net

value: Excluded:undetectable TDF


title: MSC_OPLL patient 3_rep1

description:
Gene expression after culture in osteogenic differentiation medium for 10 days.
s6

source_name: bone marrow-derived MSCs from OPLL patient (3)

tag: cell type

tag: disease state

value: ossification of the posterior longitudinal ligament (OPLL)


title: GMSB_047_PBMC_FTC/TDF

source_name: PBMC from GMSB_047 treated with FTC/TDF

tag: collectiondate

tag: age

value: prep

tag: tdfngperml

tag: tdfdetected

value: oral

tag: mpa

tag: nugent

value: Negative

value: unknown


title: GMSB_052_PBMC_FTC/TDF

source_name: PBMC from GMSB_052 treated with FTC/TDF

tag: arm

tag: drug

tag: prep

value: Yes

tag: tdfresultdate

value: Positive

tag: rin

tag: valid

value: Included


title: MSC_OPLL patient 2_rep1

description:
Gene expression after culture in osteogenic differentiation medium for 10 days.
s2

source_name: bone marrow-derived MSCs from OPLL patient (2)

value: mesenchymal stem cells

tag: tissue

value: bone marrow

tag: gender

value: female


title: MSC_healthy donor 1_rep1

description:
Gene expression after culture in osteogenic differentiation medium for 10 days.
s8

source_name: bone marrow-derived MSCs from healthy people (1)

value: healthy

value: male


title: MSC_OPLL patient 1_rep1

description:
Gene expression after culture in osteogenic differentiation medium for 10 days.
s1

source_name: bone marrow-derived MSCs from OPLL patient (1)


title: Huh7 cells, collagen_(1.0_mg/ml)_rep3

description:
counts.txt.gz
tpms.txt.gz
cg1_0_mg_ml_rep3

value: Huh7 human liver cell line

tag: passages

tag: matrix for cell growth

value: Collagen (1.0 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: 22_S5_PBMC_monocytes_Run2

tag: cell type

value: PBMC monocyte


title: GMSB_049_PBMC_FTC/TDF

source_name: PBMC from GMSB_049 treated with FTC/TDF

value: PBMC

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: B

value: FTC/TDF

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

value: injectable

tag: birthcontrollab

tag: lng

tag: eng

tag: net


title: 19_S4_IPS_monocytes_Run2

source_name: iPSC

value: iPSC-derived macrophage progenitors


title: 17_S1_IPS_monocytes_Run2


title: Huh7 cells, collagen_(1.0_mg/ml)_rep2

description:
counts.txt.gz
tpms.txt.gz
cg1_0_mg_ml_rep2

source_name: Huh7 cells

tag: passages


title: Huh7 cells, collagen_(0.5_mg/ml)_rep3

description:
counts.txt.gz
tpms.txt.gz
cg0_5_mg_ml_rep3

tag: matrix for cell growth

value: Collagen (0.5 mg/ml)


title: GMSB_044_PBMC_TDF

source_name: PBMC from GMSB_044 treated with TDF

tag: tissue

tag: arm

value: A

tag: drug

value: TDF

tag: prep

value: prep

value: No

tag: tdfresultdate

value: oral

tag: mpa

tag: nugent

value: Positive

tag: rin

tag: valid

value: Excluded:undetectable TDF


title: GMSB_043_PBMC_TDF

source_name: PBMC from GMSB_043 treated with TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: tdfngperml

tag: tdfdetected

value: Yes

value: NoHC

value: Included


title: Huh7 cells, collagen_(1.0_mg/ml)_rep1

description:
counts.txt.gz
tpms.txt.gz
cg1_0_mg_ml_rep1

tag: cell type

value: Huh7 human liver cell line

tag: passages

value: Collagen (1.0 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: GMSB_042_PBMC_TDF

source_name: PBMC from GMSB_042 treated with TDF

tag: tissue

value: PBMC

tag: arm

tag: drug

tag: prep

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

tag: lng

tag: eng

tag: net

value: Negative

value: unknown


title: 45_S23_PBMC_macrophages_m2_MCSF_IL4

source_name: PBMC

value: PBMC-derived M2 macrophage


title: GMSB_039_PBMC_Placebo

source_name: PBMC from GMSB_039 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: C

value: Placebo

value: placebo

tag: tdfresultdate

tag: mpa

tag: nugent

tag: rin

tag: valid


title: GMSB_041_PBMC_FTC/TDF

source_name: PBMC from GMSB_041 treated with FTC/TDF

tag: tissue

tag: arm

value: B

value: FTC/TDF

value: prep

tag: tdfngperml

tag: tdfdetected

value: oral


title: GMSB_038_PBMC_Placebo

source_name: PBMC from GMSB_038 treated with Placebo

tag: drug

tag: prep

tag: birthcontrolepi

value: injectable

tag: birthcontrollab

value: Positive


title: GMSB_033_PBMC_TDF

source_name: PBMC from GMSB_033 treated with TDF

tag: ptid

value: A

value: TDF

value: No

value: NoHC

tag: lng

tag: eng

tag: net

value: Excluded:undetectable TDF


title: 44_S45_PBMC_macrophages_m1_GMCSF_INFG

tag: cell type

value: PBMC-derived M1 macrophage


title: 41_S33_PBMC_macrophages_m1_GMCSF_INFG


title: GMSB_045_PBMC_TDF

source_name: PBMC from GMSB_045 treated with TDF

value: PBMC

tag: visit

tag: collectiondate

tag: age

value: Yes

tag: tdfresultdate

value: Nohist

tag: mpa

value: Included


title: Huh7 cells, collagen_(0.5_mg/ml)_rep1

description:
counts.txt.gz
tpms.txt.gz
cg0_5_mg_ml_rep1

value: Huh7 human liver cell line

tag: passages

tag: matrix for cell growth

value: Collagen (0.5 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: 43_S34_PBMC_macrophages_m0_MCSF

value: PBMC-derived M0 macrophage


title: GMSB_034_PBMC_FTC/TDF

source_name: PBMC from GMSB_034 treated with FTC/TDF

tag: tissue

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

value: implant

tag: nugent

value: Negative

tag: rin

tag: valid


title: Huh7 cells, control_rep2

description:
counts.txt.gz
tpms.txt.gz
normal_rep2

tag: cell type

value: Polystyrene coated cell culture plate


title: GMSB_036_PBMC_Placebo

source_name: PBMC from GMSB_036 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: C

value: Placebo

value: placebo

tag: tdfresultdate

value: oral

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: lng

tag: eng

tag: net

value: Excluded:MDS outlier


title: GMSB_035_PBMC_TDF

source_name: PBMC from GMSB_035 treated with TDF

tag: tissue

value: PBMC

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

value: Yes

value: injectable

value: Positive

value: Included


title: GMSB_032_PBMC_TDF

source_name: PBMC from GMSB_032 treated with TDF

value: prep

tag: tdfdetected

value: No

tag: birthcontrolepi

tag: nugent

value: unknown

tag: rin

tag: valid

value: Excluded:undetectable TDF


title: Huh7 cells, collagen_(0.5_mg/ml)_rep2

description:
counts.txt.gz
tpms.txt.gz
cg0_5_mg_ml_rep2

tag: cell type

value: Huh7 human liver cell line

tag: passages

tag: matrix for cell growth

value: Collagen (0.5 mg/ml)

tag: average insert size

tag: standard deviation

tag: directionality

value: antisense strand reads


title: GMSB_037_PBMC_TDF

source_name: PBMC from GMSB_037 treated with TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: tdfresultdate

value: Nohist

tag: birthcontrollab

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

value: Negative


title: GMSB_029_PBMC_TDF

source_name: PBMC from GMSB_029 treated with TDF

tag: tissue

value: PBMC

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

tag: nugent

tag: rin

tag: valid


title: Huh7 cells, control_rep1

description:
counts.txt.gz
tpms.txt.gz
normal_rep1

tag: cell type

tag: passages

tag: matrix for cell growth

value: Polystyrene coated cell culture plate

tag: average insert size

tag: standard deviation

tag: directionality


title: 40_S44_PBMC_macrophages_m0_MCSF

value: PBMC-derived M0 macrophage


title: GMSB_030_PBMC_FTC/TDF

source_name: PBMC from GMSB_030 treated with FTC/TDF

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: B

value: FTC/TDF

tag: tdfresultdate

value: oral

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net


title: WNT3A treatment  donor 3

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and FastX-toolkit
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using TopHat2
FPKM estimation of reference genes and transcripts using Cufflinks 2
Assembly of novel transcriptome with Cufflinks 2 and Cuffmerge
Variant calling (SNVs and small indels) with the Isaac Variant caller
Genes and isoforms differential expression using Cuffdiff2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Stem cells isolated from human exfoliated deciduous teeth

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment


title: 42_S11_PBMC_macrophages_m2_MCSF_IL4

tag: cell type

value: PBMC-derived M2 macrophage