title: 61_Batch1_61_FAA2P6HN-01_S61_L008

first: Gregory

institute: Yerkes National Primate Research Center

tag: visit

value: baseline

tag: lactobacilli

value: No

value: Unchecked


title: 58_Batch1_58_KAA2NZ84-01_S58_L008

status: Public on Sep 13 2023

type: SRA

city: Atlanta

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

library_source: transcriptomic

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: total RNA

organism: Homo sapiens

source_name: endocervical cells

growth_protocol: Cervical cytobrush samples collected at the baseline and the one month follow-up visit from 188 matched participants (n=376) were processed for RNA sequencing of cervical cells. The cervical cells were collected using a Digene cervical sampler (Digene Corporation, Gaithersburg, MD, USA). A cervical cytobrush was inserted into the endocervical os, rotated through 360 degrees and placed in a 15ml tube containing 3ml R10 media (10% heat-inactivated fetal calf serum (FCS) in RPMI supplemented with L-glutamine (50 ng/μl), anti-fungin (0.8 ng/μl), penicillin (50 U) and streptomycin (50 ng/μl)) and transported to the laboratory within 6 hours.

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

treatment_protocol: Upon arrival of the cytobrush at the laboratory, the cytobrush was rotated against the side of the tube to dislodge the cells and the transport medium was used to flush the cytobrush bristles 30 times. The tubes were centrifuged at 1200 rpm for 10 mins to pellet cells. The supernatant was removed from the tube leaving about 50 μl and the pellet gently dislodged by vortexing. 350 μl RLT buffer (QIAGEN) with 1% beta-mercaptoethanol was added to sample. The samples were vortexed for one min to disrupt cells and immediately stored at -80℃.

tag: site

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete


title: Passage 4 Pkd2KO cells with DOX, replicate 1

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Four technical repliates of each experimental group were prepared for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using Star (2.6.0c) with a qaunt mode.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: mouse inner medullary collecting duct cell line

growth_protocol: The Pkd2 knockout cells were grown on the permeable filter membrane for 10 days in the RenaLife Epithelial Basal Medium (LM-0010, LIFELINE CELL TECHNOLOGY) supplemented with a RenaLife LifeFactors Kit (LS-1048, LIFELINE CELL TECHNOLOGY) and 5% FBS.

extract_protocol:
Cells were lyzed in Trizol. Total RNA was extracted using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
To enrich mRNA, 1-3 ug of total RNA was applied to oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEW ENGLAND BioLabs Inc.) as a manufacturer’s instruction. mRNA (20-30 ng) was sequentially used for the further sequencing library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, NEW ENGLAND BioLabs Inc.) and NEBNext® Multiplex Oligos (E7335; E7500, NEW ENGLAND BioLabs Inc.). cDNA libraries were sequenced on Illumina HiSeq 4000 platform. Sequence reads (2 × 75 bp, paired-end) were aligned on Ensembl genome GRCm38p6 using STAR (2.6.0c).

treatment_protocol: Cells (passage 4 and passage 7) were grown on the permeable filters of a transwell system (6-well) for 10 days and treated with or without doxycycline (2 ug/mL) for 6 days. Media were daily changed.

tag: tissue

value: kidney

tag: dox treatment

value: with DOX

tag: genotype

value: Pkd2KO induced by DOX

tag: cell type

tag: passage


title: Passage 4 Pkd2KO cells without DOX, replicate 4

value: without DOX

value: wild type

value: mouse inner medullary collecting duct cell line


title: CD8 CD33 CAR T cells from AML patient Donor 9b, Day 0

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

description:
AML9b_CD33_41BB_CD8_0d_S46
CD8_Filtered_Rawcounts.txt

data_processing:
Samples were aligned to the Human genome (GRCh38) with STAR (v2.6.1). Gene expression was quantified with quant3p (github.com/ctlab/quant3p).
Downstream analyses were performed in R (v3.6.2). Data transformation, normalization, and differential gene expression analysis were performed with DESeq2. Genes were considered adjusted p value (p-adj)<0.05 and absolute log transformed fold-change (|log2FC|)>1, unless otherwise indicated. vst expression values were used for data visualization and unsupervised analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes filtered raw counts (filtered to have counts >0 at least in one sample) for all the CAR T cells samples divided in CD4 or CD8 cells

growth_protocol: CAR T Cell generation: Peripheral Blood Mononuclear Cells (PBMCs) were isolated with Ficoll-Paque and CD4+ and CD8+ T cells were selected using CD4 and CD8 MicroBeads (Miltenyi Biotec) in the AutoMACS Pro Separator (Miltenyi Biotec). Isolated T cells were activated with 10 µl/ml T cell TransAct (Miltenyi Biotec) for 48h and infected with the CAR lentiviral vector at MOI 2 with 10 µl/ml of LentiBoost (Sirion Biotech). CAR-T cells were expanded in RPMI 1640 culture medium supplemented with 3% human serum (Sigma), 1% penicillin/streptomycin and 625 IU/ml of human IL-7 and 85 IU/ml of human IL-15 (Miltenyi Biotec). CAR-T cells were counted, and the concentration was adjusted to 1×106 cells/ml every two days.

extract_protocol:
RNA-seq was performed following MARS-seq protocol adapted for bulk RNA-seq with minor modifications. Briefly, 7000 to 10000 cells were sorted in 100µl of Lysis/Binding Buffer (Ambion), vortexed and stored at -80ºC until further processing. Poly-A RNA was reverse-transcribed using poly-dT oligos carrying a 7 nt-index. Pooled samples were subjected to linear amplification by IVT. Resulting aRNA was fragmented and dephosphorylated.
RNA-seq libraries quantification was done with Qubit 3.0 Fluorometer (Life Technologies) and size profiles were examined using Agilent’s 4200 TapeStation System. Libraries were sequenced in an Illumina NextSeq500 at a sequence depth of 10 million reads per sample.

tag: group

value: AML patient

tag: time

value: Day 0


title: u2os_ko_3

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

institute: WashU School Of Medicine

description:
paired-end
group_u2os_ko_Differential_Expression_sanitized.tsv

data_processing:
Basecalls and de-multiplexing were performed with Illumina’s bcl2fastq software and a custom Python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-Seq reads were then aligned to Ensembl GRCh38.76 or Ensembl GRCm38.76 assembly for human or mouse samples, respectively, with STAR version 2.7.9a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: Ensembl GRCh38.76 or Ensembl GRCm38.76 assembly for human or mouse samples, respectively
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone; Osteocarcoma

growth_protocol: Human cell lines (HeLa-S, and U2OS; both originally from ATCC) were cultured in Dulbecco’s modified eagle medium (Invitrogen), supplemented with 10% fetal bovine serum (Sigma), 100 U/ml of penicillin-streptomycin (GIBCO) at 37°C and 5% CO2.

extract_protocol:
RNA was purified from cell lines using the Qiagen miRNeasy mini kit to accomodate small RNA isolation (#217004). For RNA isolation from mouse cortex, cerebral cortex was dissected in ice-cold PBS from 5 female Ttdn1-/- and 5 WT littermates at 8 weeks of age, then flash frozen. RNA was purified from cortex using the Qiagen miRNeasy mini kit.
Samples for small RNA-sequencing were prepped with TruSeq Small RNA library preparations kits; otherwise all other samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000 2x150bp with the Genome Technology Access Center at Washington University in St. Louis, typically yielding 200 million paired-end reads per sample.

treatment_protocol: Where indicated, cells were treated with 250 nM pladienolide-B for 24h.

tag: cell line

value: Bone; Osteocarcoma


title: Passage 4 Pkd2KO cells without DOX, replicate 2


title: u2os_wt_1

value: WT


title: 54_Batch1_54_4560_S54_L008

tag: visit

value: Emavundleni

value: IVD

value: nonLD

tag: lactobacilli

value: BV

value: No

value: Unchecked


title: CD4 CD33 CAR T cells from AML patient Donor 9b, Day 0

description:
AML9b_CD33_41BB_CD4_0d_S45
CD4_Filtered_Rawcounts.txt


title: Passage 4 Pkd2KO cells without DOX, replicate 3


title: u2os_ko_2


title: Passage 4 Pkd2KO cells without DOX, replicate 1


title: u2os_ko_1


title: 57_Batch1_57_BAA2NRSC-01_S57_L008

value: baseline

tag: site

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

value: Nobs

value: Never married

value: Secondary school, some or complete


title: 53_Batch1_53_3056_S53_L008

tag: bmi

tag: ngonorrhoeae


title: CD8 CD33 CAR T cells from AML patient Donor 8, Day 14

description:
AML8_CD33_41BB_CD8_14d_S42
CD8_Filtered_Rawcounts.txt

value: AML patient

value: Day 14


title: ntc_c

description:
paired-end
group_ko-group_ntc_Differential_Expression_sanitized.tsv

source_name: Uterus; Cervix; Adenocarcinoma

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: WT


title: DS368.OldMale_rep4

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

data_processing:
Genomic Sciences and Precision Medicine Center at the Medical College of Wisconsin completed sequencing on the NovaSeq6000 (Illumina) with paired-end 150 base pair reads generated at ~45 million total reads per sample.
Sequencing reads were aligned to the rat Rnor_6.0.98 (Ensemble) transcriptome and processed through the MAPR-Seq Workflow with differential expression analysis completed using Bioconductor, edgeR v 3.8.6 software.
Genes with a false discovery rate (FDR) <0.05 and an absolute fold change ≥ 2 to 4 were initially filtered and considered significantly differentially expressed.
Assembly: Rnor_6.0.98
Supplementary files format and content: GeneCount.xlsx, contains raw and normalized counts for all individual samples for all genes.
Supplementary files format and content: SigDEgene_pairwise.xlsx, contains log fold change and false discovery rate statistic for each pairwise comparison, and raw counts for individual samples

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
extracted total RNA with RNeasy Micro Kit
RNA libraries were prepared according to the manufacturer’s protocols utilizing Illumina’s TruSeq Stranded mRNA library kit.
Final assessment, quantification, and pooling of the RNAseq libraries were completed with qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and DNA high sensitivity fragment analysis (Agilent).

treatment_protocol: Animals are aged or not

value: Kidney

tag: Sex

value: Male

tag: age

value: Old

value: Homo

tag: treatment

value: No treatment


title: OP793.OldMale_rep3

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

tag: tissue


title: 51_Batch1_51_560245826601_S51_L008

value: baseline

value: KEMRI

value: IVD

value: nonLD

tag: chlamydiatrachomatis

tag: mobilincus

value: BV

tag: yeasts

tag: maritalstatus

value: Married

value: Primary school, some or complete

value: No

value: Unchecked


title: CD8 CD33 CAR T cells from AML patient Donor 8, Day 0

description:
AML8_CD33_41BB_CD8_0d_S38
CD8_Filtered_Rawcounts.txt

tag: cell type

tag: group

value: AML patient

value: Day 0


title: 48_Batch1_48_560243436601_S48_L008

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

value: Nobs

value: Secondary school, some or complete

value: Yes

value: Checked


title: OP790.OldMale_rep2

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Kidney

value: Male

value: Old

tag: genotype

value: Homo

value: No treatment


title: ntc_a

tag: cell line

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: WT


title: CD4 CD33 CAR T cells from AML patient Donor 8, Day 14

description:
AML8_CD33_41BB_CD4_14d_S41
CD4_Filtered_Rawcounts.txt

value: AML patient

tag: time

value: Day 14


title: ntc_b


title: CD4 CD33 CAR T cells from AML patient Donor 9b, Day 14

description:
AML9b_CD33_41BB_CD4_14d_S49
CD4_Filtered_Rawcounts.txt


title: CD4 CD33 CAR T cells from AML patient Donor 8, Day 0

description:
AML8_CD33_41BB_CD4_0d_S37
CD4_Filtered_Rawcounts.txt

value: Day 0


title: ko_b


title: ko_c


title: DS380.OldFemale_rep4

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Female


title: OP789.OldMale_rep1

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx


title: 47_Batch1_47_560228986601_S47_L007

tag: visit

value: baseline

tag: site

value: KEMRI

value: IIIA

value: LD

value: TRUE

value: Negative

tag: lactobacilli

value: Abs

value: Married


title: CD8 CD33 CAR T cells from AML patient Donor 11b, Day 0

description:
AML11b_CD33_41BB_CD8_0d_S62
CD8_Filtered_Rawcounts.txt


title: DS379.OldFemale_rep3

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Kidney

value: Old

value: Homo


title: CD8 CD33 CAR T cells from AML patient Donor 11b, Day 14

description:
AML11b_CD33_41BB_CD8_14d_S66
CD8_Filtered_Rawcounts.txt


title: ko_a

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma


title: wt3

description:
paired-end
group_ko_pla-group_ko_Differential_Expression_sanitized.tsv

value: Bone; Osteocarcoma

value: WT


title: 36_Batch1_36_560241966601_S36_L007

tag: rin

value: IVD

value: nonLD

tag: bmi

tag: ngonorrhoeae

value: Positive

value: Intermediate

value: Nobs

value: Primary school, some or complete

value: Yes

value: Unchecked


title: CD4 CD33 CAR T cells from AML patient Donor 11b, Day 14

description:
AML11b_CD33_41BB_CD4_14d_S65
CD4_Filtered_Rawcounts.txt

value: AML patient

value: Day 14


title: 41_Batch1_41_GAA2P5CW-01_S41_L007

value: baseline

value: WRHI

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

value: Never married

value: Post-secondary school

value: No


title: 35_Batch1_35_560238766601_S35_L007

value: KEMRI

value: IB

value: Positive

value: Married


title: 20_Batch1_20_EAA2P5SQ-01_S20_L006

value: Nobs

value: Secondary school, some or complete

value: Unchecked


title: OP796.OldFemale_rep1

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Kidney

tag: Sex

value: Female

tag: age

value: Old

value: Homo

tag: treatment

value: No treatment


title: DS399.YoungMale_rep4

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

tag: tissue

value: Male

value: Young


title: CD4 CD33 CAR T cells from AML patient Donor 11b, Day 0

description:
AML11b_CD33_41BB_CD4_0d_S61
CD4_Filtered_Rawcounts.txt

value: AML patient

value: Day 0


title: wt2

value: Bone; Osteocarcoma

value: WT


title: 19_Batch1_19_HAA2NY3X-01_S19_L006

value: baseline

value: WRHI

value: IIIA

value: LD

value: TRUE

tag: chlamydiatrachomatis

value: Negative

value: Abs

tag: mobilincus

tag: yeasts

value: Never married

value: No


title: CD8 CD33 CAR T cells from AML patient Donor 10b, Day 14

description:
AML10b_CD33_41BB_CD8_14d_S58
CD8_Filtered_Rawcounts.txt

tag: cell type

tag: group

value: Day 14


title: DS363.YoungMale_rep3

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Kidney

tag: genotype

value: Homo

value: No treatment


title: DS362.YoungMale_rep2

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Male

value: Young


title: wt3_pla

tag: cell line

value: Bone; Osteocarcoma

value: WT + 250nM pladienolide-B


title: wt1

value: WT


title: 16_Batch1_16_CAA2PDC2-01_S16_L005

tag: visit

value: WRHI

value: IVA

value: nonLD

value: Positive

value: BV

value: Nobs

tag: maritalstatus

value: Secondary school, some or complete

value: Unchecked


title: Passage 7 Pkd2KO cells without DOX, replicate 2

value: kidney

tag: dox treatment

value: without DOX

value: wild type

value: mouse inner medullary collecting duct cell line

tag: passage


title: 15_Batch1_15_BAA2P3P6-01_S15_L005

value: baseline

tag: site

tag: rin

value: TRUE

tag: bmi

value: Negative

tag: lactobacilli

value: Abs

value: Never married

value: No


title: CD4 CD33 CAR T cells from AML patient Donor 10b, Day 14

description:
AML10b_CD33_41BB_CD4_14d_S57
CD4_Filtered_Rawcounts.txt

value: AML patient

tag: time

value: Day 14


title: OP818.OldFemale_rep2

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

tag: tissue

value: Kidney

tag: Sex

value: Female

tag: age

value: Old

value: Homo

tag: treatment

value: No treatment


title: wt2_pla

value: Bone; Osteocarcoma

value: WT + 250nM pladienolide-B


title: CD4 CD33 CAR T cells from AML patient Donor 10b, Day 0

description:
AML10b_CD33_41BB_CD4_0d_S53
CD4_Filtered_Rawcounts.txt

tag: cell type

value: Day 0


title: DS361.YoungMale_rep1

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Male

value: Young


title: wt1_pla


title: DS396.YoungFemale_rep4

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx


title: ko3


title: Med12 in hMo experiment, NT Sample_3

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
RNA-seq (hMo): Raw reads quality-trimmed using trim-galore (v0.6.7) and aligned to the hg38 reference by using hisat2 (v2.2.1) with the --very-sensitive option. Transcripts were quantified with stringtie (v2.2.1).
RNA-seq (BMDCs): Raw reads were quality-trimmed using cutadapt (v2.10). Additional quality filtering was performed by the fastx package (v0.0.14). Processed reads were aligned to the mouse genome version GRCm38 (Enembl 99 release) with TopHat (v2.1.1).
ATAC-seq and ChIP-seq: Raw reads quality-trimmed using trim-galore (v0.6.7) and aligned to the mm10 reference using hisat2 (v2.2.1). picard (v2.26.10) MarkDuplicates was used to mark and removed duplicates. Bigwig files were generated using deeptools (v3.5.1), normalizing by RPKM or BPM. Heatmaps were generated using deeptools (v3.5.1). Peaks for each sample were assigned using macs (v2.2.7.1). A union peak set for all samples was constructed by merging the peaks into a set of high-confidence non-overlapping fixed-width (500 bp) peaks.
Assembly: RNA-seq (hMo) - hg38; RNA-seq(BMDCs) - Grcm38 (Ensembl 99); ATAC-seq and ChIP-seq - mm10
Supplementary files format and content: Comma-delimited files listing counts, big-wig files, peak files

source_name: CD14 positive cells isolated from buffy coat

growth_protocol: To obtain BMDCs, femurs and tibia were removed, and BM was flushed. Red blood cells were lysed using RBC lysis buffer (e-bioscience). Bone marrow cells were plated in 100 mm diameter dish (Falcon, BD, NJ, USA) at a concentration of 2X105 per ml in 10 ml of medium. The medium included RPMI 1640 (Gibco #21875-034) supplemented with 10% heat-inactivated FBS (Gibco ,#10270106), β-mercaptoethanol (50 µM, Gibco, #31350-010),1% L-glutamine (Gibco, #25030-024), 1% penicillin/streptomycin (Gibco, #15140-122), 1% MEM non-essential amino acids (Gibco, #11140035), 1% HEPES (Gibco, #15630056), 1% sodium pyruvate (Gibco, #11360-039), and murine GM-CSF (20 ng/ml; Peprotech, #315-03). For CRISPR knockout experiments six- to eight-weeks-old constitutive Cas9-expressing mice were used as the source of BMDCs. Cells were maintained at 37°C in a 5% CO2-humidified atmosphere. On day two of culture, 10 ml of fresh medium supplemented with GM-CSF was added. On day five, 10 ml of medium were gently removed and 10 ml of fresh medium with GM-CSF was added. On day seven, 5 ml of fresh medium with GM-CSF was added to the cells and on day eight, floating cells were recovered and used for downstream applications.  Peripheral blood mononuclear cells (PBMCs) were isolated using a density gradient (Lymphoprep, STEMCELL Technologies, #7851) as previously described56. One buffy coat from Hadassah medical hospital was processed for each donor using BSL2* precautions in accordance with institutional safety guidelines. The buffy coat was diluted 1:1 with PBS (BI 02-023-1A), then layered on top of the lymphoprep in a 50 ml tube (Lifegene, LBT50). Isolated PMBCs were then cryopreserved in a mixture containing FBS with 10% DMSO (40X10⁶ cells in 1 ml) and stored in liquid nitrogen, or used directly for monocyte isolation. Monocytes were isolated using the EasySep Human Monocytes Isolation Kit (STEMCELL Technologies, #19359) according to the manufacturer’s instructions. To examine isolation efficiency, fractions of cells before and after separation were stained with human anti-CD14 (1:200) antibody and analyzed with Flow Cytometry.

extract_protocol:
RNA was recovered using RNeasy plus mini kit (Qiagen #74136). Samples for ATAC-seq were prepared with the kit (Active Motif #53150) according to the instruction manual. Samples for Chip-seq were prepared according to the protocol described by Antman et al  with several modifications. We used 30x10^6 BMDCs for each experiment. Quenching of formaldehyde was done at RT on a gently rocking platform. Samples were sonicated for three cycles (30 s on, 30 s off). For immunoprecipitation, 10 µL of Cebpb antibody was added (ab32358) and 30 µL of Protein G magnetic beads. Then, 2.5% of the sample was taken as input. Chromatin was eluted from the beads by shaking them in a heat block at 800 rpm for 30 min at 65 °C and reverse crosslinking was performed at 65 °C overnight.
The libraries for RNA-seq were prepared using KAPA mRNA capture kit (Roche #07962231001) following the manufacturer’s instructions. The libraries for Chip-seq were prepared using   KAPA HyperPrep Kit (Roche #7962347001) according to the instruction manual (1 ng of immunoprecipitated sample and 100 ng of input sample were used for library preparation). The libraried for ATAC-seq were prepared using the kit (Active Motif #53150) according to the instruction manual.

treatment_protocol: For RNA-seq experiment with human monocytes CD14+ cells were electroporated on day zero with RNP complex containing Cas9 portein and gRNA (against Med12 or non-targeting guide). Electroporation was done using Nepa21 machine. For RNA-seq with mouse BMDCs, cells were infected on day two with corresponding lentivirus and on day eight cells were used for RNA extraction. For ATAC-seq experiment, on day two BMDCs were infected with either mCherry lentivirus targeting Cebpb, or BFP lentivirus targeting Med12, or mCherry non-targeting lentivirus. On day eight infected cells were sorted and around 100 000 sortecells were used per sample. For Chip-seq uninfected BMDCs were used on day eight. Around 30x10^6 cells were used per sample.

value: Mo-DC

value: WT

value: Electroporated with RNP complex (Cas9 protein + non-targeting gRNA)


title: 350_Batch5_63_560233806601_S71_L005

value: baseline

value: KEMRI

value: IVB

value: nonLD

value: LD

value: FALSE

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

value: Never married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: DS359.YoungFemale_rep3

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Kidney

value: Female

value: Young

tag: genotype

value: Homo

value: No treatment


title: Med12 in hMo experiment, NT Sample_2

value: CD14 positive cells isolated from buffy coat

value: Mo-DC

value: WT

value: Electroporated with RNP complex (Cas9 protein + non-targeting gRNA)


title: ko2

tag: cell line

value: Bone; Osteocarcoma


title: 281_Batch4_66_560240846601_S2_L001

tag: visit

value: KEMRI

value: IB

value: LD

value: nonLD

value: FALSE

value: Negative

tag: maritalstatus

value: Married

value: No schooling


title: 243_Batch4_28_560249496601_S86_L006

tag: site

tag: rin

value: Abs

value: Obs

value: Primary school, some or complete

value: Yes

value: Checked


title: DS358.YoungFemale_rep2

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx

value: Kidney

value: Female

value: Young

value: Homo

value: No treatment


title: Med12 in hMo experiment, NT Sample_1

value: CD14 positive cells isolated from buffy coat

value: Mo-DC

value: WT

value: Electroporated with RNP complex (Cas9 protein + non-targeting gRNA)


title: ko1

value: Bone; Osteocarcoma


title: DS357.YoungFemale_rep1

description:
GeneCount.xlsx
SigDEgene_pairwise.xlsx


title: CD8 CD33 CAR T cells from AML patient Donor 10b, Day 0

description:
AML10b_CD33_41BB_CD8_0d_S54
CD8_Filtered_Rawcounts.txt

tag: group

value: AML patient

value: Day 0


title: 231_Batch4_16_FAA2P7JB-01_S74_L005

value: WRHI

value: nonLD

value: FALSE

tag: bmi

value: Negative

value: Positive

tag: lactobacilli

value: Abs

value: Intermediate

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: Med12 in hMo experiment, Med12 KO_2

tag: tissue

value: CD14 positive cells isolated from buffy coat

value: Mo-DC

value: Electroporated with RNP complex (Cas9 protein + gRNA targeting Med12)


title: ko3_pla

value: Bone; Osteocarcoma

value: TTDN1 -/- + 250nM pladienolide-B


title: BMSCs-OE-FNDC5 biol rep 2

city: Guangzhou

first: Huan

last: Wei

address: Zhongshan Road 58

country: China

institute: The First Affiliated Hospital of SUMS

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

growth_protocol: BMSCs were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: To mimic hypoxia/ischemia injury in vitro, BMSCs at 70%~80% density confluence were cultured under hypoxic condition with 1% O2, 94% nitrogen (N2), and 5% CO2 in glucose-free and serum-free medium for 24 h.

value: bone marrow

value: mesenchymal stem cells

value: FNDC5 overexpression

value: hypoxia 24 hours


title: 184_Batch3_41_4496_S27_L002

value: baseline

value: Emavundleni

value: LD

value: FALSE

value: Negative


title: BMSCs-OE-FNDC5 biol rep 3


title: Human monocytes experiment, Cebpb sample 3

description:
hMo_Cebpb_3
hMo_DEseq.csv

data_processing:
Experiment1:
Raw reads were quality-trimmed with TrimGalore (v0.6.4).
Processed reads were aligned to the mouse genome version GRCm38 (Ensembl release 89) with the STAR70 (v2.7.3) aligner and quantified using Salmon (v0.14.0).
Experiment2 + Human monocytes experiment:
Raw reads were quality-trimmed and the remaining adapter sequences were removed using cutadapt (v2.10).
Processed reads were aligned to the mouse genome version GRCm38 (with genome annotations of Ensembl release 99) with TopHat66 (v2.1.1).
Assembly: Ensembl 89 (Experiment 1), Ensembl 99 (Experiment 2 + Human monocytes experiment)
Supplementary files format and content: Comma-delimited files listing counts for each biologic triplicate

source_name: CD14 positive PBMCS

growth_protocol: To obtain BMDCs, femurs and tibia were removed, and BM was flushed. Red blood cells were lysed using RBC lysis buffer (e-bioscience). Bone marrow cells were plated in 100 mm diameter dish (Falcon, BD, NJ, USA) at a concentration of 2X105 per ml in 10 ml of medium. The medium included RPMI 1640 (Gibco #21875-034) supplemented with 10% heat-inactivated FBS (Gibco ,#10270106), β-mercaptoethanol (50 µM, Gibco, #31350-010),1% L-glutamine (Gibco, #25030-024), 1% penicillin/streptomycin (Gibco, #15140-122), 1% MEM non-essential amino acids (Gibco, #11140035), 1% HEPES (Gibco, #15630056), 1% sodium pyruvate (Gibco, #11360-039), and murine GM-CSF (20 ng/ml; Peprotech, #315-03). For CRISPR knockout experiments six- to eight-weeks-old constitutive Cas9-expressing mice were used as the source of BMDCs. Cells were maintained at 37°C in a 5% CO2-humidified atmosphere. On day two of culture, 10 ml of fresh medium supplemented with GM-SCF was added. On day five, 10 ml of medium were gently removed and 10 ml of fresh medium with GM-CSF was added. On day seven, 5 ml of fresh medium with GM-CSF was added to the cells and on day eight, floating cells were recovered and used for downstream applications.  Peripheral blood mononuclear cells (PBMCs) were isolated using a density gradient (Lymphoprep, STEMCELL Technologies, #7851) as previously described56. One buffy coat from Hadassah medical hospital was processed for each donor using BSL2* precautions in accordance with institutional safety guidelines. The buffy coat was diluted 1:1 with PBS (BI 02-023-1A), then layered on top of the lymphoprep in a 50 ml tube (Lifegene, LBT50). Isolated PMBCs were then cryopreserved in a mixture containing FBS with 10% DMSO (40X10⁶ cells in 1 ml) and stored in liquid nitrogen, or used directly for monocyte isolation. Monocytes were isolated using the EasySep Human Monocytes Isolation Kit (STEMCELL Technologies, #19359) according to the manufacturer’s instructions. To examine isolation efficiency, fractions of cells before and after separation were stained with human anti-CD14 (1:200) antibody and analyzed with Flow Cytometry.

extract_protocol:
RNA was recovered using RNeasy plus mini kit (Qiagen #74136).
The libraries were prepared using KAPA mRNA capture kit (Roche #07962231001) following the manufacturer’s instructions.

value: CD14 positive PBMCS

value: MO-DCs

value: Cas9 expressing mice (JAX#026556)

value: Electroporate with RNP targeting Cebpb


title: ko2_pla


title: 258_Batch4_43_5824_S101_L007

value: Abs

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: ko1_pla

value: Bone; Osteocarcoma

value: TTDN1 -/- + 250nM pladienolide-B


title: 52_Batch1_52_560249066601_S52_L008

value: KEMRI

value: IIIA

value: nonLD

value: Intermediate

value: Married

value: Primary school, some or complete

value: No


title: Human monocytes experiment, Cebpb sample 2

description:
hMo_Cebpb_2
hMo_DEseq.csv

value: CD14 positive PBMCS

value: MO-DCs

value: Cas9 expressing mice (JAX#026556)


title: BMSCs-OE-FNDC5 biol rep 1

value: bone marrow

value: mesenchymal stem cells

value: FNDC5 overexpression

value: hypoxia 24 hours


title: 42_Batch1_42_DAA2PHST-01_S42_L007

value: WRHI

value: FALSE

value: Negative

value: Abs

value: Obs

value: Never married

value: Post-secondary school

value: Unchecked


title: wt_gfp_b

description:
paired-end
group_0_75_wt_Differential_Expression_sanitize.tsv

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: WT + GFP


title: BMSCs-OE-NC biol rep 3

value: vector control


title: wt_gfp_c


title: 372_Batch6_13_560238446601_S93_L007

value: KEMRI

value: Intermediate

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes


title: Human monocytes experiment, Cebpb sample 1

description:
hMo_Cebpb_1
hMo_DEseq.csv

value: CD14 positive PBMCS

value: MO-DCs

value: Cas9 expressing mice (JAX#026556)

value: Electroporate with RNP targeting Cebpb


title: Human monocytes experiment, NT sample 3

description:
hMo_NT_3
hMo_DEseq.csv

value: Electroporated with non-targeting RNP


title: 216_Batch4_1_KAA2NMRP-01_S59_L004

value: baseline

value: WRHI

value: Negative

value: Abs

value: BV

value: Never married

value: Secondary school, some or complete


title: Human monocytes experiment, NT sample 2

description:
hMo_NT_2
hMo_DEseq.csv


title: ko_gfp_c

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: TTDN1-/- + GFP


title: Neutrophils_Shig_flexneri_M90T_DmxiD_rep2_IP

city: London

first: Serge

last: Mostowy

address: Keppel Street, Bloomsbury

country: United Kingdom

institute: LSHTM

library_source: genomic

data_processing:
Quality control of sequencing reads was performed using FastQC
ChIP-seq reads were aligned to the UCSC GRCz10 genome using Bowtie2 version 2.4.2 and samtools verison 1.11. Only uniquely mapping reads with at most one mismatch was retained.
Duplicates from ChIP-seq mapped reads were removed with MarkDuplicates version 2.18.2.2.
DNA fragment size was predicted using macs2 predictd version 2.1.1.20160309.1
Peak calling was performed using macs2_callpeak version 2.1.1.20160309.6. Extension size was set to predicted DNA fragment size and the p-value cuttoff for peak detection was 0.01
Overlap between both replicates was determined using IDR version 2.0.3 with a threshold of 0.05
Peaks were annotated  based on UCSC GRCz10 genome using chipseeker version 1.18.0.
Assembly: GRCz10
Supplementary files format and content: bigWig, bed (except for input samples), xlsx

molecule: genomic DNA

organism: Danio rerio

source_name: Neutrophil

growth_protocol: Neutrophils were collected from zebrafish larvae at 4 days post-fertilisation. Larvae were grown in 0.5X E2 media at 28.5oC

extract_protocol:
Tg(lyz::dsRed)nz50 zebrafish larvae were dissociated using 0.5% Trypsin EDTA 10x no phenol (Fisher cat no.15400054) and incubated twice for 10 min at 28.5oC. The reaction was stopped by adding 10% fetal calf serum. The suspensions were sieved using 70 μm Nylon cell strainers (Merck CLS431751-50EA) and then gently centrifuged for 3 min at 800g. Cells were then washed with 1mL PBS with 10 mM HEPES and 1 mM EDTA. Cells were incubated with fixable APC Cy7 (1:2000, Thermofisher cat no. L34994) dye for 30 min at 4oC. cells were fixed with 1% formaldehyde for 8 min at RT with occasional mixing. To stop the reaction 100 µL of glycine 1.25 M were added and the samples were incubated for 5 min at RT. After centrifuging at 600g for 10 min at 4oC, cells were washed with ice cold PBS containing protease inhibitor cocktail (Sigma-aldrich cat no. 5892970001) and centrifuged again. Cells were then resuspended in PBS with 10mM HEPES and 1 mM EDTA and run through a Becton Dickinson FACSAria III cell sorter. Chromatin was prepared for ChIPseq using the True MicroChIP Kit (Diagenode cat no. C01010130) and was sheared using Bioruptor® Pico sonication device (Diagenode cat no. B01060001) combined with the Bioruptor® Water cooler for 5 cycles using a 30’’ [ON] 30’’ [OFF] settings.
Libraries were prepared using IP-Star® Compact Automated System (Diagenode cat no. B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode cat no. C05010013). Libraries were pooled and sequenced with Illumina Novaseq 6000, running NovaSeq Control Software 1.6.0, with paired-end reads of 50bp length.

treatment_protocol: Larvae were injected with either PBS, Shigella flexneri M90T or Shigella flexneri M90T DmxiD in the hindbrain ventricle at 2 days post-fertilisation

value: Neutrophil

value: Shigella flexneri M90T DmxiD

tag: chip antibody

value: H3K4me3 (Diagenode Cat# C15410003)


title: 242_Batch4_27_560244296601_S85_L006

value: KEMRI

value: LD

value: FALSE

value: Obs

value: Married

value: Primary school, some or complete

value: Yes

value: Checked


title: Med12 in hMo experiment, Med12 KO_1

value: CD14 positive cells isolated from buffy coat

value: Mo-DC

value: WT

tag: treatment

value: Electroporated with RNP complex (Cas9 protein + gRNA targeting Med12)


title: BMSCs-OE-NC biol rep 2

value: bone marrow

tag: cell type

value: mesenchymal stem cells

value: vector control

value: hypoxia 24 hours


title: 400_Batch6_41_4480_S121_L008

value: Emavundleni

value: IVA

value: nonLD

value: TRUE

tag: ngonorrhoeae

value: Negative

value: Abs

value: BV

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: BMSCs-OE-NC biol rep 1


title: ko_gfp_a

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: TTDN1-/- + GFP


title: Human monocytes experiment, NT sample 1

description:
hMo_NT_1
hMo_DEseq.csv

value: CD14 positive PBMCS

value: MO-DCs

value: Cas9 expressing mice (JAX#026556)

value: Electroporated with non-targeting RNP


title: Neutrophils_Shig_flexneri_M90T_DmxiD_rep1_IP

value: Neutrophil

value: Shigella flexneri M90T DmxiD

value: H3K4me3 (Diagenode Cat# C15410003)


title: ko_gfp_b


title: wt_gfp_a

value: WT + GFP


title: 399_Batch6_40_2160_S120_L008

value: baseline

value: Emavundleni

value: IVA

value: nonLD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

value: Abs

value: BV


title: 394_Batch6_35_560240116601_S115_L008

value: KEMRI

value: IIIA

value: LD

tag: mobilincus

value: Nobs

value: Married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: 0_75_wt_c

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: TTDN1-/- + DBR1TTDN1-NTD


title: MP082_ResDC

city: Epalinges

first: Mathilde

last: Foglierini-Perez

address: Chemin de Boveresses 155

country: Switzerland

institute: CHUV

data_processing:
For each sample droptag was used to generate fastq files for alignment.
Then STAR was used to align the reads against human genome hg38.
The count matrix was generated with dropEst
Cells were trimmed out based on UMIs count (>=750 & <= 4000), generating the related matrices: sampleName_filtered_feature_matrix.csv
Genome_build: hg38
Supplementary_files_format_and_content: csv files containing feature matrices

molecule: polyA RNA

source_name: Lymph node

extract_protocol:
FACS sorted LN resident and LN migratory dendritic cells were processed according to the Seq-Well S3 protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7562821/)
cDNA libraries were prepared according to Illumina protocols accompanying the Nextera XT DNA Library Preparation Kit using a Custom P5 hybrid Oligo and N700 index oligos, and were sequenced on an Illumina NextSeq 500 sequencer using a custom Read 1 primer
scRNA-seq

value: Resident dendritic cells

value: ART treated

tag: disease state

value: HIV infected


title: 0_75_wt_b

tag: genotype


title: Neutrophils_Shig_flexneri_M90T_DmxiD_rep1_input

value: Neutrophil

value: Shigella flexneri M90T DmxiD

value: H3K4me3 (Diagenode Cat# C15410003)


title: MP136_ResDC


title: Neutrophils_Shig_flexneri_M90T_rep2_IP

value: Shigella flexneri M90T


title: 383_Batch6_24_560241096601_S104_L007

value: baseline

value: KEMRI

value: IIIA

value: TRUE

value: Negative

value: Abs

tag: yeasts

value: Never married

value: Primary school, some or complete

value: No


title: 0_75_wt_a

tag: cell line

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: TTDN1-/- + DBR1TTDN1-NTD


title: 393_Batch6_34_560231716601_S114_L008

tag: visit

value: LD

value: Nobs

tag: maritalstatus

value: Married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: Neutrophils_Shig_flexneri_M90T_rep2_input

value: Neutrophil

value: Shigella flexneri M90T

value: H3K4me3 (Diagenode Cat# C15410003)


title: dbr1_ntc_c

description:
paired-end
group_dbr1_ko-group_ntc_Differential_Expression_sanitize.tsv

value: DBR1 knockdown


title: RB011_MigDC

value: Migratory dendritic cells

value: ART treated

value: HIV infected


title: Neutrophils_Shig_flexneri_M90T_rep1_IP


title: 373_Batch6_14_2112_S94_L007

value: baseline

tag: site

value: Emavundleni

tag: rin

value: IIIA

value: TRUE

value: Negative

value: Abs

value: Never married

value: No


title: RB011_ResDC

value: Resident dendritic cells


title: 374_Batch6_15_3936_S95_L007

value: LD

tag: bmi

value: Nobs

value: Secondary school, some or complete

value: Unchecked


title: dbr1_ntc_b

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: DBR1 knockdown


title: Neutrophils_Shig_flexneri_M90T_DmxiD_rep2_input

value: Neutrophil

value: Shigella flexneri M90T DmxiD

value: H3K4me3 (Diagenode Cat# C15410003)


title: Neutrophils_Shig_flexneri_M90T_rep1_input

value: Shigella flexneri M90T


title: 364_Batch6_5_560235816601_S85_L006

value: baseline

value: KEMRI

value: IIIA

value: TRUE

tag: lactobacilli

value: Married

value: Primary school, some or complete

value: Yes


title: DKO_1421

city: Buffalo

first: Michael

last: Battaglia

state: NY

address: 955 Main St

department: Microbiology and Immunology

institute: SUNY at Buffalo

data_processing:
Raw reads were analyzed for quality for FASTQC v0.11.9
Raw reads were mapped to  GRCm38 – mm10 reference genome utilizing TopHat2
Aligned reads were quanitified using featureCounts v1.5.3
Raw counts matrix was processed to generate per million normalized expression values
Differentially expressed genes relative to wild type controls were identified using DEseq2 v1.24.0 with genes being identified as statistically significantly differentially expressed with a log2fold change ≥1 and a FDR value of ≤0.1.
Assembly: GRCM38-mm10
Supplementary files format and content: comma separated file including nTPM values for each sample
Supplementary files format and content: tab-delineated file containing DEG analysis  including Log2 fold change and corresponding p values

source_name: ventral neck skin

extract_protocol:
RNA was extracted using phenol-chloroform extraction followed by Direct-zol RNA miniprep (Zymo Research)
Extracted RNA was subjected to cDNA library preparation using TrueSeq RNA sample preparation kit (Illumina)

tag: tissue

value: ventral neck skin

value: Ets1 and IL17Ra knockout


title: dbr1_ntc_a


title: MP082_MigDC

value: Migratory dendritic cells

value: ART treated

value: HIV infected


title: Neutrophils_PBS_rep2_IP

value: Control

tag: chip antibody


title: MP136_MigDC

tag: treatment


title: 360_Batch6_1_JAA2NTV1-01_S81_L006

value: WRHI

value: LD

value: Negative

value: Abs

value: Nobs

value: Secondary school, some or complete

value: No

value: Unchecked


title: WT_1419

value: WT


title: dbr1_ko_c

value: HeLa S3

value: Uterus; Cervix; Adenocarcinoma

value: DBR1 knockdown


title: WT_1406

value: ventral neck skin


title: dbr1_ko_b


title: Neutrophils_PBS_rep2_input

tag: cell type

value: Neutrophil

value: H3K4me3 (Diagenode Cat# C15410003)


title: Neutrophils_PBS_rep1_IP


title: dbr1_ko_a


title: 349_Batch5_62_560241266601_S70_L005

value: KEMRI

value: IIIA

value: TRUE

tag: ngonorrhoeae

value: Never married

value: Yes


title: 326_Batch5_39_5392_S47_L004

value: baseline

value: Emavundleni

value: IVD

value: nonLD

value: Negative

tag: chlamydiatrachomatis

value: Abs

value: BV


title: IL17RaKO_1378

value: IL17Ra knockout


title: Neutrophils_PBS_rep1_input

value: Control


title: D341 cells_siMYC_Rep 3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: hg38
Supplementary files format and content: Gene expression values normalized by DESeq2 unsing FAST DB v2022_1 annotations

source_name: Cerebellum/Medulloblastoma

growth_protocol: D341 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco), 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted and DNAse treated using RNeasy Mini Kit (Qiagen). 0.2 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology)  according to the manufacturer's instructions.

treatment_protocol: D341 cells were treated with DMSO or THZ531 (100nM) for 6 hr and transfected with siCtrl or siMYC oligos for 48 hr.

value: Cerebellum/Medulloblastoma

value: medulloblastoma cells

value: MYC amplified

value: D341 cells transfected with siMYC oligo


title: 323_Batch5_36_4928_S44_L003

tag: mobilincus

value: Nobs

value: Secondary school, some or complete

value: No

value: Unchecked


title: Ets1KO_1356

value: ventral neck skin

value: Ets1 knockout


title: Pt.F [4B]

city: Washington

first: Natalia

last: Soriano-Sarabia

state: DC

address: 2300 I St. NW

department: Microbiology Immunology and tropical Medicine

institute: George Washington University

description: Fresh frozen

data_processing:
Quality-control-passed reads were aligned to the human reference GRCh38.d1.vd1 genome using STAR v2.4.2a.
Transcript abundance estimates for each sample were performed using Salmon, an expectation-maximization algorithm using the UCSC gene definitions.
Raw read counts for all RNAseq samples were normalized with DESeq2 package.
Assembly: GRCh38.d1.vd1 genome
Supplementary files format and content: Two tab-delimited text files include (1) unnormalized data (raw counts, "dl_salmon_gene_summary_Plos_Biology.txt") and (2) DESeq2-normalized  data ( "dl_salmon_gene_summary_DESeq_normalized_Plos_Biology.txt") data for each sample.

source_name: rCD4 T cells from peripheral blood mononuclear cells (PBMCs)

extract_protocol:
Automated RNA extraction was performed (KingFisher, ThermoFisher Scientific). RNA samples were quantified by measuring Abs260 with a UV spectrophotometer. All RNA samples were assayed for integrity, concentration, and fragment size on a TapeStation system (Agilent, Inc. Santa Clara, CA).
Briefly, Total RNA was converted to RNAseq libraries using the Truseq RNA Exome library Prep Kit (Illumina) and sequenced on an Illumina HiSeq 4000 to generated paired end 2x75bp configuration

tag: subject status

value: Antiretroviral therapy (ART) -suppressed people living with HIV (PLWH)

value: Treated with 2.5mg/mL of pamidronate (PAM)

tag: time

value: 6 hours


title: Pt.E [4A]

description: Fresh frozen

value: rCD4 T cells from peripheral blood mononuclear cells (PBMCs)


title: D341 cells_siMYC_Rep 2

tag: genotype


title: 322_Batch5_35_3184_S43_L003

value: baseline

value: Emavundleni

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

tag: yeasts

value: Never married


title: D341 cells_siMYC_Rep 1

value: Cerebellum/Medulloblastoma

tag: cell line

value: medulloblastoma cells

value: MYC amplified

value: D341 cells transfected with siMYC oligo


title: 315_Batch5_28_560238356601_S36_L003

tag: visit

value: KEMRI

value: Nobs

tag: maritalstatus

value: Married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: Pt.F [3B]

description: Fresh frozen

value: rCD4 T cells from peripheral blood mononuclear cells (PBMCs)

value: Antiretroviral therapy (ART) -suppressed people living with HIV (PLWH)

value: Untreated

value: 6 hours


title: IL17RaKO_1126

value: ventral neck skin

value: IL17Ra knockout


title: Pt.E [3A]

description: Fresh frozen


title: D341 cells_siCtrl_Rep 3

value: D341 cells transfected with siCtrl oligo


title: DKO_1109

value: Ets1 and IL17Ra knockout


title: 357_Batch5_70_7888_S78_L006

tag: site

value: Emavundleni

tag: rin

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Abs

value: Never married

value: Secondary school, some or complete

value: No


title: Pt.D [2D]

description: Fresh frozen

value: rCD4 T cells from peripheral blood mononuclear cells (PBMCs)

value: Treated with 2.5mg/mL of pamidronate (PAM)


title: D341 cells_siCtrl_Rep 2

value: Cerebellum/Medulloblastoma

value: medulloblastoma cells

value: MYC amplified


title: 3_HLTF-/- cells  -/- mice

city: Lubbock

first: Beverly

middle: S

last: Chilton

state: TX

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

data_processing:
trimming
mapping
differential gene expression
gene ontology
Assembly: mm10 and hg38
Supplementary files format and content: Differential_expression_analysis_tablehumnan.csv
Supplementary files format and content: Differential_expression_analysis_tablemouse.csv
Supplementary files format and content: Significant-DEGshumnan.csv
Supplementary files format and content: Significant-DEGsmouse.csv
Supplementary files format and content: TPM_valueshumnan.csv
Supplementary files format and content: TPM_valuesmouse.csv
Supplementary files format and content: normalized_counts_human.csv
Supplementary files format and content: normalized_counts_mouse.csv
Supplementary files format and content: raw_counts_human.csv
Supplementary files format and content: raw_counts_mouse.csv
Supplementary files format and content: rlog_transformed_counts_human.csv
Supplementary files format and content: rlog_transformed_counts_mouse.csv

source_name: primary CDX tumor

extract_protocol:
flash frozen; total RNA was isolated, and evaluated for integrity and purity
Illumina stranded mRNA prep
Illumina, 2x150bp, ~350M PE reads (~105GB), single index

value: primary CDX tumor

value: HCT116 HLTF-/-

value: human CRC


title: 2_HLTF-/- cells  -/- mice


title: D341 cells_siCtrl_Rep1

value: D341 cells transfected with siCtrl oligo


title: Pt.C [2C]

description: Fresh frozen

value: Antiretroviral therapy (ART) -suppressed people living with HIV (PLWH)

value: 6 hours


title: 309_Batch5_22_560240636601_S30_L002

value: KEMRI

value: IVA

value: nonLD

value: TRUE

tag: bmi

tag: lactobacilli

value: BV

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: 1_HLTF-/- cells  -/- mice

tag: tissue


title: 314_Batch5_27_560232706601_S35_L003

value: baseline

value: IIIA

value: LD

value: Negative

value: Abs


title: Ets1KO_1361

value: ventral neck skin

value: Ets1 knockout


title: D341 cells_THZ531_Rep 3

value: Cerebellum/Medulloblastoma

value: medulloblastoma cells

value: MYC amplified

tag: treatment

value: D341 cells  treated with THZ531 for 6hr


title: 304_Batch5_17_2895_S25_L002

value: Emavundleni

value: TRUE

value: Never married

value: Secondary school, some or complete

value: No


title: D341 cells_THZ531_Rep 2

tag: cell type


title: XMLC2V;Lem2 f/f cKO rep 3 [F169-8_S3]

first: Matthew

last: Stroud

address: James Black Centre

institute: King's College London

description: E14.5 heart

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Assembly: mm10
Supplementary files format and content: raw read counts in matrix table

source_name: Whole Heart Ventricle

extract_protocol:
Promega Reliaprep RNA Tissue Miniprep system
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

value: Whole Heart Ventricle

tag: developmental stage

value: embryonic day 14.5 (E14.5)

value: XMLC2V; Lem2 f/f cKO


title: D341 cells_THZ531_Rep 1


title: 294_Batch5_7_6368_S15_L001

value: baseline

value: IVA

value: nonLD

tag: ngonorrhoeae

tag: chlamydiatrachomatis

value: Positive

value: BV

value: Nobs

value: Unchecked


title: Pt.C [1C]

description: Fresh frozen

value: rCD4 T cells from peripheral blood mononuclear cells (PBMCs)

tag: subject status

value: Antiretroviral therapy (ART) -suppressed people living with HIV (PLWH)

value: Untreated

value: 6 hours


title: Pt.A [2A]

description: Fresh frozen

value: Treated with 2.5mg/mL of pamidronate (PAM)

tag: time


title: Pt.D [1D]

description: Fresh frozen


title: XMLC2V;Lem2 f/f cKO rep 2 [F169-7_S2]

description: E14.5 heart

tag: genotype


title: D341 cells_DMSO_Rep 3

value: Cerebellum/Medulloblastoma

value: medulloblastoma cells

value: MYC amplified

value: D341 cells  treated with DMSO for 6hr


title: Pt.B [1B]

description: Fresh frozen


title: 292_Batch5_5_560232166601_S13_L001

value: KEMRI

value: TRUE

value: Negative

value: Abs

tag: mobilincus

tag: yeasts

value: Previously Married

value: Primary school, some or complete

value: No


title: D341 cells_DMSO_Rep 2

tag: cell line


title: Pt.A [1A]

description: Fresh frozen


title: Pt.B [2B]

description: Fresh frozen


title: XMLC2V;Lem2 f/f cKO rep 1 [F169-5_S1]

description: E14.5 heart

value: Whole Heart Ventricle

value: embryonic day 14.5 (E14.5)

value: XMLC2V; Lem2 f/f cKO


title: D341 cells_DMSO_Rep1


title: Lem2 f/f control rep 3 [F191-4_S5]

description: E14.5 heart

value: Lem2 f/f control


title: 308_Batch5_21_560235576601_S29_L002

tag: visit

value: baseline

value: IVA

value: nonLD

value: BV

value: Nobs

tag: maritalstatus

value: Married

value: Yes

value: Unchecked


title: Lem2 f/f control rep 2 [F169-4_S4]

description: E14.5 heart


title: 279_Batch4_64_876_S122_L008

tag: site

value: Emavundleni

tag: rin

value: IVD

value: TRUE

value: Negative

value: Never married

value: Secondary school, some or complete


title: N_9

city: Houston

first: Shervin

last: Assassi

address: 6431 Fannin St

institute: UTHouston

data_processing:
Transcript data were normalized with DESeq2.
Transcripts which had counts per million (CPM) greater than 1 in at least two samples were used for the analysis
Assembly: hg38
Supplementary files format and content: csv file format of DESeq2 normalized and log2 transformed counts.

source_name: Peripheral blood cell (whole blood)

extract_protocol:
PreSSc’s and healthy controls’ whole blood samples were col_x0002_lected in PAX gene tubes and stored at –80_x0002_C. RNA was extracted according to the manufacturer’s protocol and quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Globin genes were depleted using GLOBIN Clear kit. mRNA was enriched from total RNA using oligo(dt) beads (NEB Next Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA. The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing and adapter ligation, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer  (Life Technologies, Carlsbad, CA, USA), and then diluted to 1 ng/ul before checking insert size on an Agilent 2100 and quantified to greater accuracy by quantitative PCR (q-PCR) (library activity >2nM). Libraries were pooled into Novaseq6000 machines according to molarity and expected data volume. A paired-end 150 bp sequencing strategy was used to generate an average of 88 million reads per sample.

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: N_8

tag: cell type


title: 289_Batch5_2_KAA2NZYQ-01_S10_L001

value: WRHI

value: IIIA

value: LD

tag: bmi

tag: ngonorrhoeae

tag: lactobacilli

value: Abs

value: No


title: XMLC2V;Lem2 f/f cKO rep 4 [F191-2_S8]

description: E14.5 heart

tag: tissue

value: Whole Heart Ventricle

tag: developmental stage

value: embryonic day 14.5 (E14.5)

value: XMLC2V; Lem2 f/f cKO


title: Human oligodendrocyte precursor cells isolated from embryonic brain cortical tissue, gestational week 19

city: Bronx

first: Kosaku

last: Shinoda

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

library_source: transcriptomic single cell

data_processing:
Cell Ranger Version 3.0.2
Assembly: mm10 (mouse) and GRCh38 (human)
Supplementary files format and content: Loupe Browser File (extention .cloupe)

source_name: Brain (cortex)

extract_protocol:
Donated human brain tissues obtained with consent was dissociated, immunopanned with PDGFRa antibody,  collected with trypsinization, and frozen in freezing medium until RNA extraction. Postnatal mice were anesthetized with hypothermia, brains removed, forebrain dissected, dissociated with papain, immunopanned with PDGFRa antibody,  collected with trypsinization, and frozen in freezing medium until RNA extraction.
10X Genomics Chromium 3' gene expression RNA-seq

value: Brain (cortex)

value: oligodendrocyte precursor cells

tag: genotype

value: Gestational week 19

tag: treatment

value: healthy, no known abnormality


title: HepG2 cells, lvN3D, Day6

city: Nanchong

first: Yongang

last: Ren

state: Sichuan

address: No. 55 Dongshun Road, Gaoping District, Nanchong, Sichuan

institute: North Sichuan Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: Human liver carcinoma cells HepG2 were maintained in DMEM containing 10% (v/v) FBS and 1% (v/v) penicillin-streptomycin. Cells were grown at 37 ℃ in 5% CO2.

extract_protocol:
Successfully infected lvNC/ lvNFE2L3/ lvNFE2L3△C(557-694aa)cells were green fluorescent positive observed under fluorescence microscope after 72 h, these positive cells were cultured in puromycin medium for 7 days (3μg/ml).
RNA was harvested using TRIzol® Reagent (ThermoFisher, USA). 1.5 μg of total RNA was used for the construction of sequencing libraries.

treatment_protocol: The cells were seeded (1×105 cells/ml) into 6-well plates and incubated for 24 h to reach 50%, and then replaced with fresh medium containing 20 μl of the packaged lentiviral supernatant and 5 μg polybrene.

tag: cell line

value: human liver carcinoma cells

value: N3D overexpression

value: cell proliferation

tag: time

value: Day 6


title: 277_Batch4_62_560238786601_S120_L008

first: Gregory

last: Tharp

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: endocervical cells

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

tag: visit

value: KEMRI

value: TRUE

value: Negative

tag: chlamydiatrachomatis

tag: mobilincus

tag: yeasts

value: Obs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: 293_Batch5_6_560237516601_S14_L001

tag: site

tag: rin

value: IVA

value: nonLD

value: Abs

value: BV

value: Nobs

value: Previously Married

value: Primary school, some or complete

value: No


title: N_7

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: M


title: Lem2 f/f control rep 1 [F169-1_S7]

description: E14.5 heart

tag: tissue

value: Whole Heart Ventricle

tag: developmental stage

value: embryonic day 14.5 (E14.5)

value: Lem2 f/f control


title: 276_Batch4_61_560234866601_S119_L008

value: baseline

value: KEMRI

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: lactobacilli

value: Never married

value: Secondary school, some or complete

value: Yes


title: HepG2 cells, lvN3D, Day3

tag: cell line

value: human liver carcinoma cells

tag: genotype

value: N3D overexpression

tag: treatment

value: cell proliferation

tag: time

value: Day 3


title: N_5

value: Peripheral blood cell (whole blood)

value: Evolving PreSSc

value: Follow-up

value: F


title: Liver, iAsF1-M, biol rep 3

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

institute: Anhui Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragment per kilobase of exon model per million mapped reads (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Liver (F1)

growth_protocol: 12hr/12hr light dark cycle, fed with normal chow diet

extract_protocol:
Total RNA was extracted from liver tissues of iAsF1-M and conF1-M mice using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Paternal iAs exposure

value: Paternal iAs exposure

value: WT

tag: sex (of f1 offspring)

value: male

value: Liver (F1)


title: Lem2 f/f control rep 4 [F191-5_S6]

description: E14.5 heart

value: Whole Heart Ventricle

value: embryonic day 14.5 (E14.5)

value: Lem2 f/f control


title: HepG2 cells, lvN3D, Day0

value: Day 0


title: 267_Batch4_52_560244676601_S110_L008

city: Atlanta

address: 954 Gatewood Dr

tag: visit

tag: site

value: KEMRI

value: IIIA

value: LD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

tag: maritalstatus

value: Married

value: Primary school, some or complete

value: Yes

value: Checked


title: Liver, iAsF1-M, biol rep 2

value: Paternal iAs exposure

value: WT

value: male


title: N_55

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: Liver, iAsF1-M, biol rep 1

tag: tissue

value: Liver (F1)


title: HepG2 cells, lvN3, Day6

tag: cell line

value: human liver carcinoma cells

value: N3 overexpression

value: cell proliferation

value: Day 6


title: N_54


title: 278_Batch4_63_105_S121_L008

value: baseline

value: Emavundleni

tag: rin

value: IVD

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: lactobacilli

value: Abs

value: Intermediate

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: 266_Batch4_51_560240716601_S109_L008

tag: visit

value: KEMRI

value: IIIA

value: LD

value: Married

value: Primary school, some or complete

value: Yes

value: Checked


title: HepG2 cells, lvN3, Day0

value: human liver carcinoma cells

tag: genotype

value: N3 overexpression

tag: treatment

value: cell proliferation

tag: time

value: Day 0


title: 263_Batch4_48_4336_S106_L007

tag: site

value: Emavundleni

value: IVD

value: nonLD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

value: BV

tag: yeasts

value: No


title: Liver, conF1-M, biol rep 3

value: Paternal normal water

value: WT

tag: sex (of f1 offspring)

value: male

value: Liver (F1)


title: N_52

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

value: M


title: HepG2 cells, lvNC, Day6

tag: cell line

value: human liver carcinoma cells

value: cell proliferation

value: Day 6


title: N_51

value: HC

tag: gender

value: F


title: Liver, conF1-M, biol rep 2

tag: tissue


title: 262_Batch4_47_2736_S105_L007

value: baseline

value: Emavundleni

tag: rin

value: IVB

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: lactobacilli

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: Liver, conF1-M, biol rep 1

tag: treatment

value: Paternal normal water

tag: genotype

value: WT

value: male

value: Liver (F1)


title: 249_Batch4_34_AAA2P8GH-01_S92_L007

tag: visit

tag: site

value: WRHI

value: IVD

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

value: BV

value: Married

value: No


title: HepG2 cells, lvNC, Day0

tag: cell type

value: human liver carcinoma cells

value: cell proliferation

tag: time

value: Day 0


title: 248_Batch4_33_BAA2P2T4-01_S91_L006

value: baseline

value: nonLD

value: TRUE

value: Negative

tag: yeasts

value: Nobs


title: hESC RBFOX2 id.178146 (G14)

city: New York

first: Megan

middle: D

last: Schertzer

state: New York

address: 101 Avenue of the Americas, 4th Floor, Knowles lab

institute: New York Genome Center

description: piggyBac

data_processing:
*library strategy: PacBio long read RNA-seq
A pre-commercial version of the SMRT LINK analysis pipeline was used to generate HiFi reads, S-reads, and subsequent full-length reads and high-quality isoform sequences. After the isoseq3 refine step where full-length non-chimeric reads were obtained in bam file format, we continue with our own analysis pipeline.
Minimap2 v.2.17 (H. Li 2018) was used to align reads to GRCh38 human genome reference with -ax splice:hq -uf parameters. Secondary alignments were removed, and aligned reads were filtered for mapping quality greater than or equal to 60. The resulting bam files were converted to BED12 format and PSL format with FLAIR’s helper scripts (Tang et al. 2020)
Additional filtering was applied to select for full length reads based on overlap with annotated transcription start sites (TSS) and transcription end sites (TES). Our custom script required overlap between -10bp to +50bp of TSS and -50bp to +10bp of TES (using human GENCODE v41 Basic annotation). Reads that shared the same junction chain were grouped together and collapsed, using a custom script adapted from FLAIR collapse (Tang et al. 2020). Importantly, our custom collapse script ignores start and end coordinates of the reads, allowing reads with the same junction chain, but slight variations in TSS or TES, to be grouped together. Unspliced reads (i.e. mono-exonic reads) were excluded. Resulting full length, collapsed reads were matched with transcripts in GENCODE v41 basic annotations, and any transcripts without a match were still overlapped with the proper gene and was assigned a unique transcript ID through our custom scripts.
Assembly: hg38 using GENCODE v41 basic annoation gtf
Supplementary files format and content: PSL file summarizes the transcripts identified in the WT control. This file can be converted to gtf or bed file, if desired.
Supplementary files format and content: Text file is a table with read counts and TPM per transcript across all samples.

growth_protocol: HUES66 human embryonic stem cells (hESCs) were obtained from Harvard University. Cells were maintained at 37°C with 5% CO2 in StemFlex media (ThermoFisher Cat #A3349401) and grown on Geltrex-coated plates (ThermoFisher Cat #A1413302). For passaging, Accutase (ThermoFisher Cat #A1110501) was used to dissociate cells and 10 µM ROCK inhibitor Y-27632 dihydrochloride (Tocris Cat #1254) was added to the media for plating.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen #15596018) according to the manufacturer's protocol.
Prior to sending RNA samples to PacBio for long read sequencing, the RNA integrity number (RIN) was calculated using the RNA 6000 Nano Kit (Agilent #5067-1511). RIN scores ranged between 8.7-9.7, indicating high quality, intact RNA. Per RNA sample, we combined 1 µg of total RNA + 2 µl 1:100 ERCC RNA Spike-in Mix #1 (Invitrogen #4456740). MAS-Seq bulk Iso-Seq libraries were generated in collaboration with PacBio using a pre-commercial protocol that implements the MAS-Seq concatenation method (Al’Khafaji et al. 2023). Briefly, cDNA molecules were concatenated into an ordered array, in this case, an 8-fold array, and sequenced on the Revio system. The concatenated array is sequenced as a HiFi read and then bioinformatically de-concatenated into segmented reads (S-reads) which represent the original cDNA molecules.

treatment_protocol: 1ug/ml doxycycline

tag: cell line

value: RBFOX2 isoform KD

value: 1ug/ml doxycycline

tag: timepoint

tag: replicate


title: N_49

value: Peripheral blood cell (whole blood)

tag: group

value: HC

tag: time point

tag: pair

tag: gender

value: F


title: PDTALL46 model,  acute treated with OMP52M51, mouse #4

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

data_processing:
Quality check of the raw sequencing reads was performed using FastQC (v0.11.9)
Quality filtering and reads-check performed using Fastp (v0.20.1) parameters: length_required=36, cut_right, cut_right_window_size=4, cut_right_mean_quality=15, trim_poly_g, overrepresentation_analysis.
Mouse contaminating reads were removed by competitive mapping to the human/mouse hybrid genome using BBSplit (BBMap v38.84 ).
The alignment of high-quality human reads on the reference genome Gencode GRCh38 release 37 was performed with STAR (v2.7.8a), using the basic annotation gtf file.
Gene expression quantification was carried out using Stringtie (v2.1.5).
Assembly: Gencode GRCh38 release 37
Supplementary files format and content: paired read fastq

source_name: T-acute lymphoblastic leukemia cells

growth_protocol: T-ALL cells were intravenously injected in NSG mice and leukemia growth was monitored by blood drawings and flow cytometric analysis

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was used for the construction of sequencing libraries.
The 8 RNA-seq libraries were produced using the NEB_x0002_Next rRNA Depletion Kit (NEB), following manufacturer's protocols.

treatment_protocol: Leukemia bearing mice were intraperitoneally treated with the humanized anti-human Notch1 mAb OMP-52M51 or control antibody (Rituximab) in acute treatment: 4 days before sacrifice. Both antibodies were administrated weekly at 20mg/Kg.

tag: cell line_(pdx)

value: human T-ALL cells derived from murine infiltrated spleen

value: T-acute lymphoblastic leukemia cells

value: NOTCH1 HD, FBXW7 mut, TP53 mut

value: acute treatement with OMP-52M51


title: 265_Batch4_50_6832_S108_L008

value: Emavundleni

tag: rin

value: IIIA

value: LD

tag: bmi

tag: ngonorrhoeae

value: Positive

tag: lactobacilli

value: Abs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: N_48


title: 244_Batch4_29_JAA2P4ZM-01_S87_L006

tag: visit

value: baseline

tag: site

value: WRHI

value: IVD

value: nonLD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

tag: mobilincus

value: BV

value: Nobs

value: Married


title: hESC RBFOX2 id.178145 (G13)

description: piggyBac

tag: cell line

tag: genotype

value: RBFOX2 isoform KD

tag: treatment

value: 1ug/ml doxycycline


title: hESC RBFOX2 id.178135 (G12)

description: piggyBac

tag: timepoint

tag: replicate


title: HepG2 cells, lvN3, Day3

tag: cell type

value: human liver carcinoma cells

value: N3 overexpression

value: cell proliferation

tag: time

value: Day 3


title: hESC RBFOX2 id.178136 (G11)

description: piggyBac


title: N_47

value: Peripheral blood cell (whole blood)

tag: group

value: HC

tag: time point

tag: pair

tag: gender

value: F


title: N_46


title: PDTALL46 model,  acute treated with OMP52M51, mouse #2

tag: cell line_(pdx)

value: human T-ALL cells derived from murine infiltrated spleen

value: T-acute lymphoblastic leukemia cells

value: NOTCH1 HD, FBXW7 mut, TP53 mut

value: acute treatement with OMP-52M51


title: PDTALL46 model,  acute treated with OMP52M51, mouse #1


title: hESC RBFOX2 id.178149 (G5)

description: piggyBac


title: N_45

value: M


title: hESC RBFOX2 id.178147 (G3)

description: piggyBac


title: 237_Batch4_22_EAA2PJCD-01_S80_L006

value: WRHI

tag: rin

value: IVD

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: lactobacilli

value: Abs

value: BV

tag: yeasts

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: PDTALL46 model,  acute treated with OMP52M51, mouse #3

tag: genotype


title: N_4

value: Peripheral blood cell (whole blood)

value: Evolving PreSSc

value: Follow-up


title: 236_Batch4_21_KAA2P9HQ-01_S79_L006

tag: visit

value: baseline

tag: site

tag: chlamydiatrachomatis

tag: mobilincus

value: Intermediate

value: Nobs


title: 238_Batch4_23_3232_S81_L006

value: Emavundleni

value: No


title: 239_Batch4_24_5104_S82_L006

value: IIIA

value: LD


title: HepG2 cells, lvNC, Day3

tag: cell line

tag: cell type

value: human liver carcinoma cells

value: WT

tag: treatment

value: cell proliferation

tag: time

value: Day 3


title: 229_Batch4_14_5904_S72_L005

value: IVA

value: nonLD

value: TRUE

value: Negative

value: Positive

value: Abs

value: BV

value: Never married


title: N_44

value: Peripheral blood cell (whole blood)

tag: group

value: HC

tag: time point

tag: pair

tag: gender

value: F


title: hESC WT Control

description: piggyBac

value: 1ug/ml doxycycline

tag: timepoint

tag: replicate


title: alk3_mutant_epithelium_rep3

city: Athens

first: Hongxiang

last: Liu

state: Georgia

address: 425 Riverbend Pkwy, Apt 82

department: Animal and Dairy Science

institute: The University of Georgia

data_processing:
mapping and alignment: STAR (2.7.0a)
read count: HTSeq (0.13.5)
Assembly: mm10
Supplementary files format and content: .txt files for read count

source_name: Tongue

extract_protocol:
Trizol and RNeasy Plus kits (Qiagen)
Kapa Stranded mRNA-seq kit (KAPA Biosystems, Wilmington, MA)

tag: tissue

value: Tongue

value: epithelial cell


title: 228_Batch4_13_4000_S71_L005

value: baseline

value: Emavundleni

tag: rin

tag: bmi

tag: ngonorrhoeae

tag: lactobacilli

tag: yeasts

value: Nobs

tag: maritalstatus

value: Secondary school, some or complete

value: Unchecked


title: N_50


title: PDTALL46 model, control group, mouse #4

tag: cell line_(pdx)

value: human T-ALL cells derived from murine infiltrated spleen

value: T-acute lymphoblastic leukemia cells

tag: genotype

value: NOTCH1 HD, FBXW7 mut, TP53 mut

value: acute treatement with Ctrl Ab


title: PDTALL46 model, control group, mouse #2

tag: cell type

tag: treatment


title: alk3_mutant_epithelium_rep2


title: alk3_mutant_epithelium_rep1


title: 215_Batch3_72_7184_S58_L004

tag: visit

tag: site

value: IIIA

value: LD

value: TRUE

value: Positive

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

value: Negative

value: No


title: N_41

value: Peripheral blood cell (whole blood)

tag: group

value: HC

tag: time point

tag: pair

tag: gender

value: F


title: PDTALL46 model, control group, mouse #1


title: 214_Batch3_71_4704_S57_L004

value: baseline

value: Emavundleni

tag: rin

value: IVB

value: nonLD

tag: bmi

value: Nobs

value: Never married


title: PED-23T

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: Primary tumor cells

extract_protocol:
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina. Barcoded libraries were pooled and paired end sequenced on the Illumina HiSeq using the High output V2.5 kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary tumor cells

value: Focal anaplasia


title: 211_Batch3_68_560240316601_S54_L004

value: KEMRI

tag: ngonorrhoeae

tag: lactobacilli

value: BV

value: Married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: alk3_mutant_mesenchyme_rep3

tag: tissue

value: Tongue

value: mesenchymal cell


title: N_3

value: Peripheral blood cell (whole blood)

value: Evolving PreSSc

value: Follow-up

value: F


title: 210_Batch3_67_560235206601_S53_L004

value: baseline

value: IB

value: LD

value: TRUE

value: Negative

value: Abs

tag: yeasts

tag: maritalstatus


title: PED-22T

tag: cell type

value: Primary tumor cells

tag: genotype

value: Focal anaplasia


title: N_40

value: HC


title: alk3_mutant_mesenchyme_rep1


title: alk3_mutant_mesenchyme_rep2


title: alk3_control_epithelium_rep3

value: epithelial cell


title: 209_Batch3_66_560238136601_S52_L004

tag: visit

value: KEMRI

value: IIIA

value: Nobs

value: Never married

value: Post-secondary school

value: No

value: Unchecked


title: PDTALL46 model, control group, mouse #3

tag: cell line_(pdx)

value: human T-ALL cells derived from murine infiltrated spleen

value: T-acute lymphoblastic leukemia cells

value: NOTCH1 HD, FBXW7 mut, TP53 mut

tag: treatment

value: acute treatement with Ctrl Ab


title: PED-19T

value: ANA diffuse


title: N_43

value: Peripheral blood cell (whole blood)

value: F


title: N_39


title: PED-18T

value: Primary tumor cells


title: N_38

value: HC


title: N_42


title: alk3_control_epithelium_rep2

value: Tongue

value: epithelial cell


title: N_37


title: 201_Batch3_58_560240256601_S44_L003

tag: site

value: KEMRI

value: IIIA

value: LD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

value: Abs

tag: mobilincus

value: Married

value: Secondary school, some or complete

value: Yes


title: alk3_control_epithelium_rep1


title: PED-14T


title: PED-17T


title: N_36

tag: group

tag: time point

tag: pair


title: 200_Batch3_57_560229716601_S43_L003

value: baseline

tag: rin

tag: bmi

value: Nobs

value: Unchecked


title: N_35

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

value: Follow-up

tag: gender

value: F


title: PED-11T

value: Primary tumor cells

value: ANA diffuse


title: 191_Batch3_48_560238516601_S34_L003

value: KEMRI

value: IVB

value: nonLD

tag: ngonorrhoeae

tag: lactobacilli

value: Intermediate

value: Primary school, some or complete


title: PED-21T

value: Focal anaplasia


title: alk3_control_mesenchyme_rep2

tag: tissue

value: Tongue

value: mesenchymal cell


title: N_34

tag: cell type

value: Evolving PreSSc


title: PED-10T

tag: genotype


title: alk3_control_mesenchyme_rep1


title: N_33


title: PED-09T


title: N_32


title: ChIP-seq, Input sample_1

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

institute: The Hebrew University of Jerusalem

data_processing:
RNA-seq (hMo): Raw reads quality-trimmed using trim-galore (v0.6.7) and aligned to the hg38 reference by using hisat2 (v2.2.1) with the --very-sensitive option. Transcripts were quantified with stringtie (v2.2.1).
RNA-seq (BMDCs): Raw reads were quality-trimmed using cutadapt (v2.10). Additional quality filtering was performed by the fastx package (v0.0.14). Processed reads were aligned to the mouse genome version GRCm38 (Enembl 99 release) with TopHat (v2.1.1).
ATAC-seq and ChIP-seq: Raw reads quality-trimmed using trim-galore (v0.6.7) and aligned to the mm10 reference using hisat2 (v2.2.1). picard (v2.26.10) MarkDuplicates was used to mark and removed duplicates. Bigwig files were generated using deeptools (v3.5.1), normalizing by RPKM or BPM. Heatmaps were generated using deeptools (v3.5.1). Peaks for each sample were assigned using macs (v2.2.7.1). A union peak set for all samples was constructed by merging the peaks into a set of high-confidence non-overlapping fixed-width (500 bp) peaks.
Assembly: RNA-seq (hMo) - hg38; RNA-seq(BMDCs) - Grcm38 (Ensembl 99); ATAC-seq and ChIP-seq - mm10
Supplementary files format and content: Comma-delimited files listing counts, big-wig files, peak files

source_name: Bone marrow

extract_protocol:
RNA was recovered using RNeasy plus mini kit (Qiagen #74136). Samples for ATAC-seq were prepared with the kit (Active Motif #53150) according to the instruction manual. Samples for Chip-seq were prepared according to the protocol described by Antman et al  with several modifications. We used 30x10^6 BMDCs for each experiment. Quenching of formaldehyde was done at RT on a gently rocking platform. Samples were sonicated for three cycles (30 s on, 30 s off). For immunoprecipitation, 10 µL of Cebpb antibody was added (ab32358) and 30 µL of Protein G magnetic beads. Then, 2.5% of the sample was taken as input. Chromatin was eluted from the beads by shaking them in a heat block at 800 rpm for 30 min at 65 °C and reverse crosslinking was performed at 65 °C overnight.
The libraries for RNA-seq were prepared using KAPA mRNA capture kit (Roche #07962231001) following the manufacturer’s instructions. The libraries for Chip-seq were prepared using   KAPA HyperPrep Kit (Roche #7962347001) according to the instruction manual (1 ng of immunoprecipitated sample and 100 ng of input sample were used for library preparation). The libraried for ATAC-seq were prepared using the kit (Active Motif #53150) according to the instruction manual.

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: WT


title: N_31

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

value: Follow-up

value: M


title: 202_Batch3_59_560237076601_S45_L003

tag: visit

value: baseline

value: KEMRI

value: TRUE

value: Negative

value: Abs

tag: yeasts

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Yes

value: Checked


title: 175_Batch3_32_5040_S18_L002

tag: site

value: Emavundleni

value: IIIA

value: LD

value: Positive

value: No

value: Unchecked


title: 179_Batch3_36_GAA2PFCP-01_S22_L002

value: WRHI

tag: chlamydiatrachomatis


title: ChIP-seq, Cebpb KO sample_2

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: WT


title: rat#4-EV _hippocampus_14d

type: RNA

city: Moscow

first: Diana

last: Salikhova

address: Miklukho-Maklaya, 8

department: Institute of molecular and cellular medecine

country: Russia

institute: RUDN University

description:
Test
SAMPLE 60

data_processing:
For the normalization it uses the average of housekeeping genes: GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)
Fold Change worksheet reports control/test (median all samples PBS treatment/ median all samples EV treatment) ratios at 7 and 14 days for brain regions (cortex, striatum, hippocampus).
Genes that did not show expression were excluded.

label: SYBR Green

source_name: brain tissue

label_protocol: cDNA was synthesized using RevertAid First Strand cDNA Synthesis Kit (TermoFisher) by corresponding standard protocol. The PCRs set with qPCRmix-HS SYBR master mixes (Evrogen, Russia) were carried out in a Bio-Rad cfx96 (BioRad, USA) in the following mode: primary denaturation 95 °C for 5 min; denaturation 95 °C 20 s, annealing 56–63 °C 20 s, elongation 72 °C 20 s (40 cycles).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: EV treatment

tag: time

value: 14 days


title: N_30

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: rat#9-EV _hippocampus_14d

description:
Test
SAMPLE 59

tag: tissue


title: 143_Batch2_71_EAA2P5T2-01_S79_L006

tag: visit

tag: rin

value: IVD

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

value: Positive

tag: lactobacilli

value: Abs

tag: mobilincus

value: BV

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: alk3_control_mesenchyme_rep3

value: Tongue

tag: cell type

value: mesenchymal cell


title: ChIP-seq, Cebpb KO sample_1

city: Jerusalem

value: Bone marrow

value: BMDCs

tag: genotype

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: WT


title: 142_Batch2_70_BAA2NY5T-01_S78_L006

value: baseline

tag: site

value: WRHI

value: IVD

value: nonLD

tag: chlamydiatrachomatis

tag: yeasts

tag: maritalstatus


title: ChIP-seq, Input sample_2


title: 141_Batch2_69_KAA2NSW8-01_S77_L005

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

value: Married

value: Post-secondary school


title: N_2

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Follow-up

value: F


title: ATAC-seq, Med12 KO sample2

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Med12


title: rat#17-EV _hippocampus_14d

description:
Test
SAMPLE 57

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: EV treatment

tag: time

value: 14 days


title: 190_Batch3_47_560227706601_S33_L003

tag: visit

value: baseline

value: KEMRI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: lactobacilli

value: Abs

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: rat#11-EV _hippocampus_14d

description:
Test
SAMPLE 58

value: male

value: Wistar

tag: treatment

value: TBI

tag: tissue


title: 140_Batch2_68_KAA2NN4P-01_S76_L005

tag: site

value: WRHI

tag: chlamydiatrachomatis

tag: mobilincus

tag: yeasts

value: Post-secondary school

value: No


title: N_28

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: ATAC-seq, Med12 KO sample_1

value: Bone marrow

value: BMDCs

tag: genotype

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Med12


title: 139_Batch2_67_4416_S75_L005

tag: visit

value: Emavundleni

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete


title: rat#14-EV _hippocampus_14d

description:
Test
SAMPLE 56

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: EV treatment

tag: time

value: 14 days


title: ATAC-seq, Cebpb KO sample_3

tag: tissue

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: Infected with lentivirus that encode gRNA targeting Cebpb


title: rat#4-EV_striatum_14d

description:
Test
SAMPLE 55

value: striatum


title: N_25

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

value: Follow-up

value: F


title: ATAC-seq, Cebpb KO sample_2


title: rat#9-EV_striatum_14d

description:
Test
SAMPLE 54


title: 132_Batch2_60_5648_S68_L005

value: baseline

tag: site

value: Emavundleni

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

tag: yeasts

value: Obs

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: N_27

tag: cell type

tag: group

tag: time point

tag: pair

tag: gender


title: ATAC-seq, Cebpb KO sample_1

value: Bone marrow

value: BMDCs

tag: genotype

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Cebpb


title: 127_Batch2_55_EAA2P707-01_S63_L005

tag: visit

value: WRHI

value: IVB

value: nonLD

value: Intermediate

value: Nobs

tag: maritalstatus

value: Yes


title: N_23

value: Peripheral blood cell (whole blood)

value: Evolving PreSSc

value: Follow-up

value: F


title: ATAC-seq, NT sample_1

tag: tissue

tag: treatment

value: Infected with lentivirus that encode non-targeting gRNA


title: 125_Batch2_53_8494_S61_L004

tag: site

value: Emavundleni

tag: rin

value: TRUE

value: Negative

value: Abs

value: BV

value: Never married

value: Primary school, some or complete


title: rat#11-EV _striatum_14d

description:
Test
SAMPLE 53

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: striatum

tag: activation agent

value: EV treatment

tag: time

value: 14 days


title: N_22

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

value: Follow-up


title: 118_Batch2_46_EAA2P3ZS-01_S54_L004

value: WRHI

value: IB

value: LD

tag: bmi

tag: ngonorrhoeae

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus

tag: yeasts

value: Nobs

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: N_21

tag: time point

tag: pair

tag: gender

value: F


title: N_20


title: rat#17-EV _striatum_14d

description:
Test
SAMPLE 52

tag: animal

value: male

value: Wistar

tag: treatment

tag: tissue


title: Med12 in BMDCs experiment, NT Sample_2

value: Bone marrow

value: BMDCs

tag: genotype

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode non-targeting gRNA


title: Med12 in BMDCs experiment, NT Sample_3


title: ATAC-seq, NT sample_2


title: rat#4-EV_cortex_14d

description:
Test
SAMPLE 50

tag: Sex

tag: strain

value: TBI

value: brain

tag: brain region

value: cortex

tag: activation agent

value: EV treatment

value: 14 days


title: N_1

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

value: Follow-up


title: 138_Batch2_66_2927_S74_L005

tag: visit

value: baseline

tag: site

value: Emavundleni

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

value: Abs

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No


title: rat#9-EV_cortex_14d

description:
Test
SAMPLE 49

tag: animal

value: male

value: Wistar

value: TBI

value: brain

value: cortex

tag: time


title: Med12 in BMDCs experiment, NT Sample_1

tag: tissue

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: Infected with lentivirus that encode non-targeting gRNA


title: N_29

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: N_19

value: Evolving PreSSc

value: M


title: 117_Batch2_45_FAA2NWJJ-01_S53_L004

value: baseline

value: WRHI

value: IB

value: LD

value: TRUE

value: Negative

tag: lactobacilli

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: rat#11-EV _cortex_14d

description:
Test
SAMPLE 48

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: cortex

tag: activation agent

value: EV treatment

value: 14 days


title: rat#14-EV_striatum_14d

description:
Test
SAMPLE 51

value: striatum


title: Med12 in BMDCs experiment, Med12 KO sample3

value: Bone marrow

tag: cell type

value: BMDCs

tag: genotype

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Med12


title: N_18

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

value: Follow-up

value: F


title: 116_Batch2_44_DAA2NS56-01_S52_L004

tag: visit

tag: site

value: WRHI

tag: rin

value: IVA

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

value: Abs

value: Intermediate

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 115_Batch2_43_AAA2NMS1-01_S51_L004

value: baseline

value: IVD

tag: lactobacilli


title: Med12 in BMDCs experiment, Med12 KO sample_2

tag: tissue

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: Infected with lentivirus that encode gRNA targeting Med12


title: rat#17-EV_cortex_14d

description:
Test
SAMPLE 47

tag: animal

tag: Sex

value: male

value: Wistar

value: TBI

value: brain

value: cortex

value: EV treatment

tag: time

value: 14 days


title: N_16

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: 124_Batch2_52_4352_S60_L004

value: baseline

value: Emavundleni

value: IIIA

value: LD

value: TRUE

value: Negative

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

value: Never married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: N_15

tag: cell type

tag: group

value: Evolving PreSSc


title: rat#14-EV _cortex_14d

description:
Test
SAMPLE 46

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: cortex

tag: activation agent

value: EV treatment

value: 14 days


title: rat#1-control_hippocampus_14d

description:
control
SAMPLE 45

value: hippocampus

value: PBS treatment