title: A375_CRISPRi_sgLacZ_Rep3

city: Los Angeles

first: Jessica

middle: W

last: Tsai

state: California

address: 4650 Sunset Blvd MS #57

institute: Children's Hospital Los Angeles

data_processing:
Sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.7.3a, RRID:SCR_004463).
Differential gene expression testing was performed by DESeq2 (v1.22.1, RRID:SCR_015687).
Normalized counts were subsequently uesd to perform gene set enrichment analysis.
Assembly: hg19
Supplementary files format and content: Gene counts (csv)
Supplementary files format and content: Metadata (txt)

growth_protocol: A375 (SKCM) was grown in DMEM with 10% serum. Cells were dissociated with Trypsin-EDTA 0.25% (Gibco, 25200056).

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit (Qiagen, 74106) with on column Dnase digestion (Qiagen, 79256).
RNA-sequencing was performed by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute. Libraries were prepared using KAPA mRNA HyperPrep (Roche, KK8581) strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit Fluorometer (Thermo Fisher) and 4200 TapeStation system (Agilent, G2991BA). Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 150 bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: Melanoma cell line


title: Normal_1

status: Public on Jun 23 2022

type: SRA

city: Shanghai

first: Zheng

last: Li

state: Shanghai

address: 85th Wujin Road, Shanghai, China

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was GRh38-1.2.0.
Assembly: GRh38-1.2.0
Supplementary files format and content: matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Corpus Cavernosum

extract_protocol:
Fresh CC tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before 10× Genomics library preparation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000094, 10× Genomics) according to the manufacturer’s instructions. Final libraries were sequenced on an Illumina NovaSeq 6000.

tag: tissue

value: Corpus Cavernosum

tag: disease

value: Normal


title: Jurkat WT cells, treated, t=4, bio rep 1

city: Dunedin

first: Elizabeth

middle: C.

last: Ledgerwood

address: 710 Cumberland St

department: Biochemistry

country: New Zealand

institute: University of Otago

library_source: transcriptomic

data_processing:
Sequence reads were mapped to Hg19 using STAR (v2.7.1a)
Read counts were generated using htseq (v0.6.1)  with recommended parameters -m union and -s no
Assembly: Hg19
Supplementary files format and content: tab-delimited text files of read counts for each sample

source_name: Jurkat E6-1

growth_protocol: Jurkat cells were maintained in RMPI supplemented with 10% fetal bovine serum (FBS), 2 g/L sodium bicarbonate, 60 mg/L penicillin G and 100 mg/L streptomycin sulfate in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol according to the manufacturer's instructions
250 ng of RNA was used with the Illumina Tru-Seq library prep kit using half of the recommended reagents

treatment_protocol: Jurkat cells were resuspended in PBS at a density of 1 x 10^6 cells/mL, treated with 10 µM hydrogen peroxide, and harvested after 4 hours

tag: cell line

value: Jurkat E6-1

tag: cell type

value: Lymphoma

tag: genotype

value: WT

tag: treatment

value: 10 µM hydrogen peroxide per 1 x 10^6 cells


title: Jurkat WT cells, control, t=0, bio rep 8


title: CCMP332_Control_rep2

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

country: USA

institute: University of Arkansas

data_processing:
Adapter trimming performed with kTrim v 1.1.0 [parameters: -t 15 -p 33 -q 20 -s 36 -m 0.5 using Illumina adapters]
Mapping to genome performed with STAR v 2.7.3a [parameters: --alignIntronMin 1 --alignIntronMax 22618]; initial index development parameters: --sjdbOverhang 99 --genomeSAindexNbases 12
Counts estimated from genes with HTSeq v 0.11.3 on python platform [parameters: --format=bam --order=pos --stranded=reverse --minaqual=10 --type=gene --idattr=ID --mode=union --nonunique=none]
Differential expression was performed in EdgeR using expected counts and the quasi-liklihood (QL) framework with Benjamini-Hochberg FDR correction. Genes with less than 1 count per million (CPM) in at least 3 samples were excluded from the analysis.
Assembly: ASM1318728v1
Supplementary files format and content: All files are tab delimited text files. One file is the HTSeq gene count output (cryptica_hyposalinity_HTSeq.txt) and one file is the edgeR logFC and FDR-corrected p-values output (cryptica_hyposalinity_edgeR.txt)

molecule: polyA RNA

organism: Cyclotella cryptica

source_name: microalgae, diatom

growth_protocol: C. cryptica strain CCMP332 was grown until reaching exponential phase in artificial sea water at 24 parts per thousand salinity (ASW 24) at 15°C and 22 μmol photons m-2 s-1 irradiance under a 16:8 h light:dark cycle.

extract_protocol:
Qiagen Rneasy Plant RNA extraction
KAPA mRNA HyperPrep Kit with KAPA/Roche dual adapters

treatment_protocol: Cells were immediately exposed to freshwater (ASW 0) by centrifugation at 800 rcf for 3 min followed by resuspension and transer into ASW ). Cells were incubated at 15 ℃ and 20 μmol photons m-2 s-1 irradiance with gentle agitation

value: microalgae, diatom

tag: cell strain

value: 0 min in artificial seawater (ASW 24 ppt) at 15 C


title: Thymus_CD3pos_donor3

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

data_processing:
Fastq files were mapped using CellRanger version 6.0.1
Assembly: GRCh38
Supplementary files format and content: h5 files obtained from CellRanger

source_name: thymus

extract_protocol:
Pediatric thymus from children undergoing cardiac surgery were obtained and used according to and with the approval of the Medical Ethical Commission of Ghent University Hospital (Belgium). Thymus tissue was cut into small pieces and digested with 1.6mg/ml collagenase (Gibco, 17104-019) in IMDM medium for 30min at 37°C to generate a single cell suspension. The reaction was quenched with 10% FBS and the thymocyte suspension was passed through a 70μm filter to remove undigested tissue. Cells were frozen in FBS containing 10% DMSO and stored in liquid nitrogen until needed. Upon thawing thymocytes were FACS sorted for CD3 expression.
library construction according to protocol for 10X Genomics Chromium Single Cell 3' Kit v2

value: thymus

value: CD3+ thymocytes

tag: donor sex

value: male

tag: donor age

value: 190 days


title: Thymus_CD3neg_donor3

value: CD3- thymocytes


title: Thymus_CD3pos_donor2

value: 4867 days


title: A375_CRISPRi_sgLacZ_Rep2

department: Pediatrics


title: CCMP332_8hr_0ppt_rep3

value: 8 hours in freshwater (ASW 0 ppt) at 15 C


title: CCMP332_Control_rep1


title: CCMP332_8hr_0ppt_rep2


title: Jurkat WT cells, control, t=0, bio rep 6


title: A375_CRISPRi_sgLacZ_Rep1


title: Thymus_CD3neg_donor2


title: CCMP332_8hr_0ppt_rep1


title: Jurkat WT cells, control, t=0, bio rep 4


title: Thymus_CD3pos_donor1_rep2

value: 442 days


title: Jurkat WT cells, control, t=0, bio rep 7


title: Jurkat WT cells, control, t=0, bio rep 3


title: A375_CRISPRi_sg1_Rep1

value: Melanoma cell line


title: Thymus_CD3pos_donor1_rep1


title: A375_CRISPRi_sg1_Rep2


title: CCMP332_4hr_0ppt_rep2

value: 4 hours in freshwater (ASW 0 ppt) at 15 C


title: CCMP332_4hr_0ppt_rep3


title: CCMP332_4hr_0ppt_rep1


title: Thymus_CD3neg_donor1_rep2


title: Jurkat WT cells, control, t=0, bio rep 2


title: DIPG-IV_CRISPRi_sgLacZ_Rep3

source_name: DIPG-IV

growth_protocol: DIPG-IV was grown in tumor stem media containing a 1:1 ratio of DMEM/F-12 (Invitrogen, 11330-032) and Neurobasal-A (Invitrogen, 10888-022) with 10% each of HEPES Buffer Solution 1 M (Thermo Fisher, 15630080), sodium pyruvate solution 100 nM (Life Technologies, 11360070), MEM non-essential amino acids solution 10 mM (Thermo Fisher, 11140050), Glutamax-I Supplement (Thermo Fisher, 35050061), and Penicillin/Streptomycin solution (Life Technologies, 15140122). Media was supplemented with B27 minus Vitamin A (Invitrogen, 12587-010), epidermal growth factor (EGF, StemCell Tech Inc., 78006), fibroblast growth factor (FGF, StemCell Tech Inc., 78003), PDGF-AA (Shenandoah Biotech, 100-16), PDGF-BB (Shenandoah Biotech, 100-18), and heparin solution 0.2% (StemCell Tech Inc., 07980). Neurospheres were dissociated using Accutase (StemCell Tech Inc., 07922) and passaged every four days.

value: DIPG-IV

value: DMG cell line


title: Thymus_CD3neg_donor1_rep1


title: Jurkat WT cells, control, t=0, bio rep 5

value: Jurkat E6-1

value: Lymphoma


title: CCMP332_30m_0ppt_rep3

value: 30 min in freshwater (ASW 0 ppt) at 15 C


title: Jurkat WT cells, control, t=0, bio rep 1

value: WT


title: DIPG-IV_CRISPRi_sgLacZ_Rep2


title: A375_CRISPRi_sg1_Rep3


title: DIPG-IV_CRISPRi_sgLacZ_Rep1


title: Liver nfib-KO Normal rep3

city: Chongqing

first: Li

last: Zhou

state: China

address: No. 76, Linjiang Road, Yuzhong District, Chongqing, China 400010, Telephone:86-023-62887681, Fax:86-

institute: Department of Gastroenterology, Second Affiliated Hospital of Chongqing Medical University

description:
KO3N
KO3T-vs-KO3N-diff-pval-0.05-FC-2.gene.xls

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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: mm9
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

organism: Mus musculus

source_name: Liver

extract_protocol:
livers were removed, flash frozen on dry ice, and total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: liver

tag: age

value: nfib-/-


title: Liver nfib-KO Tumor rep3

description:
KO3T
KO3T-vs-KO3N-diff-pval-0.05-FC-2.gene.xls


title: DIPG-IV_CRISPRi_sg1_Rep3


title: liver, pediatric autoimmune hepatitis, case 4

city: Chicago

first: Alyssa

last: Kriegermeier

state: IL

address: 225 E. Chicago

department: GI/Hepatology/Nutrition

institute: Ann and Robert H. Lurie Children's Hospital of Chicago

data_processing:
Reads were trimmed using trimgalore
trimmed reads were aligned using star
aligned reads were counted using htseq-count
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: liver explant tissue

extract_protocol:
Total RNA was extracted from frozen liver samples using TRIZOL reagent (Ambion by Life Technologies, Carlsbad, CA), and cDNA was synthesized with the qScript cDNA synthesis kit (Quantabio, Beverly, MD)
The stranded mRNA-seq was conducted in the Northwestern University NUSeq Core Facility. Briefly, total RNA examples were checked for quality using RINs generated from Agilent Bioanalyzer 2100. RNA quantity was determined with Qubit fluorometer. The Illumina Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 100 ng of high-quality RNA samples (RIN>7). All 34 samples met QC standards and were used for the study. The kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation.

value: liver explant tissue

tag: disease state

value: pediatric autoimmune hepatitis


title: CCMP332_2hr_0ppt_rep3

value: microalgae, diatom

value: 2 hours in freshwater (ASW 0 ppt) at 15 C


title: liver, pediatric autoimmune hepatitis, case 5


title: CCMP332_30m_0ppt_rep2


title: DIPG-IV_CRISPRi_sg1_Rep2


title: CCMP332_30m_0ppt_rep1


title: liver, pediatric autoimmune hepatitis, case 3


title: liver, pediatric autoimmune hepatitis, case 1


title: CCMP332_2hr_0ppt_rep1


title: liver, pediatric autoimmune hepatitis, case 2


title: Liver nfib-KO Tumor rep2

description:
KO2T
NC1T-vs-KO2T-diff-pval-0.05-FC-2.gene.xls


title: CCMP332_2hr_0ppt_rep2


title: Liver WT Normal rep2

description:
NC2N
NC2T-vs-NC2N-diff-pval-0.05-FC-2.gene.xls

value: wild type


title: liver pediatric choelstatic liver disease, ALGS case 5


title: CCMP332_1hr_0ppt_rep2

value: 1 hours in freshwater  (ASW 0 ppt) at 15 C


title: liver pediatric choelstatic liver disease, ALGS case 4


title: DIPG-IV_CRISPRi_sg1_Rep1


title: Liver WT Normal rep3

description:
NC3N
NC3T-vs-NC3N-diff-pval-0.05-FC-2.gene.xls


title: AALE_Control_Rep3

source_name: AALE cells

growth_protocol: AALE cells were grown in SABM Small Airway Epithelial Cell Growth Basal Medium (Lonza, CC-3119) supplemented with SAGM Small Airway Epithelial Cell Growth Medium SingleQuots (Lonza, CC-4124).

value: AALE cells


title: liver pediatric choelstatic liver disease, ALGS case 3


title: Liver WT Tumor rep3

description:
NC3T
NC3T-vs-NC3N-diff-pval-0.05-FC-2.gene.xls


title: liver pediatric choelstatic liver disease, ALGS case 2


title: CCMP332_1hr_0ppt_rep1


title: CCMP332_15m_0ppt_rep2

value: 15 min in freshwater (ASW 0 ppt) at 15 C


title: AALE_FOXR2_Rep3


title: AALE_Control_Rep2


title: CCMP332_1hr_0ppt_rep3


title: CCMP332_15m_0ppt_rep1


title: liver, pediatric cholestatic liver disease, PFIC, case 5


title: AALE_FOXR2_Rep1


title: Liver WT Tumor rep1

description:
NC1T
NC1T-vs-KO2T-diff-pval-0.05-FC-2.gene.xls


title: AALE_Control_Rep1


title: Liver WT Tumor rep2

description:
NC2T
NC2T-vs-NC2N-diff-pval-0.05-FC-2.gene.xls


title: liver, pediatric cholestatic liver disease, PFIC, case 3


title: H9_Control_Rep4

source_name: H9 human neural stem cells

growth_protocol: Human H9-derived neural stem cells (hNSCs) are derived from the NIH approved H9 (WA09) human embryonic stem cells (Gibco, N7800-100). hNSCs were propagated in cultures on plates pre-treated for at least one hour with Geltrex LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Gibco, A1413201). hNSCs were grown in media containing a 1:1 ratio of DMEM/F-12 (Invitrogen, 11330-032) and Neurobasal-A (Invitrogen, 10888-022) with 10% each of HEPES Buffer Solution 1 M (Thermo Fisher, 15630080), sodium pyruvate solution 100 nM (Life Technologies, 11360070), MEM non-essential amino acids solution 10 mM (Thermo Fisher, 11140050), Glutamax-I Supplement (Thermo Fisher, 35050061), and Penicillin/Streptomycin solution (Life Technologies, 15140122). Media was supplemented with B27 minus Vitamin A (Invitrogen, 12587-010), epidermal growth factor (EGF, StemCell Tech Inc., 78006), fibroblast growth factor (FGF, StemCell Tech Inc., 78003), and heparin solution 0.2% (StemCell Tech Inc., 07980). Accutase (StemCell Tech Inc., 07922) was used to detach cells from Geltrex plates.

value: H9 human neural stem cells


title: liver, pediatric cholestatic liver disease, PFIC, case 2


title: H9_Control_Rep3


title: AALE_FOXR2_Rep2


title: CCMP332_10hr_0ppt_rep1

value: 10 hours in freshwater (ASW 0 ppt) at 15 C


title: H9_Control_Rep5


title: liver, pediatric cholestatic liver disease, PFIC, case 4


title: CCMP332_10hr_0ppt_rep3


title: CCMP332_15m_0ppt_rep3


title: CCMP332_10hr_0ppt_rep2


title: C19

type: RNA

city: Beijing

first: Kaijiang

last: Kang

address: No.119 South Fourth Ring West Road, Fengtai District

department: Department of Neurology

institute: Beijing Tiantan Hospital, Capital Medical University

hyb_protocol: It was performed using a Gene Expression Hybridization Kit (Agilent’s miRNA Complete Labeling and Hyb Kit-p/n5190-0456) according to the manufacturer’s instructions.

scan_protocol: Slides were washed in staining dishes with a Gene Expression Wash Buffer Kit (Agilent, Santa Clara, CA, USA) and scanned by an Agilent Microarray Scanner with default settings according to the manufacturer’s instructions.

data_processing: The data was extracted using an Agilent Feature Extraction (AFE) software (version 10.7.1.1), and the raw data were normalized by Quantile algorithm using Gene Spring Software 12.6 (Agilent Technologies).

source_name: miRNA Expression in Circulating Leukocytes  of  healthy adults

extract_protocol: Trizol Reagent (Invitrogen, Carlsbad, CA, USA) was used for leukocyte denaturation. The miRNeasy Mini Kit (Qiagen p/n 217004) was used for RNA collection and purification according to the manufacturer’s protocol. The quality evaluation of the total RNA was performed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

value: circulating leukocytes

tag: group

value: healthy control

tag: gender

value: female


title: C16

label_protocol: It was performed using a Gene Expression Hybridization Kit (Agilent’s miRNA Complete Labeling and Hyb Kit-p/n5190-0456) according to the manufacturer’s instructions.


title: liver, adult cholestatic liver disease, PBC 2

description:
9309
62yo female

value: adult cholestatic liver disease


title: H9_Control_Rep2


title: CCMP332_0m_0ppt_rep3

value: 0 min in freshwater (ASW 0 ppt) at 15 C


title: C14


title: liver, pediatric cholestatic liver disease, PFIC, case 1


title: H9_Control_Rep1


title: CCMP332_0m_0ppt_rep2


title: liver pediatric choelstatic liver disease, ALGS case 1


title: C11


title: C12


title: C13


title: liver, adult cholestatic liver disease, PBC 1

description:
9124
n/a


title: H9_FOXR2_Rep5


title: liver, adult cholestatic liver disease, PSC

description:
9402
49yo


title: H9_FOXR2_Rep4


title: C10

value: male


title: liver, pediatric normal, 9

description:
9011
3.5yo female

value: normal


title: C06


title: H2172_miR130a-3p_ 4_12

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

hyb_protocol: Samples were hybridized at 65 °C for 21 hours.

scan_protocol: Samples were purified and then loaded onto the nCounter Cartridge by using the nCounter Prep Station, and RNA was quantified by using the Digital nCounter Nanostring.

data_processing: RCC files deriving from counting process were first evaluated by using nSolver 4.0 Analysis Software (Nanostring) performing a quality control through the fields of view (FOVs) count, binding density parameter, positive control linearity and limit of detection QC and the eventual presence of any warning flags.

label: Biotin

source_name: H2172 cells, miR130a-3p, 4th Replicate

label_protocol: Briefly, 150 ng of total RNA, were bound with a Reporter CodeSet and a Capture ProbeSet.

growth_protocol: NSCLC cells were cultured in RPMI culture medium and 10% foetal bovine serum under the standard conditions with 5% CO2 atmosphere with 37°C.

extract_protocol: Total RNA, including the miRNAs, was extracted using miRNeasy (Qiagen)

treatment_protocol: 5x10^4 H2172 cells were seeded in 24 well plates and transfected with 50 nM miRCURY miR (hsa-miR-130a-3p: YM00472237-ADA, hsa-miR-17-5p: YM00471966-ADA and Negative Control 4: YM00479903-ADA miRCURY miR, Qiagen) with lipofectamine 2000 (Invitrogen/ThermoFisher Scientific), according to manufacturer’s instructions. After 72 hours, the cells were harvested for the RNA extraction.

value: NSCLC cell line (H2172; CRL-5930; American Type Culture Collection (ATCC, Manassas, Virginia, USA).


title: liver, pediatric normal, 8

description:
9035
3yo female

value: liver explant tissue


title: H9_FOXR2_Rep3


title: H2172_miR17-5p_4_11

source_name: H2172 cells, miR17-5p, 4th Replicate


title: C01


title: C02


title: H9_FOXR2_Rep1


title: CCMP332_0m_0ppt_rep1

value: microalgae, diatom


title: liver, pediatric normal, 7

description:
9101
2yo male


title: H9_FOXR2_Rep2


title: H2172_Neg_CTRL_4_10

source_name: H2172 cells, Neg CTRL, 4th Replicate


title: liver, pediatric normal, 5

description:
9608
4yo male


title: liver, pediatric normal, 6

description:
9609
4yo male


title: liver, pediatric normal, 2

description:
9023
31mo female


title: liver, pediatric normal, 4

description:
9506
3yo female


title: H2172_miR17-5p_3_06

source_name: H2172 cells, miR17-5p, 3rd Replicate


title: H2172_miR130a-3p_3_09

source_name: H2172 cells, miR130a-3p, 3rd Replicate


title: M056

source_name: miRNA Expression in Circulating Leukocytes  of Patients with asymptomatic MMD

value: asymptomatic MMD


title: M038


title: H2172_miR130a-3p_1_07

source_name: H2172 cells miR130a-3p, 1st Replicate


title: liver, pediatric normal, 1

description:
9022
5yo


title: M042


title: liver, pediatric normal, 3

description:
9036
5yo female


title: H2172_miR17-5p_2_05

source_name: H2172 cells, miR17-5p, 2nd Replicate


title: H2172_miR130a-3p_2_08

source_name: H2172 cells miR130a-3p, 2nd Replicate


title: liver, adult normal, 7

description:
9503
45yo female


title: H2172_miR17-5p_1_04

source_name: H2172 cells, miR17-5p, 1st Replicate


title: H2172_Neg_CTRL_3_03

source_name: H2172 cells, Neg CTRL, 3rd Replicate


title: M040


title: H2172_Neg_CTRL_2_02

source_name: H2172 cells, Neg CTRL, 2nd Replicate


title: M014


title: M033


title: liver, adult normal, 4

description:
9037
37yo female


title: liver, adult normal, 5

description:
9126
19yo male


title: GX1135 48h root rep2

first: Anhui

last: Guo

address: College of Agronomy and Biotechnology,

institute: College of Agronomy and Biotechnology, China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TM-1 whole genome using HISAT v2.0 with default parameters.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Florea et al.,  F1000Res, 2013. 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.
Genome_build: TM-1

organism: Gossypium hirsutum

source_name: root

extract_protocol:
Total RNA was extracted from the roots of seedlings with an improved CTAB–ammonium acetate  method (Zhao et al. 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

value: 150 mM NaCl

tag: developmental stage


title: H2172_Neg_CTRL_1_01

source_name: H2172 cells, Neg CTRL, 1st Replicate


title: M050


title: M053

source_name: miRNA Expression in Circulating Leukocytes  of Patients with ischemic MMD

value: ischemic MMD


title: M052


title: M051


title: M026


title: GX1135 48h root rep1


title: liver, adult normal, 3

description:
9001
66yo female

source_name: liver explant tissue


title: liver, adult normal, 6

description:
9203
24yo female


title: M045


title: GX1135 3h root rep3


title: GX1135 12h root rep2


title: Intestinal EV68 (s5)

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description:
rnaseq_genes_metadata.tsv
rnaseq_readcount.tsv
rnaseq_samples_metadata.tsv
reactome_enrichment_analysis.tsv

data_processing:
Reads are mapped with STAR v2.7.0f on the human genome (hg38 from UCSC)
Resulting alignment files are quantified with HTSeq (v0.9.1)
The processed data file rnaseq_readcount.tsv contains the resulting read counts
Count normalization is done by dividing the read counts per the sum of all counts per library accross all genes, and multiply by 1000000.
Normalized counts are log2 transformed with a pseudo-count of 1. These values are used to compute the fold-changes between conditions given into table "rnaseq_genes_metadata.tsv", and for most of the analysis.
Genes function annotations are taken form Reactome.org database. Hyperbolic tests are performed to determine enrichement of a given gene set for a given annotation.
Genome_build: hg38, UCSC
Supplementary_files_format_and_content: rnaseq_samples_metadata.tsv is a table with statistics about each sample (number of read, number of mapped read, tissue origin, infecting virus). rnaseq_readcount.tsv contains the expression matrix, i.e. the number of mapped read in each library for each gene. rnaseq_genes_metadata.tsv is a table describing information computed for each gene, in particular the fold-changes between the conditions. reactome_enrichment_analysis.tsv contains the result of the enrichment geneset enrichment anlysis on reactome.

source_name: Intestinal 3D tissue model

growth_protocol: According to Mattek indications for intestinal tissue; and according to Epithelix indications for respiratory tissue.

extract_protocol:
RNAeasy kit (Qiagen) following manufacturer protocol including Dnase treatment step (Qiagen)
Illumina TruSeqHT stranded mRNA

treatment_protocol: SmallAir (Respiratory tissues - 24 well plate format) and EpiIntestinal (Intestinal tissues- 96 well plate format) tissues were infected apically at 33ºC with 100μl (Respiratory tissues) or 20μl (Intestinal tissues) of medium containing 10^5 RNAcopies/μl of each virus. The viral inoculum was washed out 3 times at 3 hpi.  Tissues were lysed at 2 dpi and total RNA was extracted.

value: intestinal

tag: virus


title: liver, adult normal, 2

description:
8911
28yo female


title: GX1135 3h root rep1


title: Intestinal EV68 (s4)


title: M034


title: GX1135 12h root rep3


title: liver, adult normal, 1

description:
8907
20yo male


title: Intestinal EV94 (s3)


title: GX1135 3h root rep2


title: M027


title: M037


title: M018


title: GX1135 1h root rep3


title: M008


title: Respiratory Mock (s23)

source_name: Respiratory 3D tissue model

value: respiratory

value: mock


title: M017

value: circulating leukocytes


title: Respiratory EV68 (s18)


title: Intestinal EV94 (s2)


title: Respiratory EV68 (s16)


title: M012


title: GX100-2 48h root rep3


title: GX1135 1h root rep1


title: Respiratory Mock (s24)


title: GX1135 0h root rep2


title: Respiratory EV94 (s15)


title: GX1135 0h root rep1


title: GX100-2 48h root rep1


title: M007


title: M054

source_name: miRNA Expression in Circulating Leukocytes  of Patients with hemorrhagic MMD

value: hemorrhagic MMD


title: Intestinal Mock (s12)


title: GX1135 0h root rep3


title: M048


title: M047

value: female


title: M046


title: GX100-2 48h root rep2


title: Respiratory EV94 (s14)


title: GX100-2 12h root rep2


title: GX100-2 12h root rep1


title: 132: cell pool 5

city: Neuherberg

first: Sebastian

last: Schmidt

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München

description: Demultiplex cell clones from different donors using Demuxlet (Kang et al., 2018) based on single nucleotide polymorphism (merge_GRCh38.resorted.23_24_removed.vcf)

data_processing:
Sequencing data was processed using Cell Ranger version 2.1.1.
Spliced and unspliced counts for RNA velocity analysis were called using velocyto version 0.17.7 and samtools version 1.7
Demuxlet (Kang et al., 2018) (retrieved 17th July 2018) and the obtained single nucleotide polymorphism (SNP) data were used to demultiplex the pooled sequencing data. SNP array data was reformatted to fit the chromosome ordering in the Cell Ranger output using vcf tools version 0.1.15.
Single cell gene expression data was processed according to a recently published best practices workflow (Luecken and Theis, 2019). Data was loaded into Scanpy version 1.4.3 commit 0075c62.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 binary data format with raw gene counts for every gene and cell
Supplementary_files_format_and_content: Variant call format with donor SNPs

source_name: fibroblast-derived induced pluripotent stem cells

growth_protocol: human induced pluripotent stem cells (hiPSCs) were differentiated into human small molecule neural progenitor cells (hNPCs) by embryoid body (EB) formation following the protocol described by (Reinhardt et al., 2013) with minor adaptations. At 70 % confluency, hiPSC colonies were detached using 2 mg/ml collagenase type IV (Thermo Fisher Scientific) for 40 min at 37 °C, 5 % CO2, 21 % O2. Detached hiPSC colonies were harvested in knockout serum replacement medium (80 % KnockOut DMEM (Life Technologies) supplemented with 20 % Knockout serum replacement (Life Technologies), 10 µM SB431542 (Miltenyi Biotec), 0.5 µM purmorphamine (Tocris Bioscience), 1 µM dorsomorphin (Tocris Bioscience), 3 µM CHIR99021 (Tocris Bioscience), 4.44 nM FGF-8b (Miltenyi Biotec), 1 % non-essential amino acids (Life Technologies), 1 % L-glutamine (Life Technologies), 150 µM ascorbic acid 2-phosphate (Sigma) and 0.02 % beta-mercaptoethanol (Life Technologies)). hiPSCs were cultivated for two days on an orbital shaker at 37 °C, 5 % CO2, 21 % O2 and 80 rpm with daily media changes. At day 3, EBs were transferred into neuronal precursor medium (50 % DMEM/F12-GlutaMAX (Life Technologies), 50 % Neurobasal (Life Technologies) supplemented with 1 % B27 (minus vitamin A, 12587010, Life Technologies), 0.5 % N2 (Life Technologies), 10 µM SB431542, 0.5 µM purmorphamine, 1 µM dorsomorphin, 3 µM CHIR99021, 4.44 nM FGF-8b, 150 µM ascorbic acid 2-phosphate and 0.02 % beta-mercaptoethanol). EBs were cultivated for 4 days at 37 °C, 7 % CO2, 21 % O2 and 80 rpm with daily media changes. On day 6, EBs were transferred into neural precursor maintenance medium (neural precursor medium deprived of purmorphamine and CHIR99021). The following day, EBs were seeded unharmed on Geltrex coated plates and expanded for 3-4 days in neural precursor maintenance medium at 37 °C, 7 % CO2, 21 % O2 with daily media changes. At day 10-11 hNPCs were dissociated using Accutase (Sigma) for 10 min at 37 °C, 7 % CO2, 21 % O2, chopped with a 1000 µl pipette tip and diluted in 5 ml neural precursor maintenance medium. hNPCs were harvested at 200 g for 5 min, resuspended in 1 ml neural precursor maintenance medium and seeded on Geltrex coated plates. Thereafter, hNPCs were cultivated at 37 °C, 7 % CO2, 21 % O2 with daily medium changes and passaged with Accutase at 80 % confluency. After 2 passages, 0.5 µM purmorphamine was added to the maintenance medium.

extract_protocol:
hNPCs were maintained on Geltrex coated plates containing neural precursor maintenance medium at 37 °C, 7 % CO2, 21 % O2. At 80% confluency, hNPCs were dissociated using Accutase for 10 min at 37 °C, chopped with a 1000 µl pipette tip and diluted in 5 ml PBS containing 10 % BSA (Sigma). hNPCs were harvested at 200 g for 5 min and resuspended in 1 ml PBS containing 10 % BSA. The hNPC solution was filtered through a 35 µm cell strainer (Corning) and counted using a Neubauer improved cell counting chamber (Carl Roth).
In total 6 libraries with 13,692 hNPCs each were generated in the 10X Genomics Chromium controller according to the manufacturer's instructions and using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237, 10xGenomics) and Chromium i7 Multiplex Kit (PN-120262, 10xGenomics). Libraries were pooled and sequenced on a HiSeq4000 (Illumina) according to the Chromium Single Cell v.2 specifications and with an average read depth of 90,000 aligned reads per cell.
Transcriptome of 16 cell lines was analyzed using single-cell RNA-seq. Cells from all doners where pooled and demultiplexed after sequencing due to the unique SNP patterns of donors.

value: neural precursor cells

tag: cell clones

value: contains cells from donors UKERi1JF-R1-018, UKERiG3G-R1-039, UKERi1E4-R1-003, UKERiO3H-R1-005, UKERi82A-R1-002, UKERiJ2C-R1-015, UKERiM89-R1-005, UKERiC99-R1-007, UKERiR66-R1-007, UKERiAY6-R1-003, UKERiPX7-R1-001, UKERi88H-R1-002, Delta40.7, Internal_2

value: healthy individual:UKERi1JF-R1-018, UKERiG3G-R1-039, UKERi1E4-R1-003, UKERiO3H-R1-005, UKERi82A-R1-002; sporadic Parkinson's Disease:UKERiJ2C-R1-015, UKERiM89-R1-005, UKERiC99-R1-007, UKERiR66-R1-007, UKERiAY6-R1-003, UKERiPX7-R1-001, UKERi88H-R1-002; familial Parkinson's Disease:Delta40.7; additional cell line:Internal_2


title: 131: cell pool 4


title: GX100-2 12h root rep3

tag: tissue


title: GX100-2 3h root rep1


title: Intestinal Mock (s10)


title: M029

value: male


title: M004


title: GX100-2 3h root rep3


title: 130: cell pool 3

value: contains cells from donors UKERi1JF-R1-018, UKERiG3G-R1-039, UKERi1E4-R1-003, UKERiO3H-R1-005, UKERi82A-R1-002, UKERiJ2C-R1-015, UKERiM89-R1-005, UKERiC99-R1-007, UKERiR66-R1-007, UKERiAY6-R1-003, UKERiPX7-R1-001, UKERi88H-R1-002, TUE3_1, Internal_1

value: healthy individual:UKERi1JF-R1-018, UKERiG3G-R1-039, UKERi1E4-R1-003, UKERiO3H-R1-005, UKERi82A-R1-002; sporadic Parkinson's Disease:UKERiJ2C-R1-015, UKERiM89-R1-005, UKERiC99-R1-007, UKERiR66-R1-007, UKERiAY6-R1-003, UKERiPX7-R1-001, UKERi88H-R1-002; isogenic control delta40.7:TUE3_1; additional cell line:Internal_1


title: GX100-2 3h root rep2


title: C43(DE3)EV+IPTG [ev_iptg_plus_c43_22]

city: Clayton

first: Kirill

last: Tsyganov

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with BWA mem aligner option (Li H et al. 2013 ) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GFF and FASTA files were downloaded from RefSeq database bl21_de3 (https://www.ncbi.nlm.nih.gov/nuccore/CP001509)
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical conts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: CP001509_bl21_de3
Supplementary_files_format_and_content: raw gene counts, summar QC metrices

organism: Escherichia coli

growth_protocol: Triplicate samples were grown overnight at 37 °C and used to inoculate 25mL Luria broth (LB) cultures and grown to mid-log phase (0.4-0.6).

extract_protocol:
Cells were pelleted and total RNA was purified using RNeasy Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard MiGen protocols

treatment_protocol: No treatment

value: C43(DE3) purchased from Lucigen (#60452-1) transformed with vector pACYCDuet-1 (Novagen)

tag: genotype background

value: F– ompT gal dcm hsdSB(rB- mB-)(DE3)

value: strain grown at 37C in luria broth to mid log phase then induced with IPTG for 2 hours


title: C43(DE3)EV+IPTG [ev_iptg_plus_c43_23]


title: 133: cell pool 6


title: 128: cell pool 1


title: C43(DE3)EV+IPTG [ev_iptg_plus_c43_21]


title: amniotic fluid-non-VSD7

city: Quanzhou

first: Yiru

last: Yang

address: Zhongshan North Road

institute: the Second Affiliated Hospital of Fujian Medical University

description:
H7
miRNA_all_miRNA_exp non-VSD.txt

data_processing:
Bcl2fastq (v2.19 for myocardium and maternal serum; v2.20 for amniotic fluid) was used to perform recognition on the original image and convert it into the original sequence.
The Fastx-toolkit (v0.0.14) was used to evaluate and filter the quality.
The expression was normalized using the transcripts read number per million (TPM) method of myocardium and maternal serum and counts per million (CPM) method of amniotic fluid.
Genome_build: miRBase V22
Supplementary_files_format_and_content: The expression of txt file was normalized using the counts per million (CPM) method. DESeq was used to calculate the expression of each sample, intragroup mean and perform differential expression analysis.
Supplementary_files_format_and_content: transcripts read number per million (TPM) method of myocardium and maternal serum

organism: Rattus norvegicus

source_name: amniotic fluid

extract_protocol:
Corresponding kits were used to extract total RNA/miRNA from wax blocks of the myocardium (RecoverAll™ Total Nucleic Acid Isolation Kit, Ambion, Thermo Fisher Scientific), amniotic fluid (HiPure Universal RNA Mini Kit, Magen) and maternal serum (miRNeasy Mini Kit, QIAGEN).
A cDNA library of amniotic fluid-derived miRNAs (QIAseq miRNA Library Kit, QIAGEN) and myocardium-derived and serum-derived miRNAs (TruSeq Small RNA Library Preparation kit, Illumina) was constructed.

value: Sprague-Dawley

value: amniotic fluid

tag: embryonic day


title: 129: cell pool 2

tag: cell type


title: GX100-2 1h root rep3

value: root

value: 150 mM NaCl


title: M003


title: GX100-2 1h root rep2


title: M019


title: C41(DE3)EV+IPTG [ev_iptg_plus_c41_13]

value: C41(DE3) purchased from Lucigen (#60452-1) transformed with vector pACYCDuet-1 (Novagen)


title: amniotic fluid-non-VSD5

description:
H5
miRNA_all_miRNA_exp non-VSD.txt


title: C41(DE3)EV+IPTG [ev_iptg_plus_c41_12]


title: C41(DE3)EV+IPTG [ev_iptg_plus_c41_11]


title: M005

value: circulating leukocytes


title: M006

value: hemorrhagic MMD


title: amniotic fluid-non-VSD4

description:
H4
miRNA_all_miRNA_exp non-VSD.txt


title: GX100-2 0h root rep2


title: amniotic fluid-non-VSD3

description:
H3
miRNA_all_miRNA_exp non-VSD.txt


title: GX100-2 0h root rep1


title: BL21(DE3)EV+IPTG [ev_iptg_plus_bl21_de3_31]

value: BL21(DE3) purchased from Novagen (#70235-3) transformed with vector pACYCDuet-1 (Novagen)


title: amniotic fluid-non-VSD2

description:
H2
miRNA_all_miRNA_exp non-VSD.txt


title: CM-WSU-FSCCL [TB2]

city: Barcelona

first: Luis

last: Hernandez

address: Rossello 153, CEK building

department: Molecular Pathology

country: Spain

institute: IDIBAPS

data_processing:
Raw data quality control was performed using FastQC tool
Raw reads were mapped to human genome using tophat2 method
Low quality reads (phred score <10) were eliminate using the Picard Tools software (version 1.129)
The gene assembly was performanced using cufflinks algorithm
Gene count was calculated using HT Seq software (version 0.6.0; HTSeq a Python framework to work with high-throughput sequencing data.Anders S, Pyl PT, Huber W.Bioinformatics. 2015 Jan 15;3)
Genome_build: hG38
Supplementary_files_format_and_content: Processeddatafile_MacrophagesProject.txt file containing RPKM counts for each gene/sample

source_name: CD14+ purified monocytes followed by 7 day treatment

extract_protocol:
RNeasy Mini kit (Qiagen)
Ribosomal RNA depleted using Ribozero kit

treatment_protocol: M-CSF; GM-CSF; CM-WSU-FSCCL cell line (50%) in complete media for 7 days

value: peripheral blood

tag: polarization treatment

value: CM-WSU-FSCCL cell line (50%)


title: amniotic fluid-non-VSD1

description:
H1
miRNA_all_miRNA_exp non-VSD.txt


title: GX100-2 1h root rep1

tag: treatment


title: amniotic fluid-VSD7

description:
G7
miRNA_all_miRNA_exp VSD.txt


title: CM-WSU-FSCCL [TB1]


title: M-CSF [CB3]

value: Treatment M-CSF


title: amniotic fluid-VSD6

description:
G6
miRNA_all_miRNA_exp VSD.txt


title: amniotic fluid-non-VSD6

description:
H6
miRNA_all_miRNA_exp non-VSD.txt


title: M-CSF [CB1]


title: pH 7, prrA-T6A-DUC/∆prrA, replicate 1 (prrA T6A pH NaCl)

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

description: PrrA_T6A_DUC_del_prrA_pH7_vs_PrrA_DUC_del_prrA_pH7.csv, PrrA_T6A_DUC_del_prrA_pH7_vs_PrrA_T6A_DUC_del_prrA_pHCl.csv

data_processing:
Illumina bcl2fastq was used for demultiplexing and conversion of reads to FASTQ file format.
Trimmomatic (v0.33) was used with a 4 bp sliding window to trim adapter sequences and low quality bases. Sequence was removed when the sliding window identified read quality below 15 or read length less than 36 bp.
Bowtie (v1.1.1) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession #: AE000516) to produce SAM files.
HTseq (v0.6.1) was used to determine the number of aligned reads that map to each gene feature in the M. tuberculosis genome.
edgeR (v3.2) was used to normalize data.
R was used for differential gene expression and statistical analyses.
Assembly: M. tuberculosis CDC1551 genome (GCA_000008585.1) (NCBI accession AE000516).
Supplementary files format and content: The file is presented in the .csv file format. It contains gene expression analysis from 2 biological replicates for each condition.

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 harboring a prrA-FLAG-DAS4 (wild type prrA allele) or prrA-T6A-FLAG-DAS4 (T6A STPK-phosphoablative prrA allele) construct were grown to an OD600 of ~0.6 (mid-log phase) in standing, filter-capped T-75 flasks in 20 ml of media, originally seeded at an OD600 = 0.05.

extract_protocol:
RNA was extracted as previously described by Rohde, Abramovitch, and Russell (Cell Host and Microbe 2:352-364, 2007). In brief, RNA was stabilized with guanidine-thiocyanate lysis buffer prior to a freeze-thaw step. Once thawed, bacteria were lysed with 5 µg/ml lysozyme, followed by hot Trizol and physical disruption through silica bead agitation in a Beadbeater.  A chloroform extraction was used to further isolate the RNA before purification with an RNAeasy kit (Qiagen). DNA was degraded with Turbo DNAfree DNAse (Ambion). RNA quality was assessed with an Aligent Bioanalyzer.
The cDNA library was constructed with an Illumina Stranded Total RNA with Ribo-Zero Plus kit.

treatment_protocol: Mtb strains at mid-log phase were subcultured in 10 ml of media to an OD600 of 0.3 in standing, filter-capped T-25 flasks containing standard 7H9, pH 7 media ± 250 mM NaCl, or 7H9, pH 5.7 media ± 250 mM NaCl. Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

tag: genotype

tag: exposure condition


title: pH 7, prrA-T6A-DUC/∆prrA, 250 mM NaCl, replicate 2 (prrA T6A pH NaCl)

description: PrrA_T6A_DUC_del_prrA_pH7_vs_PrrA_T6A_DUC_del_prrA_pHCl.csv


title: pH 7, prrA-T6A-DUC/∆prrA, 250 mM NaCl, replicate 1 (prrA T6A pH NaCl)


title: amniotic fluid-VSD5

description:
G5
miRNA_all_miRNA_exp VSD.txt


title: GX100-2 0h root rep3


title: BL21(DE3)EV+IPTG [ev_iptg_plus_bl21_de3_33]


title: BL21(DE3)EV+IPTG [ev_iptg_plus_bl21_de3_32]


title: pH 7, prrA-DUC/∆prrA, 250 mM NaCl, replicate 2 (prrA T6A pH NaCl)

description: PrrA_DUC_del_prrA_pHCl_vs_PrrA_DUC_del_prrA_pH7.csv

value: prrA-DUC/{delta}prrA


title: GM-CSF [TA3]

value: Treatment GM-CSF


title: CM-WSU-FSCCL [TB3]


title: amniotic fluid-VSD3

description:
G3
miRNA_all_miRNA_exp VSD.txt


title: pH 7, prrA-DUC/∆prrA, 250 mM NaCl, replicate 1 (prrA T6A pH NaCl)


title: GM-CSF [TA1]


title: M-CSF [CB2]


title: pH 7, prrA-T6A-DUC/∆prrA, replicate 2 (prrA T6A pH NaCl)


title: M-CSF [CA3]


title: pH 7, prrA-DUC/∆prrA, replicate 2 (prrA T6A pH NaCl)

description: PrrA_DUC_del_prrA_pHCl_vs_PrrA_DUC_del_prrA_pH7.csv, PrrA_T6A_DUC_del_prrA_pH7_vs_PrrA_DUC_del_prrA_pH7.csv


title: amniotic fluid-VSD1

description:
G1
miRNA_all_miRNA_exp VSD.txt


title: amniotic fluid-VSD2

description:
G2
miRNA_all_miRNA_exp VSD.txt


title: amniotic fluid-VSD4

description:
G4
miRNA_all_miRNA_exp VSD.txt


title: WT_QNZ_1uM_1

first: Tracy

last: Tran

state: CA

address: 1425 San Pablo

institute: University of Southern California

data_processing:
base call and demultiplex by bcl2fastq
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
logCPM values were obtained with the ‘EdgeR’ package
Differential expression analysis was performed with DESeq2
Genome_build: GRCh38

source_name: organoid

growth_protocol: At day 8, the progenitor cells were dissociated and 600,000 cells seeded into each well of a 12-well EZSPHERE plate in 3μM CHIR and 10ng/ml FGF9. Each well generated ~400 mini-organoids and each mini-organoid comprised ~1,500 cells. On differentiation day (dd) 10, the medium was switched to Advanced RPMI 1640 + 1X Glutamax + 1% Penicillin-Streptomycin, denoted basal differentiation medium, with 10ng/ml FGF9. From dd13 to dd28, cultures were maintained in basal differentiation medium

extract_protocol:
Organoids and Cysts were resuspend in cell lysis buffer. We used Rneasy Micro Kit for RNA extraction following the manufacturer's protocol.
Samples were prepared according to library kit manufacturer’s protocol

treatment_protocol:
QNZ and DMSO added into culture medium on dd8 for WT organoids
QNZ and DMSO added into culture medium on dd13 for PKD2null organoids

tag: phenotype

value: normal

value: 1 uM QNZ

value: WT


title: pH 7, prrA-T6A-DUC/∆prrA, 100 µM DETA NONOate, replicate 2 (prrA T6A NO)

description: PrrA_T6A_DUC_del_prrA_Control_vs_PrrA_T6A_DUC_del_prrA_NO.csv

growth_protocol: Mtb strain CDC1551 with a deletion of the native copy of prrA, and harboring a prrA-FLAG-DAS4 (wild type prrA allele - prrA-DUC/∆prrA) or prrA-T6A-FLAG-DAS4 (T6A STPK-phosphoablative prrA allele - prrA-T6A-DUC/∆prrA) construct were grown in aerated conditions to mid-log phase (OD600 ~0.6). This entailed three passages in 12 ml of 7H9, pH 7 media each time, in filter-capped T75 flasks laid flat.

treatment_protocol: Mtb strains grown in aerated conditions at mid-log phase were subcultured to an OD600 = 0.3 in filter-capped T-75 flasks laid flat, in 12 ml of  standard 7H9, pH 7 media ± 100 µM DETA NONOate. Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

tag: strain

value: 7H9, pH 7, 100 µM DETA NONOate


title: pH 7, prrA-DUC/∆prrA, replicate 1 (prrA T6A pH NaCl)


title: WT_QNZ_0uM_3

value: 0 uM QNZ


title: WT_QNZ_1uM_3


title: pH 7, prrA-T6A-DUC/∆prrA, 100 µM DETA NONOate, replicate 1 (prrA T6A NO)


title: pH 7, prrA-T6A-DUC/∆prrA, replicate 2 (prrA T6A NO)


title: H9_WT_ChIP_HA_Rep2

first: Jessica

last: Tsai

address: 4650 Sunset Blvd MS #57

institute: Children's Hospital Los Angeles

library_source: genomic

data_processing:
A modified version of the ChiLin pipeline was used for quality control and pre-processing of the data. We used Burrows-Wheeler Aligner (BWA Version: 0.7.17-r1188, RRID:SCR_010910) as a read mapping tool to align to hg19 using default parameters.
Unique reads for a position for peak calling were used to reduce false positive peaks, and statistically significant peaks were finally selected by calculating a false discovery rate (FDR) of reported peaks. ChIP-seq peaks were called using MACS2 (v2.1.2) with a cut-off of FDR<0.01 for H3K27ac and H3K4me3, FDR<0.1 for HA.
DESeq2 (RRID:SCR_015687) was used to identify differential peaks in ChIP-seq, where gained or lost peaks were defined with the threshold of log2 fold change of 1 or 2 and an adjusted p-value<0.05.
Assembly: hg19
Supplementary files format and content: BIGWIG (bw)

molecule: genomic DNA

source_name: H9 human neural stem cells

extract_protocol:
For histone marks profiling, cells were crosslinked with 1 ml of 1% formaldehyde for 10 minutes. For CTCF and HA profiling cells were crosslinked in two steps with 2 mM of disuccinimidyl glutarate (DSG, Pierce) for 45 minutes at room temperature followed by 1 ml of 1% formaldehyde for 10 minutes. Crosslinked cells were then quenched with 0.125 M glycine for 5 minutes at room temperature and washed with PBS. After fixation, pellets were resuspended in 500 μl of 1% SDS (50 mM Tris-HCl pH 8, 10 mM EDTA) and sonicated for 5 minutes (histone marks)  or 10 minutes (HA and CTCF) using a Covaris E220 instrument (setting: 140 peak incident power, 5% duty factor and 200 cycles per burst) in 1 ml AFA fiber millitubes. Chromatin was immunoprecipitated with 10 μg of each antibody (H3K4me3 Abcam ab8580, RRID:AB_306649; H3K27ac Diagenode C15410194, RRID:AB_2637079; CTCF Millipore 07-729, RRID:AB_441965; HA Abcam ab9110, RRID:AB_307019).
5 μg of chromatin was used for histone mark ChIPs, and 40 μg of chromatin was used for HA and CTCF ChIPs. ChIP-seq libraries were made using NEBNext® Ultra™ II DNA Library Prep Kit (New England BioLabs, E7103). 75 bp paired-end reads were sequenced on a NextSeq instrument (Illumina).

tag: cell line

value: H9 human neural stem cells

tag: chip antibody

value: HA


title: amniotic fluid-NC5

description:
F5
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt

value: Sprague-Dawley

value: amniotic fluid


title: GM-CSF [TA2]


title: pH 7, prrA-T6A-DUC/∆prrA, replicate 1 (prrA T6A NO)


title: M-CSF [CA1]


title: WT_QNZ_0uM_1


title: amniotic fluid-NC4

description:
F4
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt


title: WT_QNZ_0uM_2


title: amniotic fluid-NC3

description:
F3
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt


title: H9_WT_ChIP_HA_Rep1


title: WT_QNZ_0.1uM_3

value: 0.1 uM QNZ


title: WT_QNZ_0.1uM_2


title: pH 7, prrA-DUC/∆prrA, 100 µM DETA NONOate, replicate 2 (prrA T6A NO)

description: PrrA_DUC_del_prrA_NO_vs_PrrA_DUC_del_prrA_Control.csv


title: amniotic fluid-NC6

description:
F6
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt


title: M-CSF [CA2]


title: pH 7, prrA-DUC/∆prrA, 100 µM DETA NONOate, replicate 1 (prrA T6A NO)


title: amniotic fluid-NC2

description:
F2
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt


title: H9_HA-FOXR2_ChIP_HA_Rep1


title: WT_QNZ_0.1uM_1


title: DIPG-XIII_ChIP_H3K4me3_Rep2

source_name: DIPG-XIII

value: DIPG-XIII

value: DMG cell line


title: amniotic fluid-NC1

description:
F1
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt


title: pH 7, prrA-DUC/∆prrA, replicate 2 (prrA T6A NO)


title: WT_QNZ_0.01uM_3

value: 0.01 uM QNZ


title: Phf20-/-, GlcStarv, ATAC-seq, rep2

city: Seoul

first: Se Won

last: Park

state: Gwanak-Gu

address: Gwanak-ro 1, Gwanak-gu, Seoul, Seoul Nat'l Univ Bldg504 Rm607

country: South Korea

institute: Seoul national university

data_processing:
ATAC-seq reads were mapped to mm10 reference using Burrows-Wheeler Aligner (BWA) MEM algorithm (version 0.7.12)
Peak-calling was performed using MACS2 (version 2.1.2) callpeak command with --nomodal --extensive 200 shift -100 -q 0.01 parameters
All Peaks are merged and read counts of each peaks are calculated using bedtools (v2.25.0)
The read counts were processed using DESeq2 (v1.26.0) to identity differentially opening peaks
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for genome coverage

source_name: Mouse Embryonic Fibroblast (MEF)

growth_protocol: WT and Phf20-/- MEF cells were cultured at 37 ℃ in Dulbecco’s modified Eagle medium (DMEM)supplemented with 10 % fetal bovine serum (FBS) and ZellShield in a humidified incubator with 5 % CO2.

extract_protocol:
For RNA-seq, RNA were harvested using Trizol and purified using Qiagen RNeasy Kit. For ATAC-seq, DNA was fragmented with Mnase. For ChIP-seq, crosslinked DNA was fragmented with sonication and IP with H3K4me1 or H3K4me2 antibody.
All of the libraries (RNA-seq, ATAC-seq and ChIP-seq) were constructed following standard Illumina library preparation protocol

treatment_protocol: For glucose starvation samples, cells were treated with Glucose-free DMEM supplemented with dialyzed FBS for 24hrs

value: Mouse Embryonic Fibroblast (MEF)

value: Glucose starvation 24hr

tag: assay

value: ATAC-seq


title: WT_QNZ_1uM_2


title: Phf20-/-, GlcStarv, ATAC-seq, rep1


title: WT_QNZ_0.01uM_2


title: WT_QNZ_0.01uM_1


title: DIPG-XIII_ChIP_H3K4me3_Rep1


title: DIPG-IV_ChIP_H3K4me3_Rep2

source_name: DIPG-IV

value: DIPG-IV


title: Phf20-/-, control, ATAC-seq, rep1

value: control


title: H9_HA-FOXR2_ChIP_HA_Rep2


title: DIPG-IV_ChIP_H3K4me3_Rep1


title: pH 5.7, 250 mM NaCl, ATC treated, replicate 1 (prrA OE pH NaCl)

description: prrA_OE_ATC_pH7_vs_prrA_OE_ATC_pH57NaCl.csv

growth_protocol: Mtb strain CDC1551 harboring a tet inducible prrA-FLAG construct was grown to an OD600 of 0.6 (mid-log phase) in standing, filter-capped T-75 flasks in 20 ml of media, originally seeded at an OD600 of 0.05.

treatment_protocol: Mtb strains at mid-log phase were treated with either ethanol (EtOH) as a carrier control or 200 ng/ml anhydrotetracycline (ATC) for 2 hours, before being subcultured in 10 ml of media to an OD600 = 0.3 in standing, filter-capped T-25 flasks containing standard 7H9, pH 7 media ± 250 mM NaCl, or 7H9, pH 5.7 media ± 250 mM NaCl. Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

value: Inducible prrA-FLAG

value: ATC


title: pH 7, 250 mM NaCl, ATC treated, replicate 2 (prrA OE pH NaCl)

value: 7H9, pH 7, 250 mM NaCl


title: PKD2null_org_0uM_3

value: normal

value: 0 uM QNZ


title: DIPG-XIII_ChIP_H3K27ac_Rep2


title: PKD2null_org_0uM_2


title: amniotic fluid-NC7

description:
F7
miRNA_all_miRNA_exp VSD.txt
miRNA_all_miRNA_exp non-VSD.txt


title: WT, GlcStarv, ATAC-seq, rep2

value: WT


title: pH 5.7, ATC treated, replicate 2 (prrA OE pH NaCl)


title: PKD2null_org_0uM_1


title: pH 5.7, ATC treated, replicate 1 (prrA OE pH NaCl)


title: pH 7, 250 mM NaCl, ATC treated, replicate 1 (prrA OE pH NaCl)


title: pH 5.7, 250 mM NaCl, ATC treated, replicate 2 (prrA OE pH NaCl)


title: WT, GlcStarv, ATAC-seq, rep1


title: DIPG-XIII_ChIP_H3K27ac_Rep1


title: PKD2null_org_0.1uM_3


title: pH 7, prrA-DUC/∆prrA, replicate 1 (prrA T6A NO)

value: prrA-DUC/{delta}prrA


title: PKD2null_org_0.1uM_2


title: DIPG-IV_ChIP_H3K27ac_Rep2


title: pH 7, ATC treated, replicate 1 (prrA OE pH NaCl)

description: prrA_OE_ATC_pH7_vs_prrA_OE_EtOH_pH7.csv, prrA_OE_ATC_pH7_vs_prrA_OE_ATC_pH57.csv, prrA_OE_ATC_pH7_vs_prrA_OE_ATC_NaCl.csv, prrA_OE_ATC_pH7_vs_prrA_OE_ATC_pH57NaCl.csv


title: Phf20-/-, control, ATAC-seq, rep2


title: WT, control, ATAC-seq, rep2


title: DIPG-IV_ChIP_H3K27ac_Rep1


title: PKD2null_org_0.1uM_1


title: pH 7, ATC treated, replicate 2 (prrA OE pH NaCl)


title: WT, control, ATAC-seq, rep1


title: DIPG-IV_ChIP_CTCF_Rep3

value: CTCF


title: PKD2null_cyst_1uM_3

value: cyst

value: 1 uM QNZ


title: DIPG-IV_ChIP_CTCF_Rep2

value: DMG cell line


title: DIPG-IV_ChIP_CTCF_Rep1


title: PKD2null_cyst_1uM_2


title: pH 5.7, 250 mM NaCl, EtOH treated, replicate 2 (prrA OE pH NaCl)

description: prrA_OE_EtOH_pH57NaCl_vs_prrA_OE_EtOH_pH7.csv

value: EtOH


title: BT245_ChIP_CTCF_Rep2


title: BT245_ChIP_CTCF_Rep1


title: pH 5.7, 250 mM NaCl, EtOH treated, replicate 1 (prrA OE pH NaCl)


title: PKD2null_cyst_0uM_6


title: PKD2null_cyst_1uM_1


title: CIT 3

city: Bethesda

first: Tim

last: Greten

state: Maryland

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Targeted capture libraries were prepared using BD Rhapsody Single-cell Analysis System with the targeted human immune response panel of 399 genes (BD Biosciences, https://www.bd.com/documents/specifications/genomics/GMX_BD-Rhapsody-immune-response-human-panel_SP_EN.pdf) adding 6 additional targets (CCR6 PolyA, CCR6 Reference End, CD19, CLEC4C, KLRD1, NCR2) according to manufacturer’s recommendations ((BD Biosciences). Libraries were pooled and sequenced on NextSeq 550 using pair-end runs (R1:76bps, R2:76bps). The demultiplex of sequencing run was performed using Illumina bcl2fastq version2.17. One mismatch in sample barcodes was allowed to tolerate sequencing error or PCR errors. The average sequencing yield was about 133 million raw reads per sample and these reads were stored in FASTQ format.  The FASTQ-formatted files were processed using the standard Rhapsody analysis pipeline version 1.3 on Seven Bridges (https://www.sevenbridges.com). Mate pairs in which either read was too short or too low in sequencing quality were first removed (if Read1 <66bps or Read2 < 64bps or base call quality score is less than Q20 in either mate). In addition, reads with low complexity such as strings of identical bases and tandem repeats were removed. After filtering, the average total reads per sample was about 125 million reads for scRNA-seq samples. Cell barcodes and unique molecular identifiers (UMIs) were extracted from R1 reads. R2 reads were mapped to reference sequences (Immune Amplicons reference for mRNA-seq) using Bowtie2. The percentages of uniquely aligned reads were between 70% - 90% for each sample. A mate pair was retained if and only both reads survived the above filtering and both reads mapped uniquely.  Finally, all valid R1 and R2 reads were combined and annotated to the respective molecules by applying both recursive substation error correction (RSEC) for collapsing molecules with one base difference in UMIs as well as distribution-based error correction (DBEC) algorithms to remove PCR errors in the UMI sequences from BD Rhapsody analysis pipeline. The mean DBEC sequencing depth was 416x and sequencing saturation was about 88% for scRNA-seq.    Putative cell identification was done using a basic implementation of second derivative analysis to find cut-off point with additional refinement steps in the BD Rhapsody analysis pipeline to remove false positive cells and recover false negative cells. For scRNA-seq samples from PBMCs, the putative cell counts were between 128 – 2477. The mean reads per sample after DBEC correction were about 154,000 reads/cell, and the mean molecule per cells was about 170 molecules/cell. For scRNA-seq samples from liver tissue, the putative cell counts were between 290 – 3037. The mean reads per sample after DBEC correction were about 64,500 reads/cell, and the mean molecule per cells was about 1281 molecules/cell.  The final gene expression matrices contain DBEC-adjusted molecule counts was generated in a CSV format.
Genome_build: HUMAN - hg38
Supplementary_files_format_and_content: csv; Gene expression matrix

source_name: Blood

extract_protocol:
Fresh tissue from a total of 11 HCC patients undergoing liver surgery was collected in MACS tissue storage solution (Miltenyi Biotec)(Heinrich et al., 2021b). Immediate tissue preparation was a crucial factor for yield and viability of isolated cells, therefore, single cell preparation was started directly after tissue collection and finished in an interval of less than 8 hours. Tissue weight was measured, and the digestion process was adapted accordingly. Samples were minced with a sterile blade and incubated with 2ml collagenase IV (STEMCELL technologies) and 150 µl DNAse I (STEMCELL Technologies) in a total volume of 10ml RPMI 1640 (Gibco) without FCS per 1g tissue for 90 minutes at 37°C in a rocking shaker. Cells were spun down at 1400 RPM for 5 min and washed once with RPMI plus FCS before filtering through a 100 µm filter. Cells were washed twice, and a density gradient centrifugation using 30% and 70% percoll solution was performed to separate the immune cells from the remaining liver tissue. Cells were resuspended in 30% Percoll (GE Healthcare) and layered onto 70% percoll solution. Centrifugation was performed at 2400 RPM, for 20 min at room temperature without brake. Immune cells were recovered from the middle layer and washed with RPMI once. RBC lysis was performed before cells were counted. Cells were used for immediate flow cytometry analysis, flow sorting and sequencing or were frozen for future experiments.
Single cell gene expression and protein expression analysis was done using BD Rhapsody Single cell analysis platform following manufacturer’s suggested protocol. Briefly, BD cartridge was primed with air, and washing buffers. Freshly isolated and flow sort enriched ILC populations of 1,000-10,000 single cells were resuspended in sample buffer (BD Bioscience) before loading onto microwells on the BD Rhapsody cartridges. Cartridge and cells were incubated for 15 minutes and cells were scanned in the cartridge. Cell capture beads were loaded onto the cartridge and incubated with the sample following the protocol. Two washing steps were performed before another imaging step. Next, cell lysis buffer was added to the samples and incubated for 2 min. After incubation on the large magnet, reverse transcription was performed (25min). A targeted panel of primers were used for library preparation. Libraries were sequenced on Illumina NextSeq550.

value: PBMCs

tag: disease status

value: Hepatocellular Carcinoma

tag: therapy

value: tremelimumab and durvalumab


title: BT245_ChIP_CTCF_Rep3

city: Los Angeles


title: CIT 2


title: PKD2null_cyst_0uM_5


title: PKD2null_cyst_0uM_4


title: pH 7, 250 mM NaCl, EtOH treated, replicate 1 (prrA OE pH NaCl)

description: prrA_OE_EtOH_NaCl_vs_prrA_OE_EtOH_pH7.csv


title: pH 5.7, EtOH treated, replicate 1 (prrA OE pH NaCl)

description: prrA_OE_EtOH_pH57_vs_prrA_OE_EtOH_pH7.csv


title: pH 7, 250 mM NaCl, EtOH treated, replicate 2 (prrA OE pH NaCl)


title: pH 7, EtOH treated, replicate 2 (prrA OE pH NaCl)

description: prrA_OE_ATC_pH7_vs_prrA_OE_EtOH_pH7.csv, prrA_OE_EtOH_NaCl_vs_prrA_OE_EtOH_pH7.csv, prrA_OE_EtOH_pH57_vs_prrA_OE_EtOH_pH7.csv, prrA_OE_EtOH_pH57NaCl_vs_prrA_OE_EtOH_pH7.csv


title: HCC 3


title: PKD2null_cyst_0uM_2


title: pH 7, EtOH treated, replicate 1  (prrA OE pH NaCl)


title: pH 5.7, EtOH treated, replicate 2 (prrA OE pH NaCl)


title: PKD2null_cyst_0uM_3


title: PKD2null_cyst_0uM_1


title: PKD2null_cyst_0.1uM_6

value: 0.1 uM QNZ


title: HCC 2


title: PKD2null_cyst_0.1uM_5


title: pH 7, ATC treated, 100 µM DETA NONOate, replicate 2 (prrA OE NO)

description:
prrA_OE_ATC_Control_vs_prrA_OE_ATC_NO.csv
ATC_NO_2

growth_protocol: Mtb strain CDC1551 harboring a tetracycline inducible prrA-FLAG construct was grown in aerated conditions to mid-log phase (OD600 ~0.6). This entailed three passages in 12 ml of 7H9, pH 7 media each time, in filter-capped T75 flasks laid flat.

treatment_protocol: Mtb strains grown in aerated conditions at mid-log phase were treated with either ethanol (EtOH) as a carrier control or 200 ng/ml anhydrotetracycline (ATC) for 2 hours, before being subcultured to an OD600 = 0.3 in filter-capped T-75 flasks laid flat, in 12 ml of  standard 7H9, pH 7 media ± 100 µM DETA NONOate. Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

value: 7H9, pH 7, 100 µM DETA NONOate


title: pH 7, ATC treated, 100 µM DETA NONOate, replicate 1 (prrA OE NO)

description:
prrA_OE_ATC_Control_vs_prrA_OE_ATC_NO.csv
ATC_NO_1

value: Inducible prrA-FLAG


title: HCC 1


title: pH 7, ATC treated, replicate 2 (prrA OE NO)

description:
prrA_OE_ATC_Control_vs_prrA_OE_ATC_NO.csv
ATC_cont_2

value: ATC


title: PKD2null_cyst_0.1uM_4


title: Healthy 3

value: Healthy


title: pH 7, ATC treated, replicate 1 (prrA OE NO)

description:
prrA_OE_ATC_Control_vs_prrA_OE_ATC_NO.csv
ATC_cont_1


title: CIT 1


title: PKD2null_cyst_0.1uM_2


title: PKD2null_cyst_0.1uM_3


title: pH 7, EtOH treated, 100 µM DETA NONOate, replicate 2 (prrA OE NO)

description:
prrA_OE_EtOH_NO_vs_prrA_OE_EtOH_Control.csv
EtOH_NO_2


title: Healthy 1


title: pH 7, EtOH treated, 100 µM DETA NONOate, replicate 1 (prrA OE NO)

description:
prrA_OE_EtOH_NO_vs_prrA_OE_EtOH_Control.csv
EtOH_NO_1


title: C4_2_rep3_R1881_1nM

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: transcriptional profiling (RNA sequencing)

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the hg19 genome using TopHat v2.1.0 with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene is calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Htseq-count text file

growth_protocol: culturing was performed as previously described: Esmaeili, M., Pungsrinont, T., Schaefer, A. and Baniahmad, A. (2016) A novel crosstalk between the tumor suppressors ING1 and ING2 regulates androgen receptor signaling. J. Mol. Med., 94, 1167-1179.

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, Erlangen, Germany) according to the manufacturer’s protocol.
RNA samples were further processed for Poly-A RNA-seq library preparation according to the manufacturer’s instructions (TruSeqRRNA Sample preparation v2, Illumina). Library concentrations were evaluated on Qubit 3.0 (Thermo Fisher Scientific) and quality by using the Fragment Analyzer using the High Sensitivity NGS Fragment Analysis Kit (1 bp – 6,000 bp) (Advanced Analytical).

treatment_protocol: C4-2 cells were treated for 72h with solvent control (DMSO), 1nM R1881, 100um Atraric acid or combination of Atraric acid and R1881.

value: human prostate cancer cell line


title: C4_2_rep3_R1881_AA

value: R1881_atraric acid (AA)


title: PKD2null_cyst_0.01uM_2

value: 0.01 uM QNZ


title: C4_2_rep3_AA

value: atraric acid (AA)


title: PKD2null_cyst_0.1uM_1


title: PKD2null_cyst_0.01uM_3


title: C4_2_rep2_R1881_AA


title: pH 7, EtOH treated, replicate 1 (prrA OE NO)

description:
prrA_OE_EtOH_NO_vs_prrA_OE_EtOH_Control.csv
EtOH_cont_1


title: Zambia line 470, stage 5, replicate 3

city: Davis

first: Susan

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

data_processing:
Adapter/quality trimming with Cutadapt
Mapping with HISAT2 (v. 2.1.0)
Gene level counts with featureCounts
Counts normalized to sequencing depth using DESeq2
Genome_build: Flybase D. melanogaster release 6.18
Supplementary_files_format_and_content: Dmel_RalZam_counts_data.txt

organism: Drosophila melanogaster

source_name: single whole stage 5 embryo

growth_protocol: density controlled, standard cornmeal food, 25 degreee incubator, 60% humidity, mothers were 3-10 days old

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Standard Illumina mRNA-Seq library prep protocols, using KAPA mRNA stranded reagents

tag: fly line (origin)

value: Line ZI 470 (Siavonga, Zambia)

tag: replicate number

value: embryo

tag: embryo sex

value: XY

tag: Stage


title: Zambia line 470, stage 5, replicate 1

tag: tissue


title: PKD2null_cyst_0.01uM_1

value: cyst


title: C4_2_rep3_DMSO

tag: cell type

value: DMSO


title: Zambia line 470, stage 2, replicate 3

source_name: single whole stage 2 embryo

value: unknown


title: Zambia line 470, stage 5, replicate 2


title: Healthy 2

value: PBMCs


title: Zambia line 470, stage 2, replicate 2


title: C4_2_rep2_R1881_1nM


title: leukemiaRNA_CLL6_SC2 CLL 6_SC2

city: La Jolla

first: Emanuela

middle: Maria

last: Ghia

address: 9310 Athena Circle

department: Center For Novel Therapeutics

institute: University of California San Diego

data_processing:
Data were analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt (Martin and Wang, 2011). Quality scores were assessed using FastQC (Andrews, 2010).
Reads were aligned to the Homo sapiens genome build hg19 using STAR (Dobin et al., 2013).
Individual sample reads were quantified using Htseq (Anders et al., 2015) and normalized via Relative Log Expression (RLE) using DESeq2 R library (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized gene expression for every gene and for each sample.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample collection


title: leukemiaRNA MEC1

description: leukemiaRNA


title: C4_2_rep1_R1881_1nM

tag: treatment


title: C4_2_rep1_R1881_AA


title: C4_2_rep2_DMSO


title: C4_2_rep2_AA


title: Zambia line 470, stage 2, replicate 1


title: leukemiaRNA_CLL7_SC1 CLL 7_SC1


title: leukemiaRNA_CLL6_SC1 CLL 6_SC1


title: leukemiaRNA MEC1-ROR1

description: leukemiaRNA


title: C4_2_rep1_AA


title: leukemiaRNA_CLL7_SC2 CLL 7_SC2


title: leukemiaRNA_CLL5_SC1 CLL 5_SC1


title: leukemiaRNA_CLL5_SC2 CLL 5_SC2


title: C4_2_rep1_DMSO


title: Zambia line 160, stage 2, replicate 2

value: Line ZI 160 (Siavonga, Zambia)


title: Zambia line 160, stage 5, replicate 1


title: Zambia line 160, stage 2, replicate 1


title: leukemiaRNA_CLL4_SC1 CLL 4_SC1


title: Miniature kidney organoids collected at differentiation day 14

data_processing:
From fastq files, quality control, alignment to reference genome (hg38) and generation of count tables of the five libraries were done using CellRanger 3.1 (10X Genomics).
The Seurat 3.0 package was used for scRNA-seq analyses (Stuart et al., 2019)
Genome_build: hg19
Supplementary_files_format_and_content: tar archive comprising barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: kidney organoids derived from human embryonic stem cells

growth_protocol: MAFB-P2A-eGFP H9 hESCs were differentiated following a protocol detailed in our manuscript to generate miniature kidney organoids.

extract_protocol:
Miature organoids were dissociated using cold active protease (protocol described in Ransick et al., 2019). Single cells were FACS sorted to select for DAPI- DRAQ5+ live cells, which were then profiled with a 10x Genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (10X Genomics, PN-1000075).
After recovery from the emulsion, cDNA was cleaned-up and amplified by PCR, examined on a 4200 Tape station (Agilent) for yield assessment, and then processed into barcoded library for Illumina sequencing. Paired-end sequencing on the Illumina NextSeq 500 platform was performed using the NextSeq® 500/550 High Output Kit v2 (FC-404-2002) and the 150-cycle flow cell (FC-410-1002).
scRNA-seq

value: MAFB-P2A-eGFP H9 hESC

value: Miniature kidney organoids

tag: time

value: differentiation day 14


title: leukemiaRNA_CLL3_SC2 CLL 3_SC2


title: Zambia line 160, stage 2, replicate 3


title: leukemiaRNA_CLL4_SC2 CLL 4_SC2


title: Miniature kidney organoids collected at differentiation day 28

value: differentiation day 28


title: Zambia line 160, stage 5, replicate 2


title: Miniature kidney organoids collected at differentiation day 16

value: differentiation day 16


title: Zambia line 160, stage 5, replicate 3


title: Zambia line 94, stage 5, replicate 3

value: Line ZI 94 (Siavonga, Zambia)


title: Miniature kidney organoids collected at differentiation day 8

value: differentiation day 8


title: Miniature kidney organoids collected at differentiation day 10

value: differentiation day 10


title: leukemiaRNA_CLL3_SC1 CLL 3_SC1


title: leukemiaRNA_CLL2_SC2 CLL 2_SC2


title: BXSH2O2cyto5

city: Buffalo

first: Michael

last: Farkas

state: NY

address: 3495 Bailey Ave, Bldg 20, Mail Stop 151

department: Ophthalmology

institute: State University of New York at Buffalo

data_processing:
Base calling was performed using RTA v2
Reads were aligned to human genome version hg38 using STAR v2.5.2b
Counts were generated for each transcript using Rsubread v1.32.4
RPKM values for each transcript were calculated to determine overall expression
Differential expression analsis was perfromed using DESeq
Genome_build: hg38
Supplementary_files_format_and_content: DESeq output from analyses comparing nuclear and cytoplasmic fractions of control and treated cells, and comparing control and treated nuclear fractions and control and treated cytoplasmic fractions

source_name: induced pluripotent stem cell-derived retinal pigment epithelium

growth_protocol: Human iPSC (line ATCC-BXS0114, ATCC, ACS-1028) were seeded at 500,000 cells in a 10-cm dish coated with Matrigel. Cells were maintained in TeSR-E8 media (Stem Cell Technologies) with Rock Inhibitor (Y-27632 dihydrochloride, Santa Cruz Biotechnology) at a final concentration of 1 μM/mL. Media was changed daily. To differentiate iPSC cells toward RPE, the culture was maintained in RDM until day 80, when RPE was dissected and passaged.

extract_protocol:
RNA was isolated from the nuclear and cytoplasmic fractions using Tri-Reagent
RNA-sequencing libraries were prepared using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing kit according to the manufacturer’s protocol using 100 ng total RNA, and each sample was indexed for multiplexing

treatment_protocol: Subcellular fractionation- Briefly, iPSC-RPE cells were incubated either in RDM media (untreated samples) or in media with 500 µM hydrogen peroxide (treated samples) for 3 hours, washed three times with phosphate buffered saline, incubated at 37°C for 5 minutes with Tryple Express dissociation reagent, and collected via scraping. Cells were pelleted via centrifugation and resuspended in ice-cold cell disruption buffer, then incubated on ice and homogenized. Cytoplasmic material was separated from the nuclei, and both were collected.

value: ATCC-BXS0114, ATCC, ACS-1028

tag: cell fraction

value: cytoplasm

value: 3 hours hydrogen peroxide


title: Zambia line 94, stage 5, replicate 1

value: embryo

value: XY


title: leukemiaRNA_CLL2_SC1 CLL 2_SC1


title: leukemiaRNA_CLL1_SC2 CLL 1_SC2


title: Zambia line 94, stage 2, replicate 1


title: BXSH2O2cyto3

value: induced pluripotent stem cell-derived retinal pigment epithelium


title: BXSH2O2cyto4


title: Zambia line 94, stage 2, replicate 2

value: unknown


title: BXSH2O2cyto2


title: Zambia line 50, stage 5, replicate 3

value: Line ZI 50 (Siavonga, Zambia)


title: HPDE c7 - PPCL68 EV #3

city: Washington

first: Amrita

last: Cheema

state: District of Columbia

address: 3900 Reservoir Road NW

institute: Georgetown University

data_processing:
Illumina CASAVA was used for base calling
Sequenced reads were filtered by removing reads containing adaptors, reads containing N > 10% (uncertain nucleotides) and reads with Qscore of over 50% bases below 5.
Filtered reads were mapped to hg19 genome using STAR, mismatch = 2
Quantification was achieved using HTSeq and differential gene expression analysis performed using DESeq2 (p-adj < 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Pancreas cell line

growth_protocol: hTERT-HPNE and HPDE-H6c7 cells were grown in keratinocyte serum free media with 1% penicillin-streptomycin in a 24-well plate until 50-60% confluent.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen, #74104) according to manufacturer's protocol.
Libraries were prepared using NEBNext Ultra II non-directional RNA Library Prep kit (New England BioLabs, # E7770S). Library quality and concentration was assessed with Labchip and qPCR.

treatment_protocol: Cells were treated with fresh serum free media, PANC-1 EVs (1E10 per well), PPCL-68 EVs (1E10 per well) or residual media left over from EV isolation (as a negative control) for 24 hours prior to RNA extraction.

value: HPDE

value: Normal pancreas cell

value: PPCL-68 Extracellular vesicles


title: BXSH2O2cyto1


title: leukemiaRNA_CLL1_SC1 CLL 1_SC1


title: Zambia line 50, stage 5, replicate 2


title: HPDE c7 - PPCL68 EV #2


title: HPDE c7 - PPCL68 EV #1


title: Zambia line 94, stage 5, replicate 2


title: Zambia line 94, stage 2, replicate 3


title: HPDE c7 - Neg. Control #3

value: Negative control


title: BXSH2O2nuc5

value: nucleus


title: Zambia line 50, stage 2, replicate 3


title: BXSH2O2nuc3


title: pH 7, EtOH treated, replicate 2 (prrA OE NO)

description:
prrA_OE_EtOH_NO_vs_prrA_OE_EtOH_Control.csv
EtOH_cont_2

tag: genotype

value: Inducible prrA-FLAG

value: EtOH

tag: exposure condition


title: BXSH2O2nuc2

tag: cell line


title: Zambia line 50, stage 5, replicate 1


title: HPDE c7 - Neg. Control #1


title: BXSH2O2nuc1


title: Zambia line 50, stage 2, replicate 1


title: Raleigh line 517, stage 5, replicate 3

value: DGRP line 517 (Raleigh, NC)


title: Zambia line 50, stage 2, replicate 2


title: BXScyto5


title: HPDE c7 - Neg. Control #2


title: BXScyto4


title: Raleigh line 517, stage 5, replicate 2


title: BXSH2O2nuc4


title: HPDE c7- Panc1 EV #3

value: PANC-1 Extracellular vesicles


title: BXScyto3

value: ATCC-BXS0114, ATCC, ACS-1028


title: BXScyto2

value: cytoplasm


title: HPDE c7 - Control #2

value: Control


title: Raleigh line 517, stage 5, replicate 1

value: embryo


title: HPDE c7- Panc1 EV #2


title: Raleigh line 517, stage 2, replicate 3


title: adult_R3

city: Beijin

first: Ruiyan

last: Hou

state: Beijin

address: Datun Road

department: State Key Laboratory of Integrated Management of Pest Insects and Rodents

institute: Institute of Zoology, Chinese Academy of Sciences

description: Drosophila melanogaster, resistance strain,adult,rep3

data_processing:
Quality control was done by the FastQC (version 0.11.9)
Then the high-quality reads were mapped to the reference genome by STAR
The output files of STAR then were imported to RSEM (version 1.3.3)
The edgeR (version 3.12) package from Bioconductor was used to identify different expression genes (DEGs) for the sensitive and resistance strains
Assembly: dm6
Supplementary files format and content: csv/FPKM value for each sample
Supplementary files format and content: N/A

source_name: whole body

extract_protocol:
Total RNA extraction using TRIzol method
RNA-library was prepared for sequencing using standard BGISEQ-500 protocol

value: whole body

tag: developmental stage

value: adult

value: resistance to avermectins


title: adult_S3

description: Drosophila melanogaster, sensitive strain,adult,rep3

value: wild type


title: Raleigh line 360, stage 5, replicate 3

value: DGRP line 360 (Raleigh, NC)

value: XY


title: adult_R1

description: Drosophila melanogaster, resistance strain,adult,rep1


title: Raleigh line 517, stage 2, replicate 1

value: unknown


title: HPDE c7 - Control #1

value: HPDE

value: Normal pancreas cell


title: Raleigh line 360, stage 5, replicate 2


title: BXSnuc3

value: induced pluripotent stem cell-derived retinal pigment epithelium

value: nucleus


title: HPNE - PPCL68 EV #1

value: HPNE

value: PPCL-68 Extracellular vesicles


title: BXSnuc4

value: ATCC-BXS0114, ATCC, ACS-1028


title: HPDE c7 - Control #3


title: Raleigh line 360, stage 5, replicate 1


title: HPNE - Neg. Control #3

value: Negative control


title: Raleigh line 517, stage 2, replicate 2

value: DGRP line 517 (Raleigh, NC)


title: BXSnuc2


title: BXSnuc5


title: adult_S2

description: Drosophila melanogaster, sensitive strain,adult,rep2


title: IUE_PdgfraD482V, DNp53, Control_Rep3_TP38

data_processing:
Sequence reads were aligned to the reference genome using the TopHat aligner (RRID:SCR_013035), and reads aligning to each known transcript were counted using Bioconductor packages for next-generation sequencing data analysis.
Differential gene expression testing was performed using DESeq2.
Normalized counts were subsequently uesd to perform gene set enrichment analysis.
Assembly: hg19
Supplementary files format and content: Gene counts (csv)
Supplementary files format and content: Metadata (txt)

source_name: Mouse brain tumor cells

extract_protocol:
Freshly isolated tumors were snap frozen and total RNA isolated using the NucleoSpin RNA kit. For isolation of polyA RNA, a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, E7490) was used for polyA RNA purification with a total of 1 μg good quality total RNA as input. The SMARTer Apollo NGS Library Prep System (Takara Bio, 640078) was used for automated polyA RNA isolation.
For RNA sequencing library preparation, the library for RNA-seq was prepared by using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7760). After indexing via PCR enrichment (8 cycles), the amplified libraries together with the negative control were cleaned up for quality control analysis. To study differential gene expression, individually indexed and compatible libraries were proportionally pooled (~25 million reads per sample in general) for clustering in the cBot system (Illumina, SY-301-2002). Libraries at the final concentration of 15 pM were clustered onto a single-read flow cell using the TruSeq SR Cluster Kit v3 (Illumina, GD-401-3001), and sequenced to 51 bp using the TruSeq SBS Kit v3 (Illumina, FC-401-3001) on the Illumina HiSeq system.

value: Mouse brain tumor cells

tag: strain

value: CD-1 IGS


title: Raleigh line 360, stage 2, replicate 2

value: embryo


title: HPNE - PPCL68 EV #3


title: HPNE - PPCL68 EV #2


title: Raleigh line 357, stage 5, replicate 3

value: DGRP line 357 (Raleigh, NC)


title: BXSnuc1


title: larva_S2

description: Drosophila melanogaster, sensitive strain, third-instar larve,rep2

value: whole body

value: third-instar larve

value: wild type


title: HPDE c7- Panc1 EV #1

value: PANC-1 Extracellular vesicles


title: HPNE - Neg. Control #2


title: adult_S1

description: Drosophila melanogaster, sensitive strain, adult,rep1

value: adult


title: IUE_PdgfraD482V, DNp53, FOXR2_Rep3_TP35


title: IUE_PdgfraD482V, DNp53, Control_Rep1_TP36


title: Raleigh line 357, stage 5, replicate 2

value: XY


title: BXScyto1

value: induced pluripotent stem cell-derived retinal pigment epithelium

value: cytoplasm


title: larva_S1

description: Drosophila melanogaster, sensitive strain, third-instar larve,rep1


title: Raleigh line 357, stage 5, replicate 1


title: Raleigh line 360, stage 2, replicate 3

value: DGRP line 360 (Raleigh, NC)

value: unknown


title: larva_R3

description: Drosophila melanogaster, resistance strain, third-instar larve,rep3

value: resistance to avermectins


title: HPNE - Neg. Control #1

value: HPNE

value: Normal pancreas cell

value: Negative control


title: IUE_PdgfraD482V, DNp53, FOXR2_Rep2_TP34

value: Mouse brain tumor cells

value: CD-1 IGS


title: HPNE - Control #3

value: Control


title: larva_R2

description: Drosophila melanogaster, resistance strain, third-instar larve,rep2

value: whole body


title: adult_R2

description: Drosophila melanogaster, resistance strain,adult,rep2


title: IUE_PdgfraD482V, DNp53, Control_Rep2_TP37


title: ScpB ChIP DNA of strain BSG1050 (∆parB) repeat 2

city: Ecublens VD

first: Hon-Wing

last: Liu

address: Le Biophore, CH-1015 Lausanne

institute: Université de Lausanne

description:
FD4IPP
APR ChIP2.txt
APR ChIP/WT2.txt

data_processing:
Raw ChIP-seq data pairs (L1/L2) were merged,
ChIP-seq data was trimmed using Trimmomatic-0.39 (SE -phred33, ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Mapped with bowtie2, sorted with samtools
Binning at 1kb.
Obtained .bam files were further imported to SeqMonk for Read Count Quantitation.
Assembly: NC_000964 (1A700)
Supplementary files format and content: Read Count Quantitation and generation of Probe Report in .txt format with SeqMonk (used All Reads, Correct for total read count, Correcct for Milion Reads)

organism: Bacillus subtilis

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated using a Bandelin Sonopuls HD2070.
DNA libraries were prepared by Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–250 bp. DNA libraries were prepared using the Ovation Ultralow Library Systems V2 Kit (NuGEN) including 15 cycles of PCR amplification. 20-30 million sequence reads were obtained on a NovaSeq 6000 system with 150-bp read length

value: 1A700, {delta}parB::kanR, trpC2

tag: chip antibody

value: Eurogentec SK5045 anti-ScpB


title: larva_S3

description: Drosophila melanogaster, sensitive strain, third-instar larve,rep3

value: third-instar larve

value: wild type


title: larva_R1

description: Drosophila melanogaster, resistance strain, third-instar larve,rep1


title: ScpB ChIP DNA of strain BSG5149 (parB(L69S,K70E,E101K)) repeat 2

description:
FD4IPM
APR ChIP2.txt
APR ChIP/WT2.txt

value: 1A700, parB(L69S K70E E101K)::kanR, trpC2


title: HPNE- Panc1 EV #2

value: PANC-1 Extracellular vesicles


title: HPNE - Control #1


title: Raleigh line 357, stage 2, replicate 3

value: DGRP line 357 (Raleigh, NC)

value: embryo


title: IUE_PdgfraD482V, DNp53, FOXR2_Rep1_TP33


title: Raleigh line 360, stage 2, replicate 1

value: DGRP line 360 (Raleigh, NC)

value: unknown


title: ScpB ChIP DNA of strain BSG5149 (parB(L69S,K70E,E101K)) repeat 1

description:
FD3IPM
APR ChIP.txt
APR ChIP/WT.txt


title: ScpB ChIP DNA of strain BSG5146 (WT ParB) repeat 2

description:
FD4IPWT
APR ChIP2.txt
APR ChIP/WT2.txt

value: 1A700, parB(WT)::kanR, trpC2


title: ScpB ChIP DNA of strain BSG1050 (∆parB) repeat 1

description:
FD3IPP
APR ChIP.txt
APR ChIP/WT.txt


title: HPNE- Panc1 EV #3

value: HPNE

value: Normal pancreas cell


title: Raleigh line 307, stage 5, replicate 2

value: DGRP line 307 (Raleigh, NC)

value: XY


title: Raleigh line 357, stage 2, replicate 2


title: Raleigh line 307, stage 5, replicate 1


title: Donor2_post_G-CSF_BM_10X

city: Beijing

first: Guoju

last: You

state: Beijing

address: 30 Shuangqing Street

institute: Tsinghua University

data_processing:
The Cell Ranger software pipeline (version 4.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes, map reads to the human reference genome,and filter data for valid cell barcodes and unique molecular identifiers
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every  cell

source_name: Bone marrow

extract_protocol:
The bone marrow samples were collected by aspiration on the fourth day of G-CSF treatment
RNA libraries were prepared with Chromium Single cell 3' Reagent v2 Kits accoding to the manufacturer's protocol

treatment_protocol: Healthy donors and treated them with recombinant G-CSF  at a dosage of 5μg/kg body weight per day for 5 consecutive days

value: After G-CSF treatment

tag: gender

value: Male

tag: disease state

value: Healthy

value: bone marrow


title: HPNE - Control #2

value: Control


title: HPNE- Panc1 EV #1


title: Donor2_pre_G-CSF_BM_10X

value: before G-CSF treatment


title: Raleigh line 357, stage 2, replicate 1

tag: fly line (origin)

tag: replicate number


title: ES2

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using TopHat (http://tophat.cbcb.umd.edu/, version2.0.0) software.
The mapping criteria of bowtie was as follows: sequencing reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions.
Then the region of gene were expanded following depths of sites and the operon was obtained.
In addition, the whole genome was split into multiple 15kbp windows that share 5kbp. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Endometrial stroma cells

growth_protocol: Endometrial stroma cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM)/F12 (1:1) (Invitrogen, Carlsbad, CA) medium containing 10% fetal bovine serum (FBS) (Gibico, Carlsbad, CA, USA) and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA), and then cells were incubated at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol® reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

value: normal endometrial stromal cells

value: endometrial

value: intramural myoma


title: NS3

value: adenomyotic eutopic endometrial stromal cells

value: Adenomyosis


title: △s77 strain cultured in DMEM medium

first: Bin

address: Hai Dian

department: School of Life Sciences

data_processing:
Raw data was performed bowtie2 in python2 environment
samtool was used to view and sort data
Sorted data was uploaded to galaxy online platform
reads number was counted by feature count and RPKM value was caculated
binomial test was performed in R studio
Genome_build: AE005174
Supplementary_files_format_and_content: All our processed data were listed in an excel file which includes two parts. One part only focuses on s77 locus and we use o157_LB.fastq and o157_in_vivo.fastq raw file to count. Another part is the differentially expressed genes between s77 deletion and o157 wild-type strains in DMEM medium and we use o157_DMEM.fastq and o157_s77.mutant_DMEM.fastq raw file to count.

organism: Escherichia coli O157:H7

source_name: DMEM cultured

growth_protocol: The DMEM cultured o157 WT and △s77 strain, and in vivo samples were grown under certain conditions

extract_protocol:
Total RNAs were extracted from three biological replicates, respectively.
Library construction of RNA samples was carried out using a NEBNext R UltraTM Directional RNA Library Prep Kit for Illumina R (NEB, USA), following the manufacturer’s recommendations.

tag: genotype/variation

tag: culture condition

value: DMEM cultured


title: Donor1_post_G-CSF_BM_10X

tag: tissue


title: Donor1_pre_G-CSF_BM_10X


title: Raleigh line 307, stage 5, replicate 3

value: embryo

tag: embryo sex

tag: Stage


title: Input DNA of strain BSG1050 (∆parB)

description:
FD3NP
APR Inp.txt
APR Inp/WT.txt

value: 1A700, {delta}parB::kanR, trpC2

value: Eurogentec SK5045 anti-ScpB


title: Raleigh line 307, stage 2, replicate 3

value: DGRP line 307 (Raleigh, NC)

value: unknown


title: o157 strain cultured in DMEM medium

value: wild type


title: ScpB ChIP DNA of strain BSG5146 (WT ParB) repeat 1

description:
FD3IPWT
APR ChIP.txt
APR ChIP/WT.txt

value: 1A700, parB(WT)::kanR, trpC2


title: NS2

tag: cell type


title: ES1


title: NS1


title: ES3


title: Raleigh line 307, stage 2, replicate 2


title: o157 strain in mice

source_name: mice colon colonized

value: mice colon colonized


title: Raleigh line 307, stage 2, replicate 1


title: Input DNA of strain BSG5149 (parB(L69S,K70E,E101K))

description:
FD3NM
APR Inp.txt
APR Inp/WT.txt

value: 1A700, parB(L69S K70E E101K)::kanR, trpC2


title: Healthy Donor B - Timepoint 3 (HD2_S7)

status: Public on Jun 22 2022

first: Livius

last: Penter

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Targeted TCR sequencing
HD2_3_TCRalpha.xlsx
HD2_3_TCRbeta.xlsx
See Processed_data_files.tar.gz

data_processing:
Demultiplexing of raw sequencing data
Separation of TCR alpha and beta reads using BLAST
Assembly and annotation of reads using MiXCR
Quality control and error correction
Quantification of T cell clonotypes
Assembly: GRCh38
Supplementary files format and content: Excel files include T cell clonotype count values for each Sample
Library strategy: TCR-seq

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from 5 x 10^6 PBMCs using the RNeasy Mini Kit (Qiagen)
Libraries were constructed using RNase H-dependent T-cell receptor sequencing with 40 ng input for each reaction in 4 replicates (PMID 31341290)
rhTCRseq

value: peripheral blood

value: T cells

tag: treatment

tag: time

value: Timepoint 3


title: Healthy Donor B - Timepoint 4 (HD2_S64)

description:
Targeted TCR sequencing
HD2_4_TCRalpha.xlsx
HD2_4_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Timepoint 4


title: Healthy Donor B - Timepoint 4 (HD2_S48)


title: Healthy Donor B - Timepoint 4 (HD2_S24)


title: Healthy Donor B - Timepoint 3 (HD2_S63)


title: Healthy Donor B - Timepoint 4 (HD2_S40)


title: Healthy Donor B - Timepoint 3 (HD2_S31)


title: Healthy Donor B - Timepoint 3 (HD2_S15)


title: Healthy Donor B - Timepoint 4 (HD2_S16)


title: Healthy Donor B - Timepoint 3 (HD2_S39)


title: Healthy Donor B - Timepoint 2 (HD2_S38)

description:
Targeted TCR sequencing
HD2_2_TCRalpha.xlsx
HD2_2_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Timepoint 2


title: Healthy Donor B - Timepoint 2 (HD2_S46)


title: Healthy Donor B - Timepoint 2 (HD2_S6)


title: Healthy Donor B - Timepoint 3 (HD2_S47)


title: Healthy Donor B - Timepoint 4 (HD2_S8)


title: Healthy Donor B - Timepoint 4 (HD2_S56)


title: Healthy Donor B - Timepoint 4 (HD2_S32)


title: Healthy Donor B - Timepoint 2 (HD2_S54)


title: Healthy Donor B - Timepoint 2 (HD2_S14)


title: Healthy Donor B - Timepoint 3 (HD2_S55)


title: Healthy Donor B - Timepoint 2 (HD2_S62)


title: Healthy Donor B - Timepoint 1 (HD2_S61)

description:
Targeted TCR sequencing
HD2_1_TCRalpha.xlsx
HD2_1_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Timepoint 1


title: Healthy Donor B - Timepoint 2 (HD2_S22)


title: o157 strain cultured in LB medium

source_name: LB cultured

value: LB cultured


title: Healthy Donor B - Timepoint 3 (HD2_S23)


title: Healthy Donor B - Timepoint 2 (HD2_S30)


title: Input DNA of strain BSG5146 (WT ParB)

description:
FD3NWT
APR Inp.txt
APR Inp/WT.txt

tag: genotype


title: Healthy Donor A - Timepoint 4 (HD1_S52)

description:
Targeted TCR sequencing
HD1_4_TCRalpha.xlsx
HD1_4_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Healthy Donor A - Timepoint 4 (HD1_S36)


title: Healthy Donor B - Timepoint 1 (HD2_S37)


title: Healthy Donor B - Timepoint 1 (HD2_S45)


title: Healthy Donor B - Timepoint 1 (HD2_S53)


title: Healthy Donor A - Timepoint 4 (HD1_S4)


title: Healthy Donor A - Timepoint 4 (HD1_S60)


title: Healthy Donor B - Timepoint 1 (HD2_S29)


title: Healthy Donor B - Timepoint 1 (HD2_S21)


title: Healthy Donor A - Timepoint 4 (HD1_S44)


title: Healthy Donor B - Timepoint 1 (HD2_S5)


title: Healthy Donor A - Timepoint 3 (HD1_S43)

description:
Targeted TCR sequencing
HD1_3_TCRalpha.xlsx
HD1_3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Healthy Donor A - Timepoint 4 (HD1_S28)


title: Healthy Donor A - Timepoint 3 (HD1_S51)


title: Healthy Donor A - Timepoint 3 (HD1_S19)


title: Healthy Donor A - Timepoint 4 (HD1_S12)


title: Healthy Donor A - Timepoint 4 (HD1_S20)


title: Healthy Donor A - Timepoint 3 (HD1_S35)


title: Healthy Donor A - Timepoint 3 (HD1_S3)


title: Healthy Donor A - Timepoint 2 (HD1_S42)

description:
Targeted TCR sequencing
HD1_2_TCRalpha.xlsx
HD1_2_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Healthy Donor A - Timepoint 2 (HD1_S34)


title: Healthy Donor A - Timepoint 2 (HD1_S58)


title: Healthy Donor A - Timepoint 3 (HD1_S11)


title: Healthy Donor A - Timepoint 2 (HD1_S2)


title: Healthy Donor B - Timepoint 1 (HD2_S13)


title: Healthy Donor A - Timepoint 2 (HD1_S50)


title: Healthy Donor A - Timepoint 2 (HD1_S18)


title: Healthy Donor A - Timepoint 2 (HD1_S26)


title: Healthy Donor A - Timepoint 2 (HD1_S10)


title: Healthy Donor A - Timepoint 1 (HD1_S57)

description:
Targeted TCR sequencing
HD1_1_TCRalpha.xlsx
HD1_1_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Healthy Donor A - Timepoint 1 (HD1_S41)


title: Healthy Donor A - Timepoint 3 (HD1_S59)


title: Healthy Donor A - Timepoint 1 (HD1_S49)


title: Healthy Donor A - Timepoint 1 (HD1_S33)


title: Healthy Donor A - Timepoint 1 (HD1_S25)


title: Healthy Donor A - Timepoint 1 (HD1_S1)


title: Patient E - C3 after surgery (BOB41018WB_S58)

description:
Targeted TCR sequencing
PatientE_C3_TCRalpha.xlsx
PatientE_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: SOC chemotherapy and surgery

value: After 3 cycles and surgery


title: Healthy Donor A - Timepoint 1 (HD1_S17)


title: Patient E - C3 after surgery (BOB41018WB_S42)


title: Healthy Donor A - Timepoint 3 (HD1_S27)


title: Patient E - C3 after surgery (BOB41018WB_S26)


title: Patient E - C3 after surgery (BOB41018WB_S10)


title: Patient E - Baseline (BOB40559WB_S9)

description:
Targeted TCR sequencing
PatientE_Baseline_TCRalpha.xlsx
PatientE_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: SOC chemotherapy

value: Before therapy


title: Patient E - Baseline (BOB40559WB_S25)


title: Patient D - C3 after surgery (BOB40561WB_S56)

description:
Targeted TCR sequencing
PatientD_C3_TCRalpha.xlsx
PatientD_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient D - C3 after surgery (BOB40561WB_S8)


title: Patient D - Baseline (BOB40560WB_S7)

description:
Targeted TCR sequencing
PatientD_Baseline_TCRalpha.xlsx
PatientD_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient D - C3 after surgery (BOB40561WB_S24)


title: Healthy Donor A - Timepoint 1 (HD1_S9)