title: BIN67_AFOS_BRG1_DOX_RNAseq_Rep2

department: Pathology and Laboratory Medicine

description:
BIN67 pIND20-FLAG-A-FOS cells, BRG1 Transfected, Control Treatment (+DOX)
BIN67_AFOS_RNAseq_raw_gene_counts.txt

data_processing:
Fastq files were initially analyzed by fastqc (v0.11.5). Reads were aligned with STAR (v2.5.3a) to GENCODE v24 (hg38) using the 2-pass method.  Aligned reads were quantified by salmon (v0.8.2) for transcripts per million (TPM) counts. TPMs were summarized to gene level using tximport (v1.10.1) in R. Differentially expressed genes (+/- BRG1, +/-DOX) samples using DESeq2 (v1.22.2).
IGV browser tracks (bigwig) were generated on the merged biological replicates by deeptools (v3.2.) bamCoverage with a binsize of 30 and normalized using RPKMs.
Genome_build: hg38 (GENCODE v24)
Supplementary_files_format_and_content: raw counts = raw unnormalized counts summarized to gene level using tximport (countsFromAbundance = "no"). Matrix input for DESeq2 differential expression analysis
Supplementary_files_format_and_content: DESeq2 Results = excel file of DESeq2 results

source_name: Cell Line

growth_protocol: A lentivirus construct containing pINDUCER20-Flag-A-FOS was generated as previously described (Abd S et al (2018) Oncotarget).  BIN67 pIND20-A-FOS cell lines were generated by lentiviral infection and subsequent selection in G418 containing medium (10% TET-FREE FBS  + 800 µg/ml G418,  RPMI-1640) to create mass populations.

extract_protocol:
RNA from frozen cell pellets was extracted using the Zymo Quick-RNA Miniprep Kit (Zymo cat# R1054).
Standard library preparation and sequencng was performed by Novogene (Novogene Corporation Inc, Sacramento, CA)

treatment_protocol: BIN67 pINDUCER20-FLAG-A-FOS cells incuded with 1 µg/µl of doxycycline (DOX) daily with media change for 48 hours prior to transfections. Cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then cell pellet were harvested for RNA-seq analysis. Cell pells were flash frozen and stored at -80°C until total RNA extraction. Standard library preparation and sequencng was performed by Novogene (Novogene Corporation Inc, Sacramento, CA)

tag: cell line

value: BIN67 pINDUCER20-FLAG-A-FOS

tag: transfected vector

value: DOX


title: dnmt3b_rep1

status: Public on Dec 30 2020

type: SRA

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

country: Israel

institute: Tel Aviv University

library_source: transcriptomic

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample

molecule: total RNA

organism: Physcomitrium patens

source_name: protonema

growth_protocol: 7 days on BCDAT media, 25 °C,  16-h light and 8-h dark regime

extract_protocol:
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

tag: genotype

tag: cultivar

value: Grandsen

tag: age

value: 7 days


title: Bone marrow, treated, patient 5 rep 2

type: RNA

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

hyb_protocol: Hybridization was performed according to specifications in One-Color Microarray-Based Gene Expression Analysis Protocol

scan_protocol: The data was extracted using Agilent Feature Extraction Software version 10.7.3.1 with default parameters of protocol GE1_107_Sep09.

data_processing: Data preprocessing was performed using R/Bioconductor (version 3.6)  limma (version 3.34.9) package. Briefly, raw Feature Extractor data was loaded into R and further background corrected (method=”minimum”), normalized (method=”quantile”) and filtered to remove control probes.

organism: Homo sapiens

source_name: BONE MARROW

label_protocol: Labelling was performed with the one color (Cyanine 3-CTP) Low Input Quick Amp Labeling Kit (Agilent Technologies) accordinf to manufacturer protocol.

growth_protocol: Cells were kept in culture in DMEM medium supplemented with 10% FCS.

extract_protocol: RNA was extracted using RNeasy Micro Kit - QIAGEN following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: Cells were analyzed either resting either after 16 hours stimulation with IFNg and TNFa.

tag: cell type

value: mesenchymal stem cell line

tag: treatment

value: IFNG+TNFA

tag: tissue

value: BONE MARROW

tag: patient

tag: ChIP


title: BIN67_AFOS_BRG1_CTRL_RNAseq_Rep2

city: Chapel Hill

first: Bernard

middle: E.

last: Weissman

state: NC

address: 450 West Drive

country: USA

institute: University of North Carolina at Chapel Hill

description:
BIN67 pIND20-FLAG-A-FOS cells, BRG1 Transfected, Control Treatment (-DOX)
BIN67_AFOS_RNAseq_raw_gene_counts.txt

value: Control


title: EMandNP water microbial gene2

type: genomic

city: Guangzhou

first: Lijuan

last: Ren

address: 601 Huangpu Avenue West, Guangzhou, China

country: China

institute: JinanUniversity

description:
sample in warming and nutrient-enriched mesocosms
G3

hyb_protocol: The dried and labeled DNA was resuspended in 42 μl hybridization solution, which included 1 × HI-RPM hybridization buffer, 1 × a CGH blocking agent, 0.05 μg.μl-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). Hybridizations were performed at 67°C for 24 h with a rotation of 20 rpm in a hybridization oven.

scan_protocol: The scanned images of hybridized GeoChips were converted and extracted by using Agilent Feature Extraction 11.5 software (Agilent Technologies, Inc., CA, USA)

data_processing: Raw data were uploaded to the microarray analysis pipeline (http://ieg.ou.edu/microarray/). In brief, the following steps were performed: (i) spots with a signal to noise ratio (SNR) less than 2 were removed due to poor quality; (ii) for each sample, intensities plus 1 were transformed to logarithm and divided by mean signal intensity.

molecule: genomic DNA

organism: uncultured soil microorganism

source_name: water

label_protocol: DNA (500 ng) was labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) by random priming.

extract_protocol: The whole microbial DNA was extracted and puriﬁed using the Wizard DNA clean-up kit.

treatment_protocol: In our study, we selected 16 fully mixed, outdoor, flow-through mesocosms combining two temperature scenarios (ambient temperature and warming scenario simulating the IPCC A2 + 50% with temperatures 4–5 °C higher than the ambient) and two nutrient levels with four replicates.

value: warming and nutrients


title: HNSCC, treated, patient 3 rep 2

source_name: HNSCC

value: mesenchymal stromal cells

value: HNSCC


title: BIN67_AFOS_BRG1_CTRL_RNAseq_Rep1


title: HNSCC, treated, patient 3 rep 1


title: cmt_rep3

value: cmt


title: drm12_rep3


title: EMandNP water microbial gene4

description:
sample in warming and nutrient-enriched mesocosms
H3


title: BIN67_AFOS_PCDNA3_DOX_RNAseq_Rep2

description:
BIN67 pIND20-FLAG-A-FOS cells, Control Transfected, Control Treatment (+DOX)
BIN67_AFOS_RNAseq_raw_gene_counts.txt


title: EMandNP water microbial gene1

description:
sample in warming and nutrient-enriched mesocosms
G1


title: Bone marrow, treated, patient 4 rep 1


title: EMandNP water microbial gene3

description:
sample in warming and nutrient-enriched mesocosms
H1


title: NP water microbial gene4

description:
sample in nutrient-enriched mesocosms
F3

value: nutrient enrichment


title: HNSCC, treated, patient 2 rep 2


title: HNSCC, treated, patient 2 rep1


title: HNSCC, treated, patient 1 rep2


title: NP water microbial gene2

description:
sample in nutrient-enriched mesocosms
E3


title: BIN67_AFOS_BRG1_DOX_RNAseq_Rep1


title: HNSCC, treated, patient 1 rep1


title: EM water microbial gene4

description:
sample in warming mesocosms
D3

value: warming


title: NP water microbial gene1

description:
sample in nutrient-enriched mesocosms
E1


title: NP water microbial gene3

description:
sample in nutrient-enriched mesocosms
F1


title: dnmt3b_rep2


title: Bone marrow, untreated, patient 4 rep 2


title: wt rep3

value: wt


title: Bone marrow, untreated, patient 4 rep 1


title: BIN67_AFOS_PCDNA3_DOX_RNAseq_Rep1


title: BIN67_AFOS_PCDNA3_CTRL_RNAseq_Rep2

description:
BIN67 pIND20-FLAG-A-FOS cells, Control Transfected, Control Treatment (-DOX)
BIN67_AFOS_RNAseq_raw_gene_counts.txt


title: EM water microbial gene2

description:
sample in warming mesocosms
C3


title: EM water microbial gene3

description:
sample in warming mesocosms
D1


title: BIN67_AFOS_PCDNA3_CTRL_RNAseq_Rep1


title: D1_2

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Data were analyzed using Cell Ranger™ v3.0.2 pipeline which is available in 10xGenomics website.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

source_name: Bone marrow aspirate

extract_protocol:
Unselected Bone Marrow cells were collected at baseline and relapse by Bone Marrow biopsy, purified with Ficoll and washed twice with 0.04% PBS-BSA.
Cells were loaded in the 10X Genomics Chromium at a concentration of 700 cells/µl with the aim of recovering 8,000 cells. Libraries were generated with the Chromium Single Cell 3’ Reagents Kit v2 or v3 Chemistry.
Chromium single cell 3´ v2 or v3 (10XGenomics)

value: Bone marrow aspirate

tag: disease state

value: relapsed-refractory Multiple Myeloma and extramedullary disease

value: after BCMA CAR-T cell infusion


title: F2-U: Mutant untreated

city: New Delhi

first: Sneh

middle: Lata

last: Panwar

state: Delhi

address: Lab No 106, School of life science, JNU New campus New Delhi

department: Life sciences

country: India

institute: Jawaharlal Nehru University New Delhi

description: Gene expression after 5 hours

hyb_protocol: The  labeled cRNA sample was fragmented at 60 º C and hybridized on to a Genotypic designed Candida albicans Microarray Geneexpression 8X15k arrays(AMADID No: 26377) .Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction software Version 11.5.1.1 of Agilent. Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Candida albicans

source_name: Cellular extract, 5 hrs

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps was carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight grown primary culture in YEPD media at 30ºC and 220 rpm sub-cultured into fresh YEPD media with starting O.D of 0.3. Cells were harvested after 5 hours.

extract_protocol: Total RNA, isolated using the RNeasymini kit (Qiagen), was treated with DNase I (Thermo Scientific) to remove contaminating DNA according to the manufacturer’s protocol.

treatment_protocol: No drug treatment

value: Candida albicans primary culture

tag: genotype/variation

value: IRE1 mutant


title: G2

value: before BCMA CAR-T cell infusion


title: F1-U: Mutant untreated

description: Gene expression after 5 hours


title: A1-U1: Wild type untreated

description: Gene expression after 5 hours

value: Wild type


title: EM water microbial gene1

description:
sample in warming mesocosms
C1


title: control water microbial gene4

description:
sample in control mesocosms
B3

value: control


title: control water microbial gene3

description:
sample in control mesocosms
B1


title: HNSCC, untreated, patient 2 rep1


title: SCLC_20_ca

status: Public on Dec 29 2020

city: Dallas

first: Ling

last: Cai

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center at Dallas

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: CEL files were read into an AffyBatch object by AffyBatch function under the affy R package, alternative cdf package hgu133plus2hsentrezg was downloaded from http://mbni.org/customcdf/21.0.0/entrezg.download/hgu133plus2hsentrezg.db_21.0.0.zip and was specified in the function so that the resulting expression data was processed to gene level rather than the original probe level. (Probe name follows format concatenating Entrez ID for the gene and _at. For example 3939_at corresponds to gene LDHA). The AffyBatch object was then converted to an expression set using robust multi-array average (RMA) expression measure by running the rma function under R package affy. Quantile normalization was performed by running normalize.quantiles function from R package preprocessCore

label: biotin

source_name: tumor

label_protocol: Not provided

extract_protocol: Not provided

value: small cell lung cancer tumor

tag: gender

value: M

value: Never

tag: neoadjuvant

value: NO


title: SCLC_18_ca

value: Ever


title: HNSCC, untreated, patient 2 rep 2

value: mesenchymal stromal cells

value: HNSCC


title: control water microbial gene1

description:
sample in control mesocosms
A1


title: A2-U1: Wild type untreated

description: Gene expression after 5 hours


title: SCLC_20_n

source_name: normal

value: adjacent lung


title: HNSCC, untreated, patient 1 rep1


title: HNSCC, untreated, patient 3 rep 2


title: HNSCC, untreated, patient 1 rep2


title: HNSCC, untreated, patient 3 rep 1


title: SCLC_16_n

value: YES


title: SCLC_13_n


title: SCLC_16_ca


title: control water microbial gene2

description:
sample in control mesocosms
A3


title: SCLC_15_ca


title: SCLC_15_n


title: SCLC_13_ca


title: SCLC_19_ca


title: SCLC_19_n


title: SCLC_11_n

value: F


title: SCLC_11_ca


title: SCLC_18_n


title: SCLC_14_ca


title: SCLC_10_ca


title: SCLC_14_n


title: SCLC_09_n


title: SCLC_09_ca


title: SCLC_08_ca


title: SCLC_07_ca


title: SCLC_02_n


title: SCLC_05_n


title: SCLC_03_n


title: SCLC_04_ca


title: HES2 SHMTA2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from GENERGY BIO company. 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 of GENERGY BIO.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HES2 human  embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina X ten was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: transfection


title: HES2 Scramble

source_name: HES2 human embryonic stem cells

value: scramble


title: cochlear_tissue_Cx30-/-_mice_rep3 [miRNA]

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

institute: IRIB-CNR

description:
SAMPLE 3_D10
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30-/- mice.

hyb_protocol: Purified labeled and dried RNA samples was resuspended in nuclease-free water, and then mixed with the 3rd dilution of Hyb Spike-In controls solution, blocking agent and hybridization buffer, reaching a final volume of 45ml each. The entire amount for each sample was dispensed into the center of a gasket well of Mouse miRNA Microarrays v.21.0, 8x60K (Agilent Technologies), according to the miRNA Complete Labeling and Hyb Kit Protocol (Version 3.1.1, August 2015). Once all samples were applied to the gasket slide, the chamber cover was clamped in place. The assembled slide cassette was placed into the hybridization oven and hybridized for 20 hrs at 55°C at 20 rpm. Disassembling washing step was carried out using the gene expression wash buffer 1 at room temperature, followed by the 1st wash using gene expression wash buffer 1 for 5 minutes at room temperature and the 2nd wash using gene expression wash buffer 2 for 5 minutes at 37°C.

scan_protocol: The microarrays were scanned at 3 μm resolution using a SureScan Microarray Scanner System (Agilent Technologies). The Feature Extraction Software v. 11.5.1.1 (Agilent Technologies) was used for acquisition, data extraction and quality control analysis. After the evaluation of quality control parameters for each scanned microarray images, the raw data of three replicates for wild-type and four replicates for knock-out experimental conditions were further analyzed.

data_processing: GeneSpring GX v.14.5 software (Agilent Technologies) was used to carry out data analysis, by which fluorescence signal values were thresholded to 1, log2 transformed and normalized using the 90th percentile shift method. Then, the resulting data were baselined to the median of all samples and quality-filtered on flags to include any probe detected in 100% of biological replicates in at least one out of two of tested experimental conditions. Significantly deregulated miRNAs across experimental conditions were identified using a moderate t-test followed by Benjamini-Hochberg multiple testing correction to minimize false positive cases.

organism: Mus musculus

label_protocol: A concentration of 100 ng from each sample was Cyanine-3 (Cy3) labeled using the Agilent miRNA Complete Labeling and Hybridization kit. In particular, the labeling protocol consists of a phosphatate treatment using calf phosphatase and spike-in controls, followed by sample denaturation using DMSO and Cy-3 ligation steps. Labeled RNA was then purified by spin-columns and dried through a vacuum concentrator before to proceed with hybridization phase, according to the miRNA Complete Labeling and Hyb Kit Protocol (Version 3.1.1, August 2015).

growth_protocol: A combination of three different primers was used to identify the Cx30 interruption due to LacZ insertion in Cx30-/-mice: Cx30F: 5’-GGTACCTTCTACTAATTAGCTTGG-3’, Cx30R: 5’-AGGTGGTACCCATTGTAGAGGAAG-3’, Cx30lacZ: 5’-AGCGAGTAACAACCCGTCGGATTC-3’. Mice were maintained on a pure C57BL/6N background. All experimental protocols were carried out in accordance with the relevant guidelines and regulations and approved by the Ethical Committee of Padua University and by the Italian Ministry of Health.

extract_protocol: Total RNA including miRNAs was extracted from mice cochlear tissue (at post-natal day 5) using Absolutely RNA Miniprep Kit (Agilent Technologies), according to manufacturer’s instructions. To detect possible contaminants, the ratios of absorbance were assessed at 260/280 nm and 260/230 nm using the NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific). The quality of the RNA was evaluated with Agilent 2100 Bioanalyzer microfluidic electrophoresis platform, using the Small RNA assay for miRNAs, following the manufacturer's specifications. All samples passed the quality evaluation and were processed for profiling experiments.

value: cochlear tissue

value: Post-natal day 5


title: cochlear_tissue_Cx30_Wild_Type_mice_rep4 [miRNA]

description:
SAMPLE 7_D12
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30 Wild Type mice.

value: Cx30 Wild Type


title: cochlear_tissue_Cx30_Wild_Type_mice_rep2 [miRNA]

description:
SAMPLE 5_D3
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30 Wild Type mice.


title: cochlear_tissue_Cx30_Wild_Type_mice_rep3 [miRNA]

description:
SAMPLE 6_D9
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30 Wild Type mice.


title: cochlear_tissue_Cx30-/-_mice_rep4 [miRNA]

description:
SAMPLE 4_D11
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30-/- mice.


title: SCLC_02_ca


title: SCLC_05_ca


title: SCLC_01_ca


title: SCLC_04_n


title: SCLC_08_n


title: cochlear_tissue_Cx30-/-_mice_rep2 [miRNA]

description:
SAMPLE 2_D1
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30-/- mice.


title: SCLC_07_n


title: SCLC_06_n


title: SCLC_03_ca


title: cochlear_tissue_Cx30-/-_mice_rep1 [miRNA]

description:
SAMPLE 1_C3
total RNA_micro RNA
microRNA profiling at P5 in cochlear tissue of Cx30-/- mice.


title: SCLC_06_ca


title: Liver_AAV-V HFD_12 months_rep2

city: Beijing

first: Luming

last: Wan

address: Dongda Street No.20

institute: Beijing Institute of Biotechnology

description: Gene expression of AAV-V and HFD treated mouse liver after 12 months-2

hyb_protocol: Each slide was hybridized with 1.65μg/600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit/3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Liver, 12 months, AAV-V HFD, replicate2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted from 50mg tissue sample using 1 mL Trizol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. After tissue homogenate, samples were incubated for 5 min at 15 - 30 °C. 200 μL chloroform was added into these tubes. The mixture was shaken vigorously by hand for 15 sec and incubated for 3 min at 15 - 30 °C. Next, the sample was centrifuged at 12,000 ×g for 15 min at 4 °C. The upper aqueous phase was transferred to a new tube and 500 μL isopropanol was added to the supernatant. After mixing and incubating at 15-30 °C for 10 min, the mixture was centrifuged at 12,000 ×g for 10 min at 4 °C. The RNA pellet was washed with 1 mL ethanol (75%) after removal of the supernatant. Then, the samples were subjected to vortex mixing and centrifugation at 7500 ×g for 5 min at 4 °C. The pellet was dissolved in RNase-free water and incubated at 55-60 °C for 10 min.

treatment_protocol: All the tissues were immediately frozen in liquid nitrogen and stored at - 80 °C until used.

value: liver

value: male

tag: diet

value: high fat diet

value: AAV-V

value: 12 months


title: SCLC_01_n

value: M


title: Liver_AAV-V HFD_12 months_rep3

description: Gene expression of AAV-V and HFD treated mouse liver after 12 months-3

source_name: Liver, 12 months, AAV-V HFD, replicate3


title: Liver_AAV-V HFD_12 months_rep1

description: Gene expression of AAV-V and HFD treated mouse liver after 12 months-1

source_name: Liver, 12 months, AAV-V HFD, replicate1


title: Liver_AAV-GP73_12 months_rep2

description: Gene expression of AAV-GP73 treated mouse liver after 12 months-2

source_name: Liver, 12 months, AAV-GP73, replicate2

value: normal diet


title: Lfng_rep3 [Cell_543]

city: Palo Alto

first: Marie

last: Kubota

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Genome_build: mm10 (GECm38)
Supplementary_files_format_and_content: text file with raw read counts

extract_protocol:
Cochlear ducts were dissected from two-day-old mice. The spiral ligament and the stria vascularis were removed. The sample was washed twice in PBS and incubated in 0.25% Trypsin-EDTA at 37°C and 5% CO2 for 10 min. After adding soybean trypsin inhibitor and DNAseI, the sample was mechanically dissociated and passed through a 70 µm strainer to remove aggregates.
SmartSeq2 protocol

tag: strain

value: Lfng-GFP

value: Postnatal day2

value: Cochlear Sensory Epithelium

tag: gate

tag: plate number

tag: plate position


title: Zfp541+/-_1

city: Chuo-ku

first: Kei-ichiro

last: Ishiguro

state: Kumamoto

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto university

description: Rec8-3xFLAG-HA-p2A-GFP knock-in background

data_processing:
The sequence reads were aligned to the mouse genome UCSC mm10 using using STAR ver.2.6.0a after trimmed to remove adapter sequence and low-quality ends using Trim Galore! v0.5.0 (cutadapt v1.16) 6 -M)
TPM was calculated by using RSEM v1.3.1.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: TPMs

source_name: male germ cells

growth_protocol: The meiotic prophase-enriched population was isolated from Zfp541 +/-  and Zfp541 KO testes at postnatal day 18 (P18), on the Rec8-3FH-GFP KI background by fluorescent sorting of GFP positive cells.

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher)
RNA-seq libraries were prepared according to the the Illumina Truseq protocol using Truseq Standard mRNA LT Sample Prep Kit

value: C57BL/6 and CBA mixed

tag: developmental stage

value: postnatal day 18 (P18)

value: testis

tag: genotype


title: Zfp541+/-_2


title: Lfng_rep3 [Cell_542]

tag: age


title: Liver_AAV-GP73_12 months_rep3

description: Gene expression of AAV-GP73 treated mouse liver after 12 months-3

source_name: Liver, 12 months, AAV-GP73, replicate3

tag: treatment


title: Liver_AAV-V_12 months_rep2

description: Gene expression of AAV-V treated mouse liver after 12 months-2

source_name: Liver, 12 months, AAV-V, replicate2

tag: tissue


title: Liver_AAV-GP73_12 months_rep1

description: Gene expression of AAV-GP73 treated mouse liver after 12 months-1

source_name: Liver, 12 months, AAV-GP73, replicate1


title: Zfp541KO_2


title: Lfng_rep3 [Cell_539]


title: Lfng_rep3 [Cell_540]


title: Zfp541KO_1


title: Lfng_rep3 [Cell_545]


title: Lfng_rep3 [Cell_544]


title: Lfng_rep3 [Cell_535]


title: cochlear_tissue_Cx30_Wild_Type_mice_rep4 [mRNA]

description:
SAMPLE 8_D12
Gene expression at P5 in cochlear tissue of Cx30 Wild Type mice.

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented in a reaction volume of 250 ml containing fragmentation buffer and blocking agent, following the manufacturer's instructions. On completion of fragmentation step, the hybridization buffer was added to the fragmentation mixture and 40 ul of each sample were then hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809). The assembled slide cassette was placed into the hybridization oven and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. Disassembling washing step was carried out using the gene expression wash buffer 1 at room temperature, followed by the 1st wash using gene expression wash buffer 1 for 1 minute at room temperature and the 2nd wash using gene expression wash buffer 2 for 1 minute at 37°C.

scan_protocol: The microarrays were scanned at 3 μm resolution using a SureScan Microarray Scanner System (Agilent Technologies). The scanned images were analyzed with Feature Extraction Software v. 11.5.1.1 (Agilent Technologies) for acquisition, data extraction and quality control analysis. After the evaluation of quality control parameters for each scanned microarray images, the raw data of all samples were further analyzed.

data_processing: GeneSpring GX v.14.5 software (Agilent Technologies) was used to carry out data analysis. Fluorescence signal values were thresholded to 1, log2 transformed, normalized to the 75th percentile, baselined to the median of all samples, and quality-filtered on flags to include any probe detected in 100% of biological replicates in at least one out of two of tested experimental conditions. In order to identify differentially expressed genes (DEGs) between knock-out relative to wild-type, a moderate T-test was performed, followed by Westfall-Young multiple testing correction procedure, and adjusted p-values < 0.05 were used as criteria for defining a set of deregulated candidate genes for further exploration.

label_protocol: Messenger RNA was cyanine-3 (Cy3) labeled starting from 100 ng of total RNA of each sample using the One-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labeling kit protocol (Version 6.9.1, December 2015), according to the manufacturer's instructions. This kit generates fluorescent cRNA from cDNA, by means of T7 RNA Polymerase Blend that simultaneously amplifies target material and incorporates Cy-3. Subsequently, labeled amplified cRNA purification was carried out using RNeasy mini kit (Qiagen) before to be quantified by Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific) to determine yield and specific activity.

extract_protocol: Total RNA including miRNAs was extracted from mice cochlear tissue (at post-natal day 5) using Absolutely RNA Miniprep Kit (cat number #400800, Agilent Technologies, Santa Clara, CA, USA), according to manufacturer’s instructions. To detect possible contaminants, the ratios of absorbance were assessed at 260/280 nm and 260/230 nm using the NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific). The quality of the RNA was evaluated with Agilent 2100 Bioanalyzer microfluidic electrophoresis platform, using the Small RNA assay for miRNAs, following the manufacturer's specifications. All samples passed the quality evaluation and were processed for profiling experiments.


title: cochlear_tissue_Cx30_Wild_Type_mice_rep1 [mRNA]

description:
SAMPLE 5_C1
Gene expression at P5 in cochlear tissue of Cx30 Wild Type mice.


title: Lfng_rep3 [Cell_538]


title: cochlear_tissue_Cx30_Wild_Type_mice_rep2 [mRNA]

description:
SAMPLE 7_D3
Gene expression at P5 in cochlear tissue of Cx30 Wild Type mice.


title: Lfng_rep3 [Cell_534]


title: cochlear_tissue_Cx30-/-_mice_rep3 [mRNA]

description:
SAMPLE 2_D10
Gene expression at P5 in cochlear tissue of Cx30-/- mice.


title: cochlear_tissue_Cx30-/-_mice_rep2 [mRNA]

description:
SAMPLE 3_D1
Gene expression at P5 in cochlear tissue of Cx30-/- mice.


title: cochlear_tissue_Cx30-/-_mice_rep1 [mRNA]

description:
SAMPLE 1_C3
Gene expression at P5 in cochlear tissue of Cx30-/- mice.


title: cochlear_tissue_Cx30_Wild_Type_mice_rep3 [mRNA]

description:
SAMPLE 6_D9
Gene expression at P5 in cochlear tissue of Cx30 Wild Type mice.


title: cochlear_tissue_Cx30-/-_mice_rep4 [mRNA]

description:
SAMPLE 4_D11
Gene expression at P5 in cochlear tissue of Cx30-/- mice.


title: Liver_AAV-V_12 months_rep1

description: Gene expression of AAV-V treated mouse liver after 12 months-1

source_name: Liver, 12 months, AAV-V, replicate1


title: Liver_AAV-V_12 months_rep3

description: Gene expression of AAV-V treated mouse liver after 12 months-3

source_name: Liver, 12 months, AAV-V, replicate3


title: Lfng_rep3 [Cell_536]


title: Lfng_rep3 [Cell_537]


title: Lfng_rep3 [Cell_541]


title: Lfng_rep3 [Cell_531]


title: Lfng_rep3 [Cell_533]


title: Lfng_rep3 [Cell_532]


title: Lfng_rep3 [Cell_530]


title: Lfng_rep3 [Cell_524]


title: Lfng_rep3 [Cell_527]


title: Lfng_rep3 [Cell_529]


title: Lfng_rep3 [Cell_523]


title: Lfng_rep3 [Cell_528]


title: Lfng_rep3 [Cell_525]


title: Lfng_rep3 [Cell_526]


title: Lfng_rep3 [Cell_520]


title: Lfng_rep3 [Cell_522]


title: Lfng_rep3 [Cell_521]


title: Lfng_rep3 [Cell_517]


title: Lfng_rep3 [Cell_518]


title: Lfng_rep3 [Cell_516]


title: Lfng_rep3 [Cell_519]


title: Lfng_rep3 [Cell_514]


title: Lfng_rep3 [Cell_511]


title: Lfng_rep3 [Cell_512]


title: Lfng_rep3 [Cell_510]


title: Lfng_rep3 [Cell_515]


title: Lfng_rep3 [Cell_513]


title: Lfng_rep3 [Cell_508]


title: Lfng_rep3 [Cell_507]


title: Lfng_rep3 [Cell_509]


title: Lfng_rep3 [Cell_505]


title: Lfng_rep3 [Cell_506]


title: Lfng_rep3 [Cell_504]


title: Lfng_rep3 [Cell_503]


title: Lfng_rep3 [Cell_501]


title: Lfng_rep3 [Cell_502]


title: Lfng_rep3 [Cell_498]


title: Lfng_rep3 [Cell_499]


title: Lfng_rep3 [Cell_497]


title: Lfng_rep3 [Cell_496]


title: Lfng_rep3 [Cell_493]


title: Lfng_rep3 [Cell_492]


title: Lfng_rep3 [Cell_494]


title: Lfng_rep3 [Cell_488]


title: Lfng_rep3 [Cell_489]


title: Lfng_rep3 [Cell_490]


title: Lfng_rep3 [Cell_487]


title: Lfng_rep3 [Cell_500]


title: Lfng_rep3 [Cell_495]


title: Lfng_rep3 [Cell_491]


title: Lfng_rep3 [Cell_483]


title: Lfng_rep3 [Cell_484]


title: Lfng_rep3 [Cell_482]


title: Lfng_rep3 [Cell_486]


title: Lfng_rep3 [Cell_480]


title: Lfng_rep3 [Cell_485]


title: Lfng_rep3 [Cell_478]


title: Lfng_rep3 [Cell_477]


title: Lfng_rep3 [Cell_475]


title: Lfng_rep3 [Cell_474]


title: Lfng_rep3 [Cell_476]


title: Lfng_rep3 [Cell_473]


title: Lfng_rep3 [Cell_471]


title: Lfng_rep3 [Cell_470]


title: Lfng_rep3 [Cell_469]


title: Lfng_rep3 [Cell_468]


title: Lfng_rep3 [Cell_472]


title: Lfng_rep3 [Cell_466]


title: Lfng_rep3 [Cell_465]


title: Lfng_rep3 [Cell_462]


title: Lfng_rep3 [Cell_464]


title: Lfng_rep3 [Cell_460]


title: Lfng_rep3 [Cell_459]


title: Lfng_rep3 [Cell_461]


title: Lfng_rep3 [Cell_481]


title: Lfng_rep3 [Cell_458]


title: Lfng_rep3 [Cell_457]


title: Lfng_rep3 [Cell_479]


title: SCLC_10_n

value: adjacent lung

value: Ever

value: NO


title: Lfng_rep3 [Cell_456]


title: Lfng_rep2 [Cell_454]


title: Lfng_rep2 [Cell_453]


title: Lfng_rep2 [Cell_451]


title: Lfng_rep2 [Cell_449]


title: Lfng_rep2 [Cell_455]


title: Lfng_rep2 [Cell_447]


title: Lfng_rep2 [Cell_448]


title: Lfng_rep2 [Cell_450]


title: Lfng_rep2 [Cell_452]


title: Lfng_rep3 [Cell_467]


title: Lfng_rep2 [Cell_445]


title: Lfng_rep2 [Cell_446]


title: Lfng_rep3 [Cell_463]


title: Lfng_rep2 [Cell_442]


title: Lfng_rep2 [Cell_441]


title: Lfng_rep2 [Cell_443]


title: Lfng_rep2 [Cell_438]


title: Lfng_rep2 [Cell_440]


title: Lfng_rep2 [Cell_439]


title: Lfng_rep2 [Cell_436]


title: Lfng_rep2 [Cell_437]


title: Lfng_rep2 [Cell_435]


title: Lfng_rep2 [Cell_434]


title: Lfng_rep2 [Cell_433]


title: Lfng_rep2 [Cell_432]


title: Lfng_rep2 [Cell_429]


title: Lfng_rep2 [Cell_428]


title: Lfng_rep2 [Cell_430]


title: Lfng_rep2 [Cell_425]


title: Lfng_rep2 [Cell_424]


title: Lfng_rep2 [Cell_426]


title: Lfng_rep2 [Cell_423]


title: Lfng_rep2 [Cell_427]


title: Lfng_rep2 [Cell_421]


title: Lfng_rep2 [Cell_419]


title: Lfng_rep2 [Cell_422]


title: Lfng_rep2 [Cell_444]


title: Lfng_rep2 [Cell_418]


title: Lfng_rep2 [Cell_417]


title: Lfng_rep2 [Cell_416]


title: Lfng_rep2 [Cell_413]


title: Lfng_rep2 [Cell_411]


title: Lfng_rep2 [Cell_410]


title: Lfng_rep2 [Cell_408]


title: Lfng_rep2 [Cell_420]


title: Lfng_rep2 [Cell_407]


title: Lfng_rep2 [Cell_412]


title: Lfng_rep2 [Cell_409]


title: Lfng_rep2 [Cell_404]


title: Lfng_rep2 [Cell_414]


title: Lfng_rep2 [Cell_415]


title: Lfng_rep2 [Cell_403]


title: Lfng_rep2 [Cell_431]


title: Lfng_rep2 [Cell_405]


title: Lfng_rep2 [Cell_402]


title: Lfng_rep2 [Cell_401]


title: Lfng_rep2 [Cell_399]


title: Lfng_rep2 [Cell_397]


title: Lfng_rep2 [Cell_395]


title: Lfng_rep2 [Cell_394]


title: Lfng_rep2 [Cell_393]


title: Lfng_rep2 [Cell_400]


title: Lfng_rep2 [Cell_392]


title: Lfng_rep2 [Cell_390]


title: Lfng_rep2 [Cell_391]


title: Lfng_rep2 [Cell_389]


title: Lfng_rep2 [Cell_388]


title: Lfng_rep2 [Cell_386]


title: Lfng_rep2 [Cell_387]


title: Lfng_rep2 [Cell_384]


title: Lfng_rep2 [Cell_385]


title: Lfng_rep2 [Cell_406]


title: Lfng_rep2 [Cell_383]


title: Lfng_rep2 [Cell_382]


title: Lfng_rep2 [Cell_381]


title: Lfng_rep2 [Cell_378]


title: Lfng_rep2 [Cell_379]


title: Lfng_rep2 [Cell_377]


title: Lfng_rep2 [Cell_398]


title: Lfng_rep2 [Cell_375]


title: Lfng_rep2 [Cell_380]


title: Lfng_rep2 [Cell_396]


title: Lfng_rep2 [Cell_374]


title: Lfng_rep2 [Cell_373]


title: Lfng_rep2 [Cell_372]


title: Lfng_rep2 [Cell_370]


title: Lfng_rep2 [Cell_369]


title: Lfng_rep2 [Cell_368]


title: Lfng_rep2 [Cell_367]


title: Lfng_rep1 [Cell_366]


title: Lfng_rep1 [Cell_365]


title: Lfng_rep1 [Cell_363]


title: Lfng_rep1 [Cell_364]


title: Lfng_rep1 [Cell_362]


title: Lfng_rep1 [Cell_360]


title: Lfng_rep1 [Cell_359]


title: Lfng_rep1 [Cell_358]


title: Lfng_rep1 [Cell_355]


title: Lfng_rep1 [Cell_357]


title: Lfng_rep1 [Cell_356]


title: Lfng_rep2 [Cell_376]


title: Lfng_rep1 [Cell_352]


title: Lfng_rep1 [Cell_350]


title: Lfng_rep1 [Cell_354]


title: Lfng_rep1 [Cell_348]


title: Lfng_rep1 [Cell_349]


title: Lfng_rep1 [Cell_346]


title: Lfng_rep1 [Cell_345]


title: Lfng_rep2 [Cell_371]


title: Lfng_rep1 [Cell_344]


title: Lfng_rep1 [Cell_343]


title: Lfng_rep1 [Cell_342]


title: Lfng_rep1 [Cell_339]


title: Lfng_rep1 [Cell_340]


title: Lfng_rep1 [Cell_337]


title: Lfng_rep1 [Cell_361]


title: Lfng_rep1 [Cell_338]


title: Lfng_rep1 [Cell_336]


title: Lfng_rep1 [Cell_335]


title: Lfng_rep1 [Cell_334]


title: Lfng_rep1 [Cell_333]


title: Lfng_rep1 [Cell_353]


title: Lfng_rep1 [Cell_327]


title: Lfng_rep1 [Cell_330]


title: Lfng_rep1 [Cell_331]


title: Lfng_rep1 [Cell_347]


title: Lfng_rep1 [Cell_328]


title: Lfng_rep1 [Cell_329]


title: Lfng_rep1 [Cell_326]


title: Lfng_rep1 [Cell_325]


title: Lfng_rep1 [Cell_341]


title: Lfng_rep1 [Cell_323]


title: Lfng_rep1 [Cell_321]


title: Lfng_rep1 [Cell_322]


title: Lfng_rep1 [Cell_320]


title: Lfng_rep1 [Cell_319]


title: Lfng_rep1 [Cell_332]


title: Lfng_rep1 [Cell_351]


title: Lfng_rep1 [Cell_312]


title: Lfng_rep1 [Cell_309]


title: Lfng_rep1 [Cell_308]


title: Lfng_rep1 [Cell_313]


title: Lfng_rep1 [Cell_310]


title: Lfng_rep1 [Cell_316]


title: Lfng_rep1 [Cell_314]


title: Lfng_rep1 [Cell_311]


title: Lfng_rep1 [Cell_306]


title: Lfng_rep1 [Cell_305]


title: Lfng_rep1 [Cell_324]


title: Lfng_rep1 [Cell_304]


title: Lfng_rep1 [Cell_303]


title: Lfng_rep1 [Cell_302]


title: Lfng_rep1 [Cell_301]


title: Lfng_rep1 [Cell_300]


title: Lfng_rep1 [Cell_317]


title: Lfng_rep1 [Cell_318]


title: Lfng_rep1 [Cell_315]


title: Lfng_rep1 [Cell_298]


title: Lfng_rep1 [Cell_307]


title: Lfng_rep1 [Cell_292]


title: Lfng_rep1 [Cell_291]


title: Lfng_rep1 [Cell_297]


title: Lfng_rep1 [Cell_295]


title: Lfng_rep1 [Cell_296]


title: Lfng_rep1 [Cell_294]


title: Lfng_rep1 [Cell_290]


title: Lfng_rep1 [Cell_287]


title: Lfng_rep1 [Cell_285]


title: Lfng_rep1 [Cell_289]


title: Lfng_rep1 [Cell_284]


title: Lfng_rep1 [Cell_286]


title: Lfng_rep1 [Cell_288]


title: Lfng_rep1 [Cell_299]


title: Lfng_rep1 [Cell_281]


title: Lfng_rep1 [Cell_282]


title: Lfng_rep1 [Cell_279]


title: Lfng_rep1 [Cell_280]


title: Lfng_rep1 [Cell_293]


title: Fgfr3_Sox2_rep3 [Cell_272]


title: Fgfr3_Sox2_rep3 [Cell_275]


title: Fgfr3_Sox2_rep3 [Cell_273]


title: Fgfr3_Sox2_rep3 [Cell_276]

value: emp (negative control)


title: Fgfr3_Sox2_rep3 [Cell_267]


title: Fgfr3_Sox2_rep3 [Cell_271]


title: Fgfr3_Sox2_rep3 [Cell_270]


title: Fgfr3_Sox2_rep3 [Cell_266]


title: Fgfr3_Sox2_rep3 [Cell_264]


title: Fgfr3_Sox2_rep3 [Cell_265]


title: Fgfr3_Sox2_rep3 [Cell_269]


title: Lfng_rep1 [Cell_283]


title: Fgfr3_Sox2_rep3 [Cell_263]


title: Fgfr3_Sox2_rep3 [Cell_260]


title: Fgfr3_Sox2_rep3 [Cell_259]


title: Fgfr3_Sox2_rep3 [Cell_262]


title: Fgfr3_Sox2_rep3 [Cell_268]


title: Fgfr3_Sox2_rep3 [Cell_258]


title: Fgfr3_Sox2_rep3 [Cell_256]


title: Fgfr3_Sox2_rep3 [Cell_274]


title: Fgfr3_Sox2_rep3 [Cell_251]


title: Fgfr3_Sox2_rep3 [Cell_250]


title: Fgfr3_Sox2_rep3 [Cell_247]


title: Lfng_rep1 [Cell_278]


title: Fgfr3_Sox2_rep3 [Cell_254]


title: Fgfr3_Sox2_rep3 [Cell_253]


title: Fgfr3_Sox2_rep3 [Cell_252]


title: Lfng_rep1 [Cell_277]


title: Fgfr3_Sox2_rep3 [Cell_255]


title: Fgfr3_Sox2_rep3 [Cell_249]


title: Fgfr3_Sox2_rep3 [Cell_261]


title: Fgfr3_Sox2_rep3 [Cell_257]


title: Fgfr3_Sox2_rep3 [Cell_248]


title: Fgfr3_Sox2_rep3 [Cell_246]


title: Fgfr3_Sox2_rep3 [Cell_238]


title: Fgfr3_Sox2_rep3 [Cell_237]


title: Fgfr3_Sox2_rep3 [Cell_244]


title: Fgfr3_Sox2_rep3 [Cell_239]


title: Fgfr3_Sox2_rep3 [Cell_241]


title: Fgfr3_Sox2_rep3 [Cell_234]


title: Fgfr3_Sox2_rep3 [Cell_245]


title: Fgfr3_Sox2_rep3 [Cell_242]


title: Fgfr3_Sox2_rep3 [Cell_243]


title: Fgfr3_Sox2_rep3 [Cell_236]


title: Fgfr3_Sox2_rep3 [Cell_235]


title: Fgfr3_Sox2_rep3 [Cell_229]


title: Fgfr3_Sox2_rep3 [Cell_230]


title: Fgfr3_Sox2_rep3 [Cell_240]


title: Fgfr3_Sox2_rep3 [Cell_233]


title: Fgfr3_Sox2_rep3 [Cell_231]


title: Fgfr3_Sox2_rep3 [Cell_226]


title: Fgfr3_Sox2_rep3 [Cell_225]


title: Fgfr3_Sox2_rep3 [Cell_227]


title: Fgfr3_Sox2_rep3 [Cell_222]


title: Fgfr3_Sox2_rep3 [Cell_221]


title: Fgfr3_Sox2_rep3 [Cell_223]


title: Fgfr3_Sox2_rep3 [Cell_224]


title: Fgfr3_Sox2_rep3 [Cell_219]


title: Fgfr3_Sox2_rep3 [Cell_217]


title: Fgfr3_Sox2_rep3 [Cell_220]


title: Fgfr3_Sox2_rep3 [Cell_218]


title: Fgfr3_Sox2_rep3 [Cell_232]


title: Fgfr3_Sox2_rep3 [Cell_216]


title: Fgfr3_Sox2_rep3 [Cell_214]


title: Fgfr3_Sox2_rep3 [Cell_213]


title: Fgfr3_Sox2_rep3 [Cell_215]


title: Fgfr3_Sox2_rep3 [Cell_212]


title: Fgfr3_Sox2_rep3 [Cell_207]


title: Fgfr3_Sox2_rep3 [Cell_205]


title: Fgfr3_Sox2_rep3 [Cell_203]


title: Fgfr3_Sox2_rep3 [Cell_210]


title: Fgfr3_Sox2_rep3 [Cell_209]


title: Fgfr3_Sox2_rep3 [Cell_199]


title: Fgfr3_Sox2_rep3 [Cell_198]


title: Fgfr3_Sox2_rep3 [Cell_197]


title: Fgfr3_Sox2_rep3 [Cell_196]


title: Fgfr3_Sox2_rep3 [Cell_208]


title: Fgfr3_Sox2_rep3 [Cell_206]


title: Fgfr3_Sox2_rep3 [Cell_204]


title: Fgfr3_Sox2_rep3 [Cell_202]


title: Fgfr3_Sox2_rep3 [Cell_211]


title: Fgfr3_Sox2_rep3 [Cell_191]


title: Fgfr3_Sox2_rep3 [Cell_201]


title: Fgfr3_Sox2_rep3 [Cell_193]


title: Fgfr3_Sox2_rep3 [Cell_190]


title: Fgfr3_Sox2_rep3 [Cell_194]


title: Fgfr3_Sox2_rep3 [Cell_188]


title: Fgfr3_Sox2_rep3 [Cell_195]


title: Fgfr3_Sox2_rep3 [Cell_192]


title: Fgfr3_Sox2_rep3 [Cell_189]


title: Fgfr3_Sox2_rep3 [Cell_186]


title: Fgfr3_Sox2_rep3 [Cell_187]


title: Fgfr3_Sox2_rep3 [Cell_185]


title: Fgfr3_Sox2_rep2 [Cell_183]


title: Fgfr3_Sox2_rep3 [Cell_184]


title: Fgfr3_Sox2_rep2 [Cell_180]


title: Fgfr3_Sox2_rep2 [Cell_179]


title: Fgfr3_Sox2_rep2 [Cell_178]


title: Fgfr3_Sox2_rep2 [Cell_176]


title: Fgfr3_Sox2_rep2 [Cell_181]


title: Fgfr3_Sox2_rep2 [Cell_182]


title: Fgfr3_Sox2_rep2 [Cell_174]


title: Fgfr3_Sox2_rep2 [Cell_177]


title: Fgfr3_Sox2_rep2 [Cell_175]


title: Fgfr3_Sox2_rep2 [Cell_170]


title: Fgfr3_Sox2_rep2 [Cell_171]


title: Fgfr3_Sox2_rep2 [Cell_172]


title: Fgfr3_Sox2_rep2 [Cell_173]


title: Fgfr3_Sox2_rep2 [Cell_167]


title: Fgfr3_Sox2_rep2 [Cell_163]


title: Fgfr3_Sox2_rep2 [Cell_164]


title: Fgfr3_Sox2_rep2 [Cell_165]


title: Fgfr3_Sox2_rep2 [Cell_166]


title: Fgfr3_Sox2_rep2 [Cell_169]


title: Fgfr3_Sox2_rep2 [Cell_168]


title: Fgfr3_Sox2_rep2 [Cell_160]


title: Fgfr3_Sox2_rep2 [Cell_161]


title: Fgfr3_Sox2_rep2 [Cell_162]


title: Fgfr3_Sox2_rep2 [Cell_159]


title: Fgfr3_Sox2_rep2 [Cell_158]


title: Fgfr3_Sox2_rep2 [Cell_157]


title: Fgfr3_Sox2_rep2 [Cell_156]


title: Fgfr3_Sox2_rep2 [Cell_155]


title: Fgfr3_Sox2_rep2 [Cell_153]


title: Fgfr3_Sox2_rep2 [Cell_152]


title: Fgfr3_Sox2_rep2 [Cell_154]


title: Fgfr3_Sox2_rep2 [Cell_151]


title: Fgfr3_Sox2_rep2 [Cell_150]


title: Fgfr3_Sox2_rep2 [Cell_149]


title: Fgfr3_Sox2_rep2 [Cell_145]


title: Fgfr3_Sox2_rep2 [Cell_144]


title: Fgfr3_Sox2_rep2 [Cell_146]


title: Fgfr3_Sox2_rep2 [Cell_142]


title: Fgfr3_Sox2_rep2 [Cell_143]


title: Fgfr3_Sox2_rep2 [Cell_148]


title: Fgfr3_Sox2_rep2 [Cell_147]


title: Fgfr3_Sox2_rep2 [Cell_141]


title: Fgfr3_Sox2_rep2 [Cell_139]


title: Fgfr3_Sox2_rep2 [Cell_135]


title: Fgfr3_Sox2_rep2 [Cell_138]


title: Fgfr3_Sox2_rep2 [Cell_140]


title: Fgfr3_Sox2_rep2 [Cell_136]


title: Fgfr3_Sox2_rep2 [Cell_134]


title: Fgfr3_Sox2_rep2 [Cell_128]


title: Fgfr3_Sox2_rep2 [Cell_132]


title: Fgfr3_Sox2_rep2 [Cell_133]


title: Fgfr3_Sox2_rep2 [Cell_130]


title: Fgfr3_Sox2_rep2 [Cell_129]


title: Fgfr3_Sox2_rep2 [Cell_127]


title: Fgfr3_Sox2_rep2 [Cell_131]


title: Fgfr3_Sox2_rep2 [Cell_125]


title: Fgfr3_Sox2_rep2 [Cell_122]


title: Fgfr3_Sox2_rep2 [Cell_123]


title: Fgfr3_Sox2_rep2 [Cell_124]


title: Fgfr3_Sox2_rep2 [Cell_137]


title: Fgfr3_Sox2_rep2 [Cell_119]


title: Fgfr3_Sox2_rep2 [Cell_120]


title: Fgfr3_Sox2_rep2 [Cell_115]


title: Fgfr3_Sox2_rep2 [Cell_118]


title: Fgfr3_Sox2_rep2 [Cell_114]


title: Fgfr3_Sox2_rep2 [Cell_117]


title: Fgfr3_Sox2_rep2 [Cell_113]


title: Fgfr3_Sox2_rep2 [Cell_112]


title: Fgfr3_Sox2_rep2 [Cell_111]


title: Fgfr3_Sox2_rep2 [Cell_110]


title: Fgfr3_Sox2_rep2 [Cell_109]


title: Fgfr3_Sox2_rep3 [Cell_228]


title: Fgfr3_Sox2_rep2 [Cell_108]


title: Fgfr3_Sox2_rep2 [Cell_107]


title: Fgfr3_Sox2_rep2 [Cell_106]


title: Fgfr3_Sox2_rep2 [Cell_100]


title: Fgfr3_Sox2_rep2 [Cell_105]


title: Fgfr3_Sox2_rep2 [Cell_104]


title: Fgfr3_Sox2_rep2 [Cell_102]


title: Fgfr3_Sox2_rep2 [Cell_101]


title: Fgfr3_Sox2_rep2 [Cell_103]


title: Fgfr3_Sox2_rep2 [Cell_126]


title: Fgfr3_Sox2_rep2 [Cell_121]


title: Fgfr3_Sox2_rep2 [Cell_99]


title: Fgfr3_Sox2_rep2 [Cell_98]


title: Fgfr3_Sox2_rep2 [Cell_116]


title: Fgfr3_Sox2_rep2 [Cell_96]


title: Fgfr3_Sox2_rep2 [Cell_97]


title: Fgfr3_Sox2_rep2 [Cell_94]


title: Fgfr3_Sox2_rep2 [Cell_95]


title: Fgfr3_Sox2_rep2 [Cell_93]


title: Fgfr3_Sox2_rep2 [Cell_92]


title: Fgfr3_Sox2_rep1 [Cell_90]


title: Fgfr3_Sox2_rep1 [Cell_91]


title: Fgfr3_Sox2_rep1 [Cell_88]


title: Fgfr3_Sox2_rep1 [Cell_87]


title: Fgfr3_Sox2_rep1 [Cell_89]


title: Fgfr3_Sox2_rep1 [Cell_84]


title: Fgfr3_Sox2_rep1 [Cell_85]


title: Fgfr3_Sox2_rep1 [Cell_83]


title: Fgfr3_Sox2_rep1 [Cell_81]


title: Fgfr3_Sox2_rep1 [Cell_77]


title: Fgfr3_Sox2_rep1 [Cell_78]


title: Fgfr3_Sox2_rep1 [Cell_76]


title: Fgfr3_Sox2_rep1 [Cell_80]


title: Fgfr3_Sox2_rep1 [Cell_75]


title: Fgfr3_Sox2_rep3 [Cell_200]


title: Fgfr3_Sox2_rep1 [Cell_73]


title: Fgfr3_Sox2_rep1 [Cell_70]


title: Fgfr3_Sox2_rep1 [Cell_69]


title: Fgfr3_Sox2_rep1 [Cell_71]


title: Fgfr3_Sox2_rep1 [Cell_68]


title: Fgfr3_Sox2_rep1 [Cell_74]


title: Fgfr3_Sox2_rep1 [Cell_65]


title: Fgfr3_Sox2_rep1 [Cell_67]


title: Fgfr3_Sox2_rep1 [Cell_86]


title: Fgfr3_Sox2_rep1 [Cell_58]


title: Fgfr3_Sox2_rep1 [Cell_82]


title: Fgfr3_Sox2_rep1 [Cell_62]


title: Fgfr3_Sox2_rep1 [Cell_59]


title: Fgfr3_Sox2_rep1 [Cell_63]


title: Fgfr3_Sox2_rep1 [Cell_61]


title: Fgfr3_Sox2_rep1 [Cell_60]


title: Fgfr3_Sox2_rep1 [Cell_57]


title: Fgfr3_Sox2_rep1 [Cell_56]


title: Fgfr3_Sox2_rep1 [Cell_54]


title: Fgfr3_Sox2_rep1 [Cell_79]


title: Fgfr3_Sox2_rep1 [Cell_55]


title: Fgfr3_Sox2_rep1 [Cell_53]


title: Fgfr3_Sox2_rep1 [Cell_52]


title: Fgfr3_Sox2_rep1 [Cell_51]


title: Fgfr3_Sox2_rep1 [Cell_50]


title: Fgfr3_Sox2_rep1 [Cell_49]


title: Fgfr3_Sox2_rep1 [Cell_48]


title: Fgfr3_Sox2_rep1 [Cell_47]


title: Fgfr3_Sox2_rep1 [Cell_66]


title: Fgfr3_Sox2_rep1 [Cell_64]


title: Fgfr3_Sox2_rep1 [Cell_45]


title: Fgfr3_Sox2_rep1 [Cell_44]


title: Fgfr3_Sox2_rep1 [Cell_43]


title: Fgfr3_Sox2_rep1 [Cell_42]


title: Fgfr3_Sox2_rep1 [Cell_39]


title: Fgfr3_Sox2_rep1 [Cell_35]


title: Fgfr3_Sox2_rep1 [Cell_34]


title: Fgfr3_Sox2_rep1 [Cell_38]


title: Fgfr3_Sox2_rep1 [Cell_33]


title: Fgfr3_Sox2_rep1 [Cell_37]


title: Fgfr3_Sox2_rep1 [Cell_72]


title: Fgfr3_Sox2_rep1 [Cell_29]


title: Fgfr3_Sox2_rep1 [Cell_31]


title: Fgfr3_Sox2_rep1 [Cell_36]


title: Fgfr3_Sox2_rep1 [Cell_30]


title: Fgfr3_Sox2_rep1 [Cell_27]


title: Fgfr3_Sox2_rep1 [Cell_28]


title: Fgfr3_Sox2_rep1 [Cell_26]


title: Fgfr3_Sox2_rep1 [Cell_46]


title: Fgfr3_Sox2_rep1 [Cell_22]


title: Fgfr3_Sox2_rep1 [Cell_24]


title: Fgfr3_Sox2_rep1 [Cell_23]


title: Fgfr3_Sox2_rep1 [Cell_25]


title: Fgfr3_Sox2_rep1 [Cell_20]


title: Fgfr3_Sox2_rep1 [Cell_40]


title: Fgfr3_Sox2_rep1 [Cell_19]


title: Fgfr3_Sox2_rep1 [Cell_18]


title: Fgfr3_Sox2_rep1 [Cell_15]


title: Fgfr3_Sox2_rep1 [Cell_32]


title: Fgfr3_Sox2_rep1 [Cell_13]


title: Fgfr3_Sox2_rep1 [Cell_11]


title: Fgfr3_Sox2_rep1 [Cell_8]


title: Fgfr3_Sox2_rep1 [Cell_6]


title: Fgfr3_Sox2_rep1 [Cell_7]


title: Fgfr3_Sox2_rep1 [Cell_5]


title: Fgfr3_Sox2_rep1 [Cell_4]


title: Fgfr3_Sox2_rep1 [Cell_41]


title: Fgfr3_Sox2_rep1 [Cell_2]


title: Fgfr3_Sox2_rep1 [Cell_1]


title: D-BP 2

city: Indianapolis

first: Jaeyeon

last: Kim

state: IN

address: 635 Barnhill Drive, MS4053

department: Department of Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Bilateral ovariectomy DKO with P4 Replicate A2

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version unknown pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:16. Custom perl scripts along with FASTX-Toolkit version 0.0.14 with the following parameters, “-l 17 -v -M 1 -i “, were used to look for partial adapters within the reads
Trimmed reads were mapped against GRCm38 TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100
Read counts for each gene were created using featureCounts from the Subread package version 1.5.0-p3 and Gencode M14 as the annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts of reads mapped to genes using Gencode M14 as the annotation

extract_protocol:
Total RNA was isolated from fallopian tubes :early-stage fallopian tube tumors (ET), bilateral ovariectomy fallopian tubes (B) and bilateral ovarietomy DKO mice with treated P4(BP). Additionally, RNA was isolated from normal fallopian tubes (Ovid, oviducts) of respective control mice for DKO and TKO mice. Total RNA was isolated using TRIzol (Invitrogen) and purified using RNeasy MinElute Cleanup Kit (Qiagen, Germantown, MD, USA), according to manufacturer’s instructions.
Total RNA (1 -1.2μg) was used for mRNA library preparation. Library preparation was performed using the TruSeq Stranded mRNA HT Library preparation kit (Illumina).

treatment_protocol: Ovaries were removed at 4-5weeks of age and P4 pellet (25 mg) was implanted. At 4-5 months of age early-stage tumor samples were collected.

value: fallopian tube tissue

value: Early stage fallopian tube tumors

value: Dicer fl/fl Pten f/f/ Amhr2 Cre/+

value: Dicer Pten conditional KO

tag: group

value: Bilateral ovariectomy DKO with P4


title: D-BP 1

description: Bilateral ovariectomy DKO with P4 Replicate A1


title: Fgfr3_Sox2_rep1 [Cell_16]


title: D-BP 5

description: Bilateral ovariectomy DKO with P4 Replicate A3


title: D-ET5

description: DKO Early Replicate A1

source_name: DKO Early Replicate A1

value: DKO Early


title: D-ET7

description: DKO Early Replicate A3

source_name: DKO Early Replicate A3


title: D-ET6

description: DKO Early Replicate A2

source_name: DKO Early Replicate A2


title: D-Ovid3

description: DKO Control Replicate A3

source_name: DKO Control Replicate A3

value: Normal fallopian tubes

value: Dicer fl/fl Pten f/f/

value: Dicer Pten conditional KO(no Cre activity)

value: DKO Control


title: Fgfr3_Sox2_rep1 [Cell_14]

value: Postnatal day2

value: Cochlear Sensory Epithelium


title: D-B 8

description: Bilateral ovariectomy DKO Replicate A1

source_name: Bilateral ovariectomy DKO Replicate A1

treatment_protocol: Ovaries were removed at 4-5weeks of age. At 4-5 months of age, we collected normal-looking fallopian tube tissues

value: Bilateral ovariectomy DKO


title: Fgfr3_Sox2_rep1 [Cell_17]


title: D-Ovid1

description: DKO Control Replicate A1

source_name: DKO Control Replicate A1


title: Fgfr3_Sox2_rep1 [Cell_9]


title: D-Ovid2

description: DKO Control Replicate A2

source_name: DKO Control Replicate A2


title: X7.femur.Mac.3

first: Xia

last: Chengxiang

state: Guangdong

address: Kai Yuang Road 190

institute: GIBH

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome by HISAT2 and generated raw counts values by featureCounts of Subread package.
Gene expression levels of different saMacles were normalized by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw count table was a csv file

growth_protocol: All mice in this study were kept in C57BL/6J background. Macrophages were sorted from MSC-treated tibias and untreated femurs of two individual mice.

extract_protocol:
Total RNA was extracted using the Rneasy micro kit with on-column Dnase treatment (Qiagen, 74004).
Library was constructed using VAHTSTM mRNA -seq V3 Library Prep Kit for Illumian (Vazyme , NR 611).

treatment_protocol: Target cells were sorted from the bone marrow nucleated cells.

value: untreated femurs

tag: cell type

value: bone marrow nucleated cells

tag: cells subtype

value: macrophage


title: X7.femur.Mac.1


title: Fgfr3_Sox2_rep1 [Cell_3]


title: X19.femur.Mac.1


title: X19.femur.Mac.3


title: Fgfr3_Sox2_rep1 [Cell_21]


title: X7.femur.Mac.2


title: X19.femur.Mac.2


title: Fgfr3_Sox2_rep1 [Cell_10]


title: D-B 9

description: Bilateral ovariectomy DKO Replicate A2

source_name: Bilateral ovariectomy DKO Replicate A2

tag: disease state


title: X19.tibia.Mac.3

value: MSC-treated tibias

value: MSC-educated macrophages


title: D-B 10

description: Bilateral ovariectomy DKO Replicate A3

source_name: Bilateral ovariectomy DKO Replicate A3

value: fallopian tube tissue


title: Fgfr3_Sox2_rep1 [Cell_12]


title: X7.tibia.Mac.3


title: X19.tibia.Mac.1


title: E-Mac-4

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome by HISAT2 and generated raw counts values by featureCounts of Subread package.
Gene expression levels of different samples were normalized by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

molecule: polyA RNA

growth_protocol: Leukemia macrophages were cultured alone or co-cultured with MSC in vitro for 12h.

treatment_protocol: Target cells were sorted from the cultured leukemia macrophages (Mac) or MSC-educated leukemia macrophages (E-Mac), which were co-cultured with MSC in vitro for 12h.

value: Leukemia macrophages

tag: co-culture

value: Mesenchymal stromal cells


title: X7.tibia.Mac.2


title: E-Mac-3

source_name: MSC-educated leukemia macrophages (E-Mac)


title: Mac-4

source_name: leukemia macrophages (Mac)


title: PO_24hr_2_4

city: Syracuse NY

first: Caitlin

middle: E

last: McDonough

state: NY

address: 107 College Place, 114 Life Science Complex

department: Syracuse University Biology Department

institute: Syracuse University

data_processing:
sequenced reads were cleaned to remove adapter sequences and exclude reads with > 10% unknown bases of > 50% low-quality bases
sequenced reads were aligned to the D. melanogaster reference genome (r6.21) using hisat 2.1.0 with default settings plus the sam option to suppress reads that do not align or represent novel splice sites
read counts per million (CPM) were generated using StringTie
Genome_build: D. melanogaster reference genome (r6.21)
Supplementary_files_format_and_content: tab deliminated text file includes CPM value for each sample

organism: Drosophila melanogaster

source_name: Parovaria

extract_protocol:
Females were etherized (unmated, 6hrs, or 24hrs post-mating) and the female reproductive tract (FRT)  removed in a drop of 1x PBS. The FRT was then microdissected into 6 discrete tissues. Tissues were rinsed in PBS and transferred directly to Trizol. Pooled tissue collections were homogenized with a pellet pestle and RNA was isolated using a phenol-chloroform extraction with phase-lock gels (ThermoFisher) and an overnight precipitation in isoproponal and 3M sodium acetate with 1.5ul glycogen (LifeTechnologies) at -18 C to maximize RNA recovery. The precipitation was followed by DNAse I (LifeTechnologies) treatment for 30 min at 37 C and a second RNA isolation. RNA was re-suspended in RNase-free H2O
RNA libraries were prepared for sequencing using standard protocols by Beijing Genomics Institute (BGI)

tag: time relative to matng

value: 24hr Postmating

value: LHM

value: 3-8 days old

tag: sequencing run


title: PO_2hhr_2_3


title: E-Mac-1


title: Mac-3


title: E-Mac-2


title: Mac-2


title: X19.tibia.Mac.2


title: Mac-1


title: PO_6h_1_2

value: 6hr Postmating


title: Recovered MSC4

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.bt2 files to generate accepted_hits.bam file by tophat, and the used cuffquant scripts (cufflinks-2.2.1) to calculated genes expression level.
Gene expression levels of different samples were normalized by cuffnorm scripts (cufflinks-2.2.1), and finally generated genes.fpkm_table
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_table was generated by cuffnorm
Supplementary_files_format_and_content: gene expression value

source_name: MSC

growth_protocol: All mice in this study were kept in C57BL/6J backgroud. MSCs were sorted from pre-leukemic mice, control mice, and MSC-treated pre-leukemic mice.

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA is based on published methods(PMID:20203668).
Libraries were prepared according to Illumina's instructions accompanying the  illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).

treatment_protocol: Target cells were sorted from the nucleated cell mixtures of bone marrow and compact bones.

value: Bone marrow


title: PO_6hr_2_3


title: PO_U_2_4

value: Unmated


title: Pre-leukemia MSC5


title: X7.tibia.Mac.1


title: PO_24hr_1_1


title: PO_U_2_3


title: PO_U_1_1


title: Pre-leukemia MSC4


title: Recovered MSC1


title: ST_24hr_2_4

source_name: Spermatheca


title: ST_24hr_2_3


title: PO_24hr_1_2


title: PO_U_1_2


title: Pre-leukemia MSC1


title: Pre-leukemia MSC3


title: ST_6hr_2_3


title: Pre-leukemia MSC2


title: ST_24hr_1_1


title: Healthy hemeostatic MSC3


title: ST_6h_1_2


title: ST_6hr_2_4


title: PO_6hr_2_4


title: Recovered MSC2


title: Healthy hemeostatic MSC2


title: Recovered MSC3


title: Healthy hemeostatic MSC1


title: ST_U_2_4


title: FM-C-02

city: Jinan

first: Jing

last: Wang

address: No. 324, jingwuweiqi road, huaiyin district

institute: Shandong Provincial Hospital

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.  After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001
The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: text file with abundance

source_name: plasma

extract_protocol: The cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, 134–160-bp PCR-amplified fragments (corresponding to small RNAs that were each 14–40 nt in length) were extracted and purified from an agarose gel.

treatment_protocol: Total RNAs that were extracted from plasma were pretreated with rtStar tRF & tiRNA Pretreatment Kits to remove RNA modifications that interfere with the construction of small RNA-seq libraries.

value: symptomatic and supportive treatment


title: Pre-leukemia MSC6


title: FM-C-03


title: ST_U_1_2


title: FM-A-03


title: SR_24hr_2_3

source_name: Seminal receptacle


title: CON-3

value: untreated


title: ST_24hr_1_2


title: ST_U_2_3


title: FM-C-01


title: CON-2


title: ST_U_1_1


title: FM-A-01


title: SR_6hr_2_4


title: SR_24hr_1_1


title: CON-1


title: SR_6hr_2_3


title: SR_U_2_3


title: FH-KHSRP_PARCLIP_0.5Uul_RNaseT1_ad2902

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Bcl2fastq (v2.20.0) was used to demultiplex and convert BCL basecall files from the sequencer to fastq files
Cutadapt (cutadapt 1.15 with Python 3.6.4) (19) was used to demultiplex adapter barcoded samples (without removing adapters). For demultiplexing libraries with a 5’ adapter barcode, the 5’ adapter barcode anchored to the 5’ end of the read was removed during demultiplexing (without removing UMIs)
PARpipe (https://github.com/ohlerlab/PARpipe) was used for further pre-processing, implementation of paralyzer
To allow the use of additional UMIs in the new protocol and preserve the true number of reads in the final bam file, during preprocessing fastq sequences were collapsed prior to adapter and UMI removal to remove potential PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: clusters(binding sites) csv files

growth_protocol: Flp-In™ 293 T-REx cells with stably integrated transgenic FLAG-HA tagged RBP of interest were cultured at 80% confluency in DMEM supplemented with 10% FBS and1x Pen/Strep

extract_protocol:
Following crosslinking, cells were collected in PBS and centrifuged at 500 x g for 5 minutes at 4°C. For chromatin associated RNPs (e.g U2AF1) cells were lysed by gentle resuspension in a modified HLB buffer (10 mM Tris at pH 7.5, 50 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 10% glycerol) for 2 min and spun for 2 min at 200 x g. The nuclei were washed twice with the same buffer and extracted using MWS buffer (10 mM Tris-HCl at pH 7.0, 4 mM EDTA, 0.3 M NaCl, 1 M urea, and 1% [v/v] NP-40). The chromatin pellet was washed twice in MWS buffer and resuspended in RIPA buffer(10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1%, sodium deoxycholate, 0.1% SDS, 140 mM NaCl supplemented with protease inhibitor cocktail (cOmplete, Sigma Aldrich 4693159001) followed by sonication in a bath sonicator (Bioruptor 300, Diagenode) 3 times for 30 seconds at medium amplitude at 4°C. 0.1 U/µl RNase I was added and incubation for 10 min at 22°C. For KHSRP, the cell pellet was lysed in 3 volumes of RIPA buffer and sonicated followed by addition of 0.1 U/µl RNase I and incubation for 10 min at 22°C. For cytoplasmic RBPs, cells were lysed in 3 volumes of NP40 lysis buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, 0.5 mM DTT) on ice for 15 minutes with optional addition of 0.1 U/µl RNase I and incubation for 10 min at 22°C. The cell extract was cleared at 15,000 x g for 15 minutes at 4°C.
Library conctraction was performed either with the radiolabel protocol or with fPAR-CLIP protocol

treatment_protocol: 8-12 hours before crosslinking, 4-thiouridine (4SU) was added to the cell culture medium at a final concentration of 100 µM. For U2AF1 PAR-CLIP, 4SU-labeling was reduced to 2 hours at a final concentration of 250 µM. Cells were washed once with 1x PBS and crosslinked with 0.3 J/cm2 of 312 or 365 nm UVA or UVB light for PAR-CLIP or 0.3 J/cm2 of 254 nm UVC light for regular CLIP in a Spectrolinker XL-1500 (Spectronics Corporation) or comparable instrument equipped with the appropriate UV lamps

tag: cell line

value: Flp-In T-REx 293

tag: protein

value: KHSRP

tag: protocol

value: PAR-CLIP-Seq

tag: clip antibody

value: Anti-FLAG® M2 Magnetic Beads, Millipore, M8823

value: NNACACTCTGGAATTCTCGGGTGCCAAGG


title: FH-KHSRP_fPARCLIP_0.15Uul_RNaseI

value: fPAR-CLIP-Seq

value: NNTGACTGTGGAATTCTCGGGTGCCAAGG


title: SR_6h_1_2

tag: strain


title: FH-KHSRP_fPARCLIP_1.5Uul_RNaseI


title: ST_6h_1_1


title: FM-A-02


title: SR_U_2_4


title: SR_6h_1_1


title: FH-FUBP3_PARCLIP_0.5Uul_RNaseT1_ad2903

value: NNACAGAGTGGAATTCTCGGGTGCCAAGG


title: FH-FUBP3_fPARCLIP_1.5Uul_RNaseI


title: OVD_24hr_2_2

source_name: Oviduct


title: OVD_24hr_2_3


title: SR_U_1_2


title: FH-FUBP3_fPARCLIP_0.5Uul_RNaseI


title: FH-FUBP3_fPARCLIP_0.15Uul_RNaseI


title: FH-KHSRP_fPARCLIP_0.5Uul_RNaseI


title: OVD_24hr_1_1


title: FH-AGO2_fPARCLIP_1.5Uul_RNaseI


title: OVD_6h_2_2


title: FH-CPSF1_fPARCLIP_0.5Uul_RNaseI


title: FH-AGO2_fCLIP_UV254_1.5Uul_RNaseI

value: fCLIP-Seq


title: OVD_U_2_2


title: SR_24hr_2_4

value: 24hr Postmating


title: OVD_U_1_1

value: LHM


title: OVD_U_2_3

value: 3-8 days old


title: FH-AGO2_fCLIP_UV254_0.15Uul_RNaseI


title: FH-AGO2_fPARCLIP_0.15Uul_RNaseI


title: FB_24hr_2_3

source_name: Fat body


title: TT_IPF_ATAC

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

description:
snATAC-seq.rds
snATAC-seq_fragments.bed.gz
snATAC-seq_fragments.bed.gz.tbi

library_source: genomic

data_processing:
For single nucleus RNA-seq fastq files were trimmed, quality-filtered and aligned to the hg38 reference genome using standardized Cell Ranger analysis pipelines from 10X Genomics. The output of this pipeline included a sparse count table containing cellular barcodes by gene IDs.
For single nucleus RNA-seq count tables were imported into Seurat (v. 3; https://satijalab.org/seurat), selected to exclude samples with >10% mitochondrial reads and integrated using the sctransform wrapper (Seurat v. 3), which applies a regularized, negative binomial regression approach to per-cell read depth as a normalization across samples. Principle components were calculated and selected by looking at the inflection point of a histogram of principal components by standard deviation. Dimensionality was reduced and cell groups defined by unbiased hierarchical clustering using the Uniform Manifold Approximation and Projection method (UMAP; available through Seurat v. 3).
For single nucleus RNA-seq cell types were identified using several approaches, including marker analysis to summarize discriminating genes between clusters and graphical approaches testing for known cell type-specific markers. Details of this analysis are included in the manuscript.
For single nucleus ATAC-seq, fastq files were trimmed, filtered, and aligned to the hg38 reference genome using SnapATAC (https://github.com/r3fang/SnapATAC). Resulting BAM files were converted into fragment files using Sinto (https://timoast.github.io/sinto/index.html), and peak calls and counts tables for each sample were constructed with Genrich (https://github.com/jsh58/Genrich#atacseq).
For single nucleus ATAC-seq, count matrices were imported into Signac (v. 0.1.6; https://github.com/timoast/signac), unaligned counts were removed, and cells with nucleosome signal >10, transcription start site enrichment <2, alignment to error-prone regions >5% and <15% read fractions in peaks were filtered out. Sample integration and dimensionality reduction were performed in Signac using term frequency-inverse document frequency (TF-IDF) weighted integration, singular value decomposition, and latent semantic indexing dimensionality reduction.
Cell type labels were transferred from cells labeled using the snRNA-seq pipeline above by performing canonical correlation analysis across datasets with UMAP. All statistical analyses utilized R (v. 3.6.1; R Foundation for Statistical Computing, Vienna, Austria).
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, raw matrix, barcode, and feature files are included for each sample, and an aggregated, normalized R analysis object is provided as a processed data file. For ATAC-seq, raw fragment files and peak ranges are included for each sample, and an aggregated, normalized R analysis object is provided (excluding the failed Sample2/TT_Control) as a processed data file.

source_name: Tissue-nucleus

extract_protocol:
Nuclei were isolated from frozen lung tissue by pulverizing in liquid nitrogen using a mortar and pestle, lysed in PBS containing 2% BSA, 0.1% TritonX-100, 1X protease inhibitors (Roche), 0.2 U/µl RNase inhibitor (Promega), and 1 mM DTT. Nuclei were washed by centrifugation at 500 x g, resuspended in PBS containing 2% BSA, 1 mM EDTA, 0.2 U/µl RNase inhibitor, and 1:100 DRAQ7 (Cell Signaling) and isolated for DRAQ7+ nuclei using a microfluidic Sony SH800 cell sorter. Nuclei were collected in PBS containing 5% BSA and 1 U/µl RNase inhibitor and quantified prior to library preparation.
For snRNA-seq, nuclei were loaded onto a 10X Chromium platform for 3-prime library preparation per manufacturer protocols. For snATAC-seq, 2K nuclei were resuspended in 17% dimethylformamide-containing buffer and incubated with 1 µl Tn5 transposase containing combinatorial barcodes.
For snRNA-seq, libraries were sequenced on an Illumina HiSeq4000 sequencer using 50 bp paired-end reads and custom sequencing primers at the University of California San Diego Institute for Genomic Medicine.
For ATAC-seq, libraries were sequenced on a NextSeq500 sequencer using 50 bp paired-end reads and custom sequencing primers at the University of California San Diego Institute for Genomic Medicine.

tag: source barcode

tag: Sex

value: male

tag: race

value: white

tag: ethnicity

value: non-hispanic

tag: disease

value: ipf

value: TT


title: GG_IPF_ATAC

tag: age

tag: genotype

value: GG


title: FB_6hr_2_3

value: 6hr Postmating


title: FB_24hr_2_4


title: GG_control_ATAC

value: normal


title: BEAS-2B_1b

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the BBMap Suite (v. 38.05) bbduk.sh tool with arguments ‘ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20’.
Trimmed reads were mapped to the human genome (hg38) using hisat2 (v. 2.1.0) and hg38 indexes downloaded from UCSC with settings '--very-sensitive and --no-spliced-alignment'.
Resulting SAM files were converted to BAM format using samtools view (v. 1.8) with arguments ‘-S -b’ and then sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.25.0) with arguments ‘-bg -ibam -g hg38 -strand +’.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files are non-normalized coverage files.

source_name: BEAS-2B airway epithelial cells

growth_protocol: Primary human tracheobronchial epithelial cells were obtained from the Human Primary Cell Core at National Jewish Health. Cells were expanded in collagen-coated 6 cm tissue culture plates and cultured on collagen-coated 12 mm Transwell-Clear Polyester Inserts (0.4 um pore size; Corning). Cells were cultured at air-liquid interface (ALI) for a minimum of 14 days before processing. Bronchial brushings obtained during consented bronchoscopy at National Jewish Health were placed in PBS on ice prior to processing. BEAS-2B transformed normal human airway epithelial cells were grown in DMEM containing 10% FBS and 1% pen/strep.

extract_protocol:
Cells were washed twice with 1X PBS and collected by scraping or pelleting prior to counting. Approximately 50K cells were pelleted and processed in duplicate as described in the Omni-ATAC-seq protocol published by Corces et al (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NextSeq instrument using 75 bp single-end (Norm-1a and Norm-1b) or 37 bp paired-end (all others) reads.

treatment_protocol: ATAC-seq was performed in primary airway epithelial cells cultured at ALI, cells from fresh bronchial brushes or BEAS-2B cells cultured to confluence; all cells were collected under basal conditions (i.e., were untreated).

tag: tissue

value: BEAS-2B airway epithelial cells

tag: primary cell tissue donor disease status


title: TT_control_ATAC


title: FB_U_2_3

value: Unmated


title: FB_U_1_2


title: FB_U_2_4


title: Brush-1a

source_name: fresh bronchial brush

value: fresh bronchial brush


title: ILD-1b

source_name: primary airway epithelial cells

value: primary airway epithelial cells

value: Interstitial Lung Disease (ILD)


title: BEAS-2B_1a


title: Brush-1b


title: OVD_6hr_2_3


title: hND6_3

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Ribodepleted RNA
Fragments per Kilobase per Million Mapped Reads (FPKM)

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the MM10 (GRCm38) transcriptome using STAR
Genome_build: MM10 (GRCm38)
Supplementary_files_format_and_content: Count files were generated using HTSeq-count.

source_name: RNA-seq

extract_protocol:
Qiagen RNEasy
TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA)

treatment_protocol: Mice received injections of lentivirus containing mutant human ND6 into their eyes.

tag: cell type

value: Optic Nerve

tag: treatment

value: Mutant human ND6T14484C


title: BUR_24hr_2_4

source_name: Bursa

tag: time relative to matng

value: 24hr Postmating

value: LHM

tag: sequencing run


title: FB_U_1_1

value: 3-8 days old


title: hND6_2


title: hND6_1


title: Norm-2b

value: Normal (Norm)


title: ILD-1a


title: BUR_24hr_2_3


title: mCherry_3

value: mCherry


title: mCherry_2


title: BUR_24hr_1_2


title: Norm-2a


title: mCherry_1


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep4_Experiment_1

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sample 1-16: The 51 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 37) using TopHat (version 2.0.6).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 66. Additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using HTSeq-count.
Sample 17-40: The 51/65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: Ensembl build 37 / build 38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: IghTer5H/Ter5H _Bone_Marrow

growth_protocol: Single cells suspensions were prepared from the Bone Marrow of 6-8-week-old mice and subjected to erylysis.

extract_protocol:
Pro or PreB cells were flow cytometrically sorted and resuspended in Trizol (Ambion Life Technologies) for the subsequent extraction of total RNA using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). Total RNA was extracted using according to the manufacturer’s protocol.
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0 as assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared using standard Illumina protocols, analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: Following erythrocyte lysis, Bone marrow cells were stained with flourescence conjugated monoclonal atibodies against CD19, B220, IgM, c-Kit and CD25 to identify their cell surface expression. ProB cells were identified as CD19+B220+IgM-c-Kit+CD25- and PreB cells were identified as CD19+B220+IgM-c-Kit-CD25+.

value: Bone Marrow


title: 12378 GRO-Seq in vitro pro-B cell

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

description: 12378 GRO-Seq in vitro pro-B cell Rag2(–/–)

data_processing:
Library strategy: GRO-seq
All sequence reads that passed the Illumina quality filtering were considered for alignment after adapter trimming. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 0.12.5, [Langmead et al, 2009; 2014]. Additional four bases were trimmed after adapter trimming and filtered against the rDNA with Bowtie version 2.1.0 before mouse genome alignment.
Read coverage bigwig files were created using the Jnomics suite [Tamir, unpublished], which basically extends reads by a set fragment size and calculates the read coverage, normalized to reads per million.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base, normalized to reads per million

source_name: in vitro Pro-B cell

extract_protocol:
phenol-chloroform extraction
Illumina TruSeq

tag: cell preparation

value: 5 days in-vitro expansion

tag: chip antibody

value: anti-BrdU agarose beads (Santa Cruz IIB5)

tag: molecule

value: BrdU-incorporated RNA


title: 12377 GRO-Seq in vitro pro-B cell

description: 12377 GRO-Seq in vitro pro-B cell Rag2(–/–)

tag: strain


title: BUR_24hr_1_1


title: BUR_6hr_2_4

value: 6hr Postmating


title: Norm-1a


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep2_Experiment_1


title: Rag1ko/ko_Bone_Marrow_ProB_rep4_Experiment_1


title: Rag1ko/ko_Bone_Marrow_ProB_rep3_Experiment_1


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep3_Experiment_1


title: BUR_6hr_2_3


title: Rag1ko/ko_Bone_Marrow_ProB_rep2_Experiment_1


title: LC2PROseq-2

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the BBMap Suite (v. 38.05) bbduk.sh tool with arguments ‘literal=AAAAAAAAAAAAAAAAAAAAAAA ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=25’.
Trimmed reads were mapped to the human genome (hg38) using hisat2 (v. 2.1.0) and hg38 indexes downloaded from UCSC with settings '--very-sensitive and --no-spliced-alignment'.
Resulting SAM files were converted to BAM format using samtools view (v. 1.8) with arguments ‘-S -b’ and then sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.25.0) for both positive and negative strands with arguments ‘-bg -ibam -g hg38 -strand [+/-]’. The fourth column (read coverage) of the negative strand file was negated and then concatenated with the positive strand file to generate a strand-differentiated bedGraph file.
FStitch (v. 1.0) was first used to filter regions of inactive transcription in all samples to lessen downstream compute processing requirements. FStitch train was used with arguments ‘-r (sample.positiveStand.bedGraph) -t (trainingFile.bed) -o (outputTrainingParameters.hmminfo)’ using the IGV (v. 2.3.75) Region Navigator tool to produce a BED format training file generated from one of the 10 min dex-treated samples that was determined to be most representative of the data in terms of read coverage, complexity, and total reads mapped.
FStitch segment was then run on all single-strand non-normalized bedGraph files with arguments ‘-r (sample.pos.bedgraph) -w (outputTrainingParameters.hmminfo) -o (sample.bed)’. Positive and negative strand files were then concatenated and sorted using sortBed in the BEDTools suite (v. 2.25.0).
Tfit (v. 1.0) was used to generate the predictions of bidirectionals/eRNAs. BED file annotations of preliminary bidirectional calls were generated using the Tfit bidir old module with arguments ‘-ij (sample.concatenated.bedGraph) -N (bidir old) -k (sample.concatenatedFStitch.bed) -mle 1 -o (output directory) -log out (output directory) -tss (hg38 RefSeq gene transcription start site file).
Using the bidirectional predictions file, the Tfit model module was run to get higher confidence calls with arguments ‘-ij (sample.concatenated.bedGraph) -k (preliminaryBidirectionals.bed) -N (tfit mod) -log out (output directory) -o (output directory) -config (config file)’ to produce a final BED annotation file of predicted bidirectionals.
Using the RefSeq : NCBI Reference Sequences for hg38, including both NM and NR accession types (downloaded from the UCSC track browser on May 18, 2018), counts were calculated for each sorted BAM file using multibBamCov in the BEDTools suite (v. 2.25.0). Genes (NM accession type) and lncRNAs (NR accession type) were then filtered such that only the isoform with the highest number of reads per annotated length was kept in order to minimize duplicate samples being included in differential transcription analysis.
DESeq2 (v. 1.20.0, Bioconductor release v. 3.7) was then used to determine which genes were differentially transcribed between the different cell types. For bidirectional/enhancer comparisons, all bidirectional prediction Tfit calls were first merged using mergeBed (argument -d 60) from the BEDTools suite (v. 2.25.0) to generate an annotation file. Counts were then calculated for each sample using multicov from the BEDTools suite (v. 2.25.0) and DESeq2 was used to calculate differentially transcribed bidirectionals/eRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files are non-normalized, strand-differentiated coverage files, as described above.

source_name: LC-2/ad airway epithelial cells

growth_protocol: A549 human lung epithelial adenocarcinoma cells (ATCC) were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Corning) with L-glutamine and 4.5 g/L glucose supplemented with 5% Fetal Bovine Serum (FBS; VWR) and 1% penicillin/streptomycin (pen/strep; Corning). LC-2/ad human lung epithelial adenocarcinoma cells were grown in a 1:1 mixture of RPMI-1640 (Corning) and Ham’s F-12 Medium with L-glutamine (Corning) supplemented with 10% FBS and 1% pen/strep. BEAS-2B transformed normal human airway epithelial cells were grown in DMEM containing 10% FBS and 1% pen/strep.

extract_protocol:
Plates were washed in PBS and cells were scraped in Lysis Buffer prior to isolation of nuclei. Nuclear run-on reactions were performed on aliquots of 10 million nuclei (two reactions were combined per library for LC-2/ad cells) in the presence of Biotin-11-CTP, then total RNA was isolated using TRIzol LS Reagent (Invitrogen). RNA was hydrolyzed with NaOH to yield fragments ~100 bp long and nascent RNA was enriched using M-280 Streptavidin Dynabeads (Invitrogen).
Sequencing adapters were ligated onto 3' ends of nascent RNA and then a second enrichment was performed using streptavidin beads. 5' ends were de-capped (RppH) and repaired (PNK) prior to ligation of sequencing adapters and the third and final streptavidin bead enrichment. Reverse transcription was then performed and purified cDNA libraries were amplified for sequencing in PCR reactions containing Illumina TruSeq Small RNA PCR Index Primers to differentially barcode the libraries and enable multiplexing. PCR-amplified libraries were size-selected for a range of ~140–350 bp (average fragment length ~250 bp) using Agencourt AMPure XP beads (Beckman Coulter) at a volume of 1X as instructed by the manufacturer. Libraries were then pooled and sequenced on an Illumina NextSeq instrument using 75 bp single-end reads.

treatment_protocol: For PRO-seq, BEAS-2B, A549 and LC-2/ad cells were each plated on 2 x 15 cm tissue culture dishes and grown to confluence. Cells were harvested under basal culture conditions (i.e., were untreated).

tag: cell line


title: LC2PROseq-1


title: FB_6h_1_1


title: BUR_6h_1_2


title: BUR_6h_1_1


title: WT_Bone_Marrow_PreB_rep4_Experiment_1

source_name: WT Bone Marrow

value: WT


title: WT_Bone_Marrow_PreB_rep3_Experiment_1


title: Rag1ko/ko_Bone_Marrow_ProB_rep1_Experiment_1


title: Norm-1b


title: WT_Bone_Marrow_PreB_rep2_Experiment_1


title: WT_Bone_Marrow_PreB_rep1_Experiment_1


title: A549PROseq-2

source_name: A549 airway epithelial cells


title: BUR_U_2_4

value: Unmated


title: WT_Bone_Marrow_ProB_rep4_Experiment_1


title: B2B30PROseq-E


title: BUR_U_2_3


title: WT_Bone_Marrow_ProB_rep1_Experiment_1


title: IghTer5H/Ter5H _Bone_Marrow_ProB_rep1_Experiment_1


title: BUR_U_1_2


title: WT_Bone_Marrow_ProB_rep3_Experiment_1


title: A549PROseq-1


title: WT_Bone_Marrow_ProB_rep2_Experiment_1


title: BUR_U_1_1


title: Day5_Ascl1_Batch2

city: Shanghai

first: Ran

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: Astrocytes infected with FUGW-Ascl1 at day 5, sequencing batch 2

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each Sample

growth_protocol: Astrocyte controls were cultured on 12 cm dish with astrocyte medium (DMEM/F-12+10% FBS+1% PS+ 2% B27 + 10 ng/ml EGF + 10 ng/ml FGF2), and all other induction samples were cultured on 6-well cell plate with inducing medium (DMEM/F-12+1% PS+ 2% B27).

extract_protocol:
Total RNAs were extracted with Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing according to standard Illumina protocols.

treatment_protocol: Astrocyte controls without treatment, and other astrocyte samples were infected with lentivirus FUGW or FUGW-Ascl1.


title: Day2_Ascl1_Batch2

description: Astrocytes infected with FUGW-Ascl1 at day 2, sequencing batch 2


title: FB_6hr_2_4


title: B2B30PROseq-E2


title: Day5_control_Batch2

description: Astrocytes infected with FUGW at day 5, sequencing batch 2


title: WF_U_2_2

source_name: Whole Female without FRT


title: N3 Group

city: Tehran

first: mehrdad

last: noruzinia

address: jalal ale ahmad

country: Iran

institute: Tarbiat Modares University

description: miRNA

data_processing:
The obtained RNA-seq data were subjected to adaptor trimming, and they were mapped to the hg19 human reference genome by the Bowtie2 software (Langmead & Salzberg, 2012). Afterward, they were annotated to the mirbase 21 release (http://www.mirbase.org/).  Preprocessed cleaned data were normalized and then analyzed using the R package DeSeq2 (Love, Huber, & Anders, 2014). Genes were considered differentially-expressed when the FC was above ±2 and the false discovery rate (FDR)-adjusted p-value < 0.05.
Genome_build: hg19

extract_protocol:
The RNA contents were extracted from the plasma samples using the miRCURY RNA Isolation Kits-Biofluids (Exiqon, Denmark) according to the manufacturer’s instructions.
In the present study, we recruited NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, Massachusetts, USA) to construct the miRNAs library according to the manufacturers’ instructions.

value: plasma

tag: health status

value: Healthy Controls

tag: menstrual phase

value: proliferative

tag: endometriosis stage


title: Day2_control_Batch2

description: Astrocytes infected with FUGW at day 2, sequencing batch 2


title: N2 Group

description: miRNA

value: secretory


title: N1 Group

description: miRNA

value: early secretory


title: Day0_Astrocyte_2_Batch2

description: Astrocytes control without virus infection at day 0, sequencing batch 2


title: WF_U_2_1


title: P6 Group

description: miRNA

value: Non-Endometriosis


title: Day5_Ascl1_Batch1

description: Astrocytes infected with FUGW-Ascl1 at day 5, sequencing batch 1


title: Day2_Ascl1_Batch1

description: Astrocytes infected with FUGW-Ascl1 at day 2, sequencing batch 1


title: FHG-2(Both DBP and DiBP)

city: Zhenjiang

first: Hui

last: Chen

address: Xuefu Road

institute: jiangsu university

data_processing:
Data filtering was performed on Raw Data, the linker sequences and low-quality reads were removed to obtain high-quality Clean Data.
HISAT2 v2.1.0 was used to sequence alignment.
The reads numbers mapped to each gene were counted by HTSeq v0.6.0.
The number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to estimate the gene expression levels of each gene which was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/danio_rerio/dna/Danio_rerio.GRCz10.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: larvae

extract_protocol:
120 hpf F1 larvae were snap frozened in liquid nitrogen, and total RNA was  harvested using Trizol reagent. The sequencing libraries were established with 3 μg RNA per sample by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were sequenced by an Illumina platform and 150 bp paired-end reads (Annoroad Gene Technology Corporation)

value: AB

value: 120 h post-fertilization

value: larvae

value: wild type

tag: agent

value: Both DBP and DiBP


title: Day5_control_Batch1

description: Astrocytes infected with FUGW at day 5, sequencing batch 1


title: P5 Group

description: miRNA

source_name: plasma

value: Endometriosis

value: stage 3-4


title: FHG-3(Both DBP and DiBP)

tag: age


title: ChIP-seq_Ascl1

description: ChIP-seq for Ascl1 in astrocytes at day 2 after virus infection

data_processing:
The quality of the reads was evaluated using the FASTQC tool.
Raw reads were mapped to mm10 version of mouse genome using bowtie2 (version: 2.3.1) program.
Enriched peaks were identified using HOMER (version 4.2) program with default parameters.
The enrichment tags were visualized using Integrative Genomics Viewer (IGV, version 2.4).
Genome_build: mm10
Supplementary_files_format_and_content: 2 bedGraph files for visualization, 1 textfile includes all binding peaks.

source_name: Astrocytes infected with FUGW-Ascl1 at day 2

growth_protocol: Astrocytes were cultured on 12 cm dish with inducing medium (DMEM/F-12+1% PS+ 2% B27).

extract_protocol:
Cells were lysed and sonicated to generate DNA fragments, then protein-DNA complexes were isolated with antibody and DNA was extracted by phenolic chloroform.
DNA library was constructed by using ChIP-Seq Sample Prep Kit (Illumina).

treatment_protocol: Astrocytes were infected with lentivirus FUGW-Ascl1.


title: P4 Group

description: miRNA

value: stage 1-2


title: ChIP-seq_Input

description: Astrocytes infected with FUGW-Ascl1 at day 2


title: FHG-1(Both DBP and DiBP)

tag: genotype


title: P3 Group

description: miRNA

tag: tissue


title: DiBPG-3(DiBP)

value: DiBP


title: P2 Group

description: miRNA


title: P1 Group

description: miRNA


title: DiBPG-1(DiBP)


title: DiBPG-2(DiBP)


title: DBPG-3(DBP)

value: DBP


title: Day2_control_Batch1

description: Astrocytes infected with FUGW at day 2, sequencing batch 1


title: DBPG-2(DBP)


title: Piriformospora 23

city: Wuerzburg

first: William

middle: Andrés

last: López Arboleda

state: Bavaria

address: Klara-Oppenheimer-Weg 32

department: Biology

institute: University of Wuerzburg

data_processing:
Quantification of transcripts was performed using Salmon v0.7.2.
Quantification files were read into R environment (version 3.5.1) and formatted to downstream analysis using DESeq2
Condition Mock vs. Infected was tested for all cell layers in each Pathogen
Supplementary_files_format_and_content: Tab-delimited file containing TPM

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Per plate, 50-100 surface-sterilized seeds were placed on the cut surface. After 2 d of stratification in darkness at 4 °C, plants were germinated and seedlings were grown vertically in poly klima ® growth chambers (poly klima GmbH, Germany) at 22 °C ± 1 °C under long day conditions (16 h light / 8 h darkness). As soon as the roots reached the infection channel (9- 11 d old seedlings), the inoculation was started with freshly harvested fungal spores

extract_protocol:
The Infection systems were combined with Translating Ribosome Affinity Purification followed by RNA sequencing (iTRAPseq). Cell-layer specific FLAG-RPL18 expressing lines (pGL2::FLAG-RPL18, pPEP::FLAG-RPL18, pSCR::FLAG-RPL18 and pSHR::FLAG-RPL18) were used to obtain supernatants with purified polysomes. This supernants were transferred for RNA isolation. This step became necessary to remove the ribosomal proteins. For this, the RNeasy ® Micro Kit (Qiagen, Germany) was used according the manufacturer’s instructions. A volume of 15 μl RNA extract was obtained in the end (RNA concentrations > 13 ng/μl).
RNA quality and fragmentation size were checked using an Experion TM RNA HighSens Analysis Kit (Bio-Rad Laboratories, Inc.). Similarly, the quality of cDNA at the end of library preparation was checked with Experion TM DNA Chips (Bio-Rad Laboratories, Inc.). Thereby, cDNA concentrations were determined to pool the samples in equal amounts. High-throughput sequencing was performed on an Illumina Genome Analyzer IIx (GAIIx) platform following the manufacturer’s instructions.

treatment_protocol: Spore solutions were prepared in Milli-Q water supplemented with 1⁄4 MS. Every infection channel was filled with 500 μl of spore solution or a mock solution (Milli-Q water supplemented with 1⁄4 MS without microorganisms). At the indicated time points, roots were collected by removing the leaves with a scalpel, flipping of the medium and carefully plucking the roots out of the Agar with forceps. The material was flash-frozen in liquid nitrogen.

tag: cell layer

value: Rhizodermis

tag: pathogen

value: Serendipita indica

value: Mock


title: Piriformospora 22

tag: treatment