title: NF1Mam20

description: PS whole_mammary_pad


title: CCB-04

status: Public on May 08 2023

type: genomic

city: Gliwice

first: Joanna

last: Tobiasz

address: Akademicka 2A

department: Department of Data Science and Engineering

country: Poland

institute: Silesian University of Technology

description:
Copy number variation data from patient id15.
id15

hyb_protocol: PCR producte were purified using magnetic beads (Agencourt AMPure, Beckman Coulter, Beverly, MA) and subsequently endlabeled with biotin and hybridized to the array. Arrays were washed and stained using a GeneChip Fluidics Station 450.

scan_protocol: Scanning used the Affymetrix GeneChip Scanner 3000 7G. Scanned data files were generated using Affymetrix GeneChip Command Console Software (version 1.2) and analyzed with the Chromosome Analysis Suite.

data_processing:
The data were processed with Chromosome Analysis Suite 3.1 tool.
Log2 Ratios

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell culture, no specific treatment

label_protocol: 250ng of genomic DNA was digested with the restriction enzyme NspI and then ligated to an adapter, followed by polymerase chain reaction (PCR) amplification using a single pair of primers that recognized the adapter sequence.

growth_protocol: Contact-inhibited (about 90% in G0-G1) fibroblast cell cultures.

extract_protocol: DNA was extracted from non-irradiated fibroblast cell cultures using Puregene DNA Purification Kit (Gentra System, Qiagen, Minneapolis, MN, USA) according to the manufacturer’s instruction.

treatment_protocol: No particulat treatment was applied prior to genomic DNA extraction. For clonogenic survival curves, X-Ray 320 kv (dose range 0-4 Gy) was used to generate survival curves.

tag: tissue

value: non-irradiated fibroblasts

tag: surviving fraction after 2 gy

tag: Sex

value: F


title: Th17Control_2_ATAC

type: SRA

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

library_source: genomic

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
ATAC-seq reads were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)  using Bowtie2.
Normalization was performed using RPGC method with Bamcoverage of Deeptools.
Assembly: mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Supplementary files format and content: Excel files include TPM values for each Sample
Supplementary files format and content: wig files were generated using "Deep tools".

organism: Mus musculus

source_name: Spleen

growth_protocol: See method in article

extract_protocol: QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN) and ATAC-Seq (ACTIVE MOTIF) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: See method in article

value: Spleen

tag: cell type

value: CD4 T cell

tag: genotype

value: Wild type

tag: treatment

value: Vehicle


title: NF1Mam10

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

country: USA

institute: Van Andel Institute

description: PS whole_mammary_pad

library_source: transcriptomic

data_processing:
Raw reads were trimmed of sequencing adapters with Trim_Galore
Trimmed reads were mapped to Rnor 6.0 assembly with STAR v2.5.2b using options ‘--twopassMode Basic’ and ‘--quantMode GeneCounts’ to directly output counts for all features from the ensemble annotation 6.0.90
Assembly: Rnor 6.0
Supplementary files format and content: raw_counts.tsv has the raw counts output from STAR mapping for features in the ensemble 6.0.90 annotation.

molecule: total RNA

organism: Rattus norvegicus

extract_protocol:
For RNA extraction of whole fat pads and tumors, fresh harvested samples were cut up and added to MPbio lysing matrix E tube. Cells were homogenized for 20 seconds in an MPbio homogenizer, then RNA was isolated from the supernatant using the Trizol-chloroform-isopropanol RNA extraction method. For RNA extraction of mature adipocytes, RNA was isolated using the Trizol-chloroform-isopropanol RNA extraction method. For RNA extraction of cultured epithelial cells and fibroblast, 1.2105 cells were plated into one well of a six-well plate. At 90-100% confluency, RNA was isolated using QIAGEN QIAshredder and RNeasy Kit manufacturer’s instructions.
Libraries were prepared by the Van Andel Institute Genomics Core from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).Individually indexed libraries were pooled and 50 bp, paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2 sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 45M reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

value: PS


title: HF-46

description:
Copy number variation data from patient id24.
id24

value: M


title: iFoxk1_ND_D5_rep1

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

description: NoDox

data_processing:
Illumina used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ATAC-seq peaks were called by MACS2
Assembly: mm10
Supplementary files format and content: peak files
Supplementary files format and content: bigwig files

source_name: EB

growth_protocol: iHA-Foxk1 and Foxk1 KO ESCs were cultured in media containing 15% fetal bovine serum (FBS), 2 mM Glutamax, 1X penicillin/streptomycin, 0.1 mM β-mercaptoethanol, and 1,000 U/mL LIF, at 37°C in 5% CO2 together with irradiated mouse embryonic fibroblasts as a feeder layer. We differentiated iHA-Foxk1 and Foxk1 KO ESCs into embryoid bodies (EBs) using mesodermal differentiation conditions. Briefly, ESCs were separated into single cells using 0.25% trypsin and plated for 50 minutes to remove fibroblast cells from the feeder layer (de-MEF step). Following de-MEF, ESCs were differentiated in mesodermal media using the shaking method in media containing 15% FBS (Foundation GeminiBio), 1X penicillin / streptomycin, 1X GlutaMAX, 50 μg/ml Fe-saturated transferrin, 450 mM monothioglycerol, 50 μg/ml ascorbic acid in IMDM media (Thermo).

extract_protocol:
iHA-Foxk1 and Foxk1 KO EBs were collected at different time periods during differentiation and disaggregated in 0.25% trypsin at 37C for 3 min incubation with gentle agitation followed by inactivation with culture medium containing 10% FBS. Cells were collected by centrifugation at 500g for 5 minutes at 4 degrees celcius and washed once with ice-cold PBS. ATAC reaction was performed with 50,000 cells as previously described38 using the Tn5 transposase (Illumina) and libraries were created at the University of Minnesota Genome Center. Libraries were then sequenced on a NextSeq Illumina platform (2x50 bp) aiming for 25 million reads per sample.
Library Creation:   ATAC-Seq library prep was performed in accordance with the ATAC-Seq protocol as described by Buenrostro, et al. In brief, transposed DNA was amplified for 5 cycles using Nextera-compatible indexed sequencing adapters. 5 ul from the PCR reaction was ran on qPCR to assess the number of additional PCR cycles required without reducing library diversity. All samples underwent additional PCR cycling as determined by their qPCR amplification curve. Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Libraries are normalized, pooled, and subjected to a double-sided AmPure to deplete un-tagmented material. Pools are QC’ed via Picogreen, Agilent BioAnalyzer High-Sensitivity, and KAPA qPCR (to assess library functionality) before normalization for sequencing.
Cluster generation and sequencing:  Pooled libraries are denatured and diluted to the appropriate clustering concentration. The libraries are then loaded onto the NovaSeq paired end flow cell and clustering occurs on board the instrument.  Once clustering is complete, the sequencing reaction immediately begins using Illumina’s 2-color SBS chemistry.  Upon completion of read 1, 2 separate 8 or 10 base pair index reads are performed.  Finally, the clustered library fragments are re-synthesized in the reverse direction thus producing the template for paired end read 2.    Primary analysis and de-multiplexing:  Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software.  The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute.  Primary analysis and de-multiplexing are performed using Illumina’s bcl2fastq v2.20.  The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released to client accounts for subsequent analysis by the mapping software and aligner of their own choosing.

tag: time

value: Day 5


title: iFoxk1_ND_D3_rep2

description: NoDox

value: Day 3


title: Th17Control_1_ATAC


title: NF1Mam18

description: IFPS whole_mammary_pad

value: IFPS


title: iFoxk1_ND_D3_rep1

description: NoDox


title: HF-06

description:
Copy number variation data from patient id13.
id13


title: Th17TOFA+LPE_2_ATAC

value: TOFA + LPE


title: NF1Mam17

description: IFPS whole_mammary_pad


title: CCT-23

description:
Copy number variation data from patient id21.
id21


title: Th17_TOFA_3_RNA_LPE

value: TOFA


title: Th17_Control_3_RNA_LPE


title: HFC-06

description:
Copy number variation data from patient id12.
id12


title: Meljuso_RDA816_RDA986_RepC

city: Cambridge

first: John

last: Doench

state: MA

address: 75 Ames St

department: Genetic Perturbation Platform

institute: Broad Institute

description: MelJuSo cells expressing 5x-tag-dCas12a-VP64 and nanobody-VP64 without the cassette containing three CD4-targeting guides

data_processing:
Sequencing reads from Genewiz were aligned to the human Genome Reference Consortium Human Build 38 (hg38) using the STAR aligner.
Transcript abundances were quantified using RNA-Seq by Expectation Maximization (RSEM).
Assembly: human Genome Reference Consortium Human Build 38 (hg38)
Supplementary files format and content: compressed tab-delimited text files include raw count values for each Sample

source_name: MelJuSo

extract_protocol:
Cells were cultivated as normal in preparation for RNA sequencing. When cells reached confluency, they were scraped from their flasks using cell scrapers, with existing media still present. 10 mL serological pipettes were used to break up cell clumps and cell-containing media was transferred to conicals. Cell mixtures were counted using a Coulter Counter to ensure that each pellet contained >1e6 cells. Cells were then pelleted by centrifugation at 321 x g for 5 minutes. Media was aspirated, pellets were resuspended in PBS, and the PBS-cell mixture was aliquoted into Eppendorf tubes. Cells were pelleted once more by centrifugation in a table-top centrifuge at maximum speed for 2 minutes. The supernatant was aspirated and pellets were flash frozen on dry ice, then frozen at -80 C, and submitted to Genewiz from Azenta Life Sciences for RNA extraction and sequencing.
RNA libraries for RNA-seq were prepared by Genewiz from Azenta Life Sciences

tag: cell line

value: MelJuSo

tag: tag vector

tag: nanobody vector

tag: group

value: CD4 guides -  FALSE


title: NF1Mam16

description: IFPS whole_mammary_pad


title: CCB-10

description:
Copy number variation data from patient id11.
id11


title: IA_Young

type: RNA

city: CHANDIGARH

first: Rashmi

last: Kumar

state: Punjab

address: CSIR-Institute of microbial technology,sector 39A chandigarh, IMTECH, housing, Type 1 A6, IMTECH, housing, Type 1 A6

country: India

institute: CSIR-Institute of microbial technology

description: Gene expression after 24hrs of LPS treatment in different groups as mentioned

hyb_protocol: Cy3-labelled mRNA samples were hybridized onto a mouse 8x60K Gene Expression V2 Array kit, G4858A (Agilent Technologies, Palo Alto, CA, USA) for 16 h at 55°C in a rotator oven and subsequently washed.

scan_protocol: The array slides were scanned using a DNA microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Hybridization signals were extracted using the Agilent Feature Extraction software 10.5 (Agilent Technologies, Palo Alto, CA, USA). Thereafter, quantitative microarray data were normalized by using the quantile normalization method from the limma R package. Estimation of differential features was performed with limma R package by using lmFit (function to fit a linear model to expression data of each feature) and eBayes (empirical Bayes function used to determine adj.P.value and logFC. Significant differential features were obtained by using thresholds adj.P.value<=0.05 and abs(logFC)>=0.5. Enrichment of functional annotation was performed with R package gprofiler2. Gene ontology summarization and treemap plot were generated with R package rrvgo.

source_name: Bone marrow derived dendritic cells

label_protocol: 500 ng of total RNA were labelled with a (Cy3 fluorochrome) one-colour  Low-Input Quick Amp labelling kit, 5190-2305 (Agilent Technologies, Palo Alto, CA, USA).

growth_protocol: Bone marrow cells were flushed away with RPMI media from mice femurs and tibiae and after RBC lysis by ACK lysis buffer and counting, 2x106 cells were plated per well in a 6-well plate. Cells were grown in RPMI-1640 with 10% FCS supplemented with penicillin (100 U/ml), L-glutamine (100 mM), streptomycin (100 mg/ml), rmGM-CSF (recombinant murine granulocyte-macrophage colony-stimulating), 2ng/ml- 554586, Biosciences (San Diego, CA, USA) and rmIL-4 (recombinant murine interleukin-4), 4ng/ml-550067, Biosciences (San Diego, CA, USA), for DC cultures. The culture was supplemented with fresh complete RPMI media containing GM-CSF (2 ng/ml) and rIL-4 (4 ng/ml) at half of its initial volume on the third day of culture. On day 7, loosely adherent cells were harvested by gentle pipetting and counted for further experiments. The methodology was followed as per the already mentioned protocol (Lutz et al., 1999).

extract_protocol: TRIzol reagent was used to isolate total RNA from DCs after LPS stimulation (1μg/ml) according to the manufacturer's protocol (Invitrogen, Carisbad, CA, USA). DNA contamination if any, was removed by incubating RNA samples with amplification grade DNase1 enzyme. Taking 260/280 ratio of 1.9-2.0 as a standard ratio for RNA purity

treatment_protocol: Later, for maturation of BMDCs (2x106/well) were stimulated with LPS-1μg/ml, L2630- Sigma-Aldrich (St. Louis, MO, USA) in 6 well plate.

tag: age

tag: gender

value: female

tag: agent


title: Th17TOFA+LPE_1_ATAC


title: NF1Mam14

description: wildtype whole_mammary_pad

value: wildtype


title: FoxK1_KO_D3_rep2

description: NoDox


title: HF-55

description:
Copy number variation data from patient id10.
id10

value: non-irradiated fibroblasts


title: Th17_TOFA+LPE_2_RNA_LPE


title: CCT-65

description:
Copy number variation data from patient id18.
id18

value: F


title: Meljuso_RDA763_RDA988_RepC

description: MelJuSo cells expressing 5x-tag-dCas12a and without the cassette containing three CD4-targeting guides

value: nanobody


title: HFC-16

description:
Copy number variation data from patient id17.
id17


title: HFC-02

description:
Copy number variation data from patient id16.
id16


title: Th17_Control_2_RNA_LPE

value: Spleen

value: CD4 T cell


title: NF1Mam12

description: PS whole_mammary_pad


title: Meljuso_RDA763_RDA988_RepA


title: NF1Mam3

description: wildtype whole_mammary_pad


title: Meljuso_RDA816_RDA811_RepB

description: MelJuSo cells expressing 5x-tag-dCas12a-VP64 and nanobody-p65 with the cassette containing three CD4-targeting guides

value: CD4 guides - True


title: NF1Mam2

description: wildtype whole_mammary_pad


title: Th17TOFA_1_ATAC

value: Wild type


title: Meljuso_RDA816_RDA987_RepC

description: MelJuSo cells expressing 5x-tag-dCas12a-VP64 and nanobody-p65 without the cassette containing three CD4-targeting guides


title: Th17_TOFA+LPE_1_RNA_LPE


title: CCF-71

description:
Copy number variation data from patient id14.
id14


title: Meljuso_RDA816_RDA811_RepA


title: NF1Mam9

description: IF whole_mammary_pad

value: IF


title: Meljuso_RDA816_RDA987_RepB


title: Th17_TOFA+LPE_3_RNA_LPE


title: NF1Mam8

description: IF whole_mammary_pad


title: Meljuso_RDA816_RDA987_RepA


title: Meljuso_RDA816_RDA810_RepC

description: MelJuSo cells expressing 5x-tag-dCas12a-VP64 and nanobody-VP64 with the cassette containing three CD4-targeting guides


title: HF-79

description:
Copy number variation data from patient id5.
id5

value: M


title: HF-66

description:
Copy number variation data from patient id8.
id8


title: Th17_Control_1_RNA_LPE

value: Vehicle


title: Meljuso_RDA816_RDA986_RepB


title: NF1Mam7

description: IF whole_mammary_pad


title: NF1Mam6

description: IFPS whole_mammary_pad

value: IFPS


title: H3K9me2_rep2

city: Seeland OT Gatersleben

first: Anne

last: Fiebig

address: Correnstraße 3

department: BIT

country: Germany

institute: IPK Gatersleben

description: The original chromatin DNA was isolated from flowers of Chionographis japonica and sonicated to 150-400 bp in length.

data_processing:
The adaptor trimmed pair-end illumina reads of ChIPseq and RNAseq in length of 150 bp were mapped to the C. japonica genome assembly using Bowtie2 with default parameters.
The Deeptools bamCompare was used to generate ChIPseq signal tracks of the average of log2-ratio of read counts in IP over input in genome-wide 10 kb windows.
Deeptools multiBigWigSummary and plotCorrelation were used to calculate and plot the Spearman correlation between different ChIPseq and RNAseq targets as a heatmap.
Assembly: GCA_947650365.1
Supplementary files format and content: bigwig

organism: Chionographis japonica

source_name: leaf

growth_protocol: Chionographis japonica plants which were grown in a shady greenhouse condition: 16 h light (from 6 AM to 10 PM), day temperature 16 °C, night temperature 12 °C) in IPK Gatersleben. Seeds of Secale cereale (inbred line Lo7) were germinated at room temperature to collect young leaf tissue.

extract_protocol:
Flowers of Chionographis japonica plants and young leaves of Secale cereale were collected, fixed, and used for chromatin preparation. The flower and leaf tissues were ground with liquid nitrogen and isolated nuclei were fixed with 1% PFA. Isolated chromatin DNAs were sonicated into 150-400 bp used for immunoprecipitation.
The ChIP-seq libraries were prepared by using NEBNEXT® UltraTM II DNA Library Prep Kit (New England Biolabs).
Low-pass genome sequencing was performed, generating 2 × 150 bp paired-end (PE) reads using NovaSeq 6000 system (Illumina).

value: leaf

tag: developmental stage

value: flowering stage

tag: replicate

value: Koshiki

tag: chip antibody


title: NF1Mam5

description: IFPS whole_mammary_pad

tag: tissue


title: Meljuso_RDA816_RDA986_RepA

value: MelJuSo

value: CD4 guides -  FALSE


title: HF-35

description:
Copy number variation data from patient id9.
id9

tag: surviving fraction after 2 gy


title: Th17_TOFA_2_RNA_LPE

value: TOFA


title: H3K4me2_rep2


title: Th17_ QKO_2_RNA_Select

value: Gene deletion of Gpam, Gpat3/Agpat9, Lplat1/Agpat1, Pla2g12a, and Scd2


title: NF1Mam4

description: IFPS whole_mammary_pad


title: Meljuso_RDA816_RDA811_RepC


title: Th17_ QKO_1_RNA_Select


title: Th17_TOFA_1_RNA_LPE


title: HF-76

description:
Copy number variation data from patient id4.
id4

value: non-irradiated fibroblasts

tag: Sex

value: F


title: NF1Mam1

description: wildtype whole_mammary_pad

value: wildtype


title: Meljuso_RDA816_RDA810_RepB


title: Integument of EG at 32 DAP Rep1

city: Wuhan

first: Liqing

last: Lu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
Cutadapt was used to remove the 3’ sequencing adapters (at least 10bp overlap) and allow 20% mismatches
The full-length isoform produced by pacbio sequencing were used to establish index using bowtie2 with default parameters
The software RSEM were used to calculate readcount of each transcript and transform into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value
The differential expression analysis was performed by DESeq R package with a criterion of |log2FoldChange| > 1 and P value < 0.05
Supplementary_files_format_and_content: Tab-delimited text files include read count and FPKM values for each sample

organism: Citrus reticulata

source_name: Integument

extract_protocol:
RNA was extracted from cell mass captured by laser capture microdissection following the manufacturer’s suggested protocol (Arcturus Picopure kit, Kit0204). About 10-20ng total RNA of 36 samples (contained three biological replications) was used for cDNA synthesis and amplification using an Ovation RNA-seq System V2 Kit (Nugen Technologies).
The first strand cDNA were synthesized using random hexamer primers and dNTPs, and the second strand cDNA were synthesized using the first strand cDNA as a template with same reaction mix as above. The purification steps were carried out in accordance with the protocol. The product was used to SPIA cDNA amplification following by the purification again with QIAGEN MinElute Reaction Cleanup Kit to guarantee no primer and dNTP remains. The cDNA libraries were sequenced with the paired-end (PE, 2 x 150bp) strategy on the Hiseq X ten platform / NovaSeq 6000 (Illumina)

value: Ovule

tag: development stage

value: 32 day after pollening

tag: cultivar

value: "Egan No.1" ponkan


title: HFC-07

description:
Copy number variation data from patient id7.
id7


title: Monocyte derived macrophages (MDM) S3C

city: San Antonio

first: Larry

middle: S

last: Schlesinger

state: Texas

address: 8715, W Military Drive, Larry Schlesinger Laboratory, Texas Biomedical Research Institute

department: Host Pathogen Interactions program

institute: Texas Biomedical Research Institute

description:
Monocyte derived macrophages (MDM)
Sample 5 (S3C)

data_processing:
Raw sequencing reads were preprocessed using Trim Galore! to trim the adapters and low-quality sequences. Trimmed reads were mapped to the human hg38 reference genome using HISAT2.
Read counts for each sample were obtained using feature Counts. Differential gene expression analysis was carried out using  DESeq2.
The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR), and the shrunken log2 fold changes (LFCs) were calculated using the adaptive shrinkage (ash) estimator with an Empirical Bayes approach. Genes with FDR-adjusted p-value <0.05 and LFC of more than 1 or less than -1 were considered to be differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: norm.counts.csv

source_name: Human PBMC, donor-3

growth_protocol: Human AMs were isolated from BAL, and purified from BAL fluid through centrifugation. Human PBMCs were isolated from healthy donor by Ficoll-Paque gradient centrifugation. Cells were cultured in the sterile Teflon wells (2x10^6/ml) with RPMI+10% autologous serum and incubated at 37°C/5% CO2 for 6 days to allow differentiation of monocytes into AML cells and untreated monocyte derived macrophages (MDM). To generate alveolar macrophage like (AML) cells, lung associated components and specific cytokines were added (Three doses). On day 6, cells were harvested and adhered to tissue culture dishes for 2h in RPMI with 10% autologous serum, lymphocytes were washed away, and then all experiments were performed. Such MDM/AML monolayers are 99% pure and viable.

extract_protocol:
Freshy isolated human alveolar macrophages (HAM) and 2h adherent cells (MDM, AML) were washed once with 1X DPBS (GIBCO), then lysed in TRIzol (Invitrogen) and RNA was isolated using Direct-zol RNA Miniprep kit, R2052 (Zymo Research) as per the manufacturer’s instructions (Zymo Research). The isolated RNA was quantified and assessed using the Qubit 4 Fluorimeter (Invitrogen). RNA quality was assessed with the 4200 TapeStation System (Agilent). Samples with an RNA integrity number (RIN) lower than 7 were discarded.
Then RNA-seq libraries were prepared from 300ng of total RNA using the mRNA-seq library preparation and 50bp single read sequencing with about 25-30M reads per sample in the NEB Next RNA Ultra Kit (Qiagen, Redwood City, CA) with poly (A) enrichment.

tag: cell types

value: PBMC derived MDM cells


title: HFS

description:
Copy number variation data from patient id3.
id3

value: M


title: Th17_ RORgt KO_2_RNA_Select

value: Spleen

tag: cell type

value: CD4 T cell

tag: genotype

value: RORgt KO

tag: treatment

value: Vehicle


title: Alveolar macrophage like (AML) cells S4B

description:
Alveolar macrophage like (AML) cells
Sample 7 (S4B)

source_name: Human PBMC, donor-2

value: PBMC derived AML cells


title: H3K9me2_rep1

value: leaf

value: flowering stage

value: Koshiki


title: Monocyte derived macrophages (MDM) S3A

description:
Monocyte derived macrophages (MDM)
Sample 3 (S3A)

source_name: Human PBMC, donor-1


title: PM1 strain, SDA 7d, 25℃ [Illumina_KD_mycelium_2(KD3M)]

city: Beijing

first: Xueyan

last: Hu

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: Peking University Health Science Center

data_processing:
cut adapter and low quanlity filter (cutadapt for Illumina and porechop for Nanopore)
circRNA identification (CIRI2 for Illumina and CIRI-long for Nanopore)
circRNA merge and quatification (CIRIquant)
linear RNA quantification (HISAT2 + Stringtie)
feature identification (in house scripts)
Assembly: De novo assembly of T. marneffei PM1 (PRJNA967827)
Supplementary files format and content: comma-delimited text files include Counts values for each Sample

organism: Talaromyces marneffei

extract_protocol:
E.Z.N.A. fungal RNA kit (Omega Bio-Tek)
VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina and circFL for Nanopore

tag: strain

value: circDS-1 KD

value: cultured at 25degreeC in SDB for 3 d


title: Meljuso_RDA816_RDA810_RepA

tag: cell line

value: MelJuSo

tag: tag vector

tag: nanobody vector

tag: group

value: CD4 guides - True


title: Integument of EG at 28 DAP Rep1

value: Ovule

value: 28 day after pollening


title: Th17_ Control_1_RNA_Select

value: Wild type


title: Integument of EG at 32 DAP Rep3

value: 32 day after pollening

value: "Egan No.1" ponkan


title: Alveolar macrophage like (AML) cells S4C

description:
Alveolar macrophage like (AML) cells
Sample 8 (S4C)


title: Integument of EG at 18 DAP Rep3

value: 18 day after pollening


title: HF-59

description:
Copy number variation data from patient id2.
id2

value: non-irradiated fibroblasts

value: M


title: H3K4me2_rep1

tag: developmental stage


title: Integument of EG at 18 DAP Rep2


title: 200d KO Hypothalamus 3

city: New York

first: Nneka

last: Southwell

state: New York

address: 407 E 64th St Fl 5

department: Brain and Mind Research Institute

institute: Weill Cornell Graduate School

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequence reads were processed using the BBDuk program in the BBMap package
Trimmed reads were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version 2.5.0a for Liver and Muscle samples, 2.7.9a for Hypothalamus).
SAM files were converted to BAM to read overlapping reads per gene using HTseq-count (version 0.6.1)

source_name: Hypothalamus

extract_protocol:
Liver, calf muscle, and hypothalamus were removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol and the Qiagen RNeasy Mini Kit (Cat# 74104). The Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hypothalamus

value: COX10 KO

tag: age (d)

value: Male


title: PM1 strain, SDA 7d, 37℃ [Illumina_KD_yeast_3(KD4Y)]

value: cultured at 37degreeC in SDB for 3 d


title: Integument of EG at 32 DAP Rep2


title: Integument of EG at 18 DAP Rep1


title: 200d KO Hypothalamus 2


title: Alveolar macrophage like (AML) cells S4A

description:
Alveolar macrophage like (AML) cells
Sample 6 (S4A)

value: PBMC derived AML cells


title: Th17_TOFA_2_RNA_Select

value: Spleen

value: CD4 T cell

value: TOFA


title: Th17_ RORgt KO_1_RNA_Select

value: RORgt KO

value: Vehicle


title: Integument of EG at 28 DAP Rep3

value: Ovule

value: 28 day after pollening


title: PM1 strain, SDA 7d, 37℃ [Illumina_KD_yeast_1(KD2Y)]

value: circDS-1 KD


title: PM1 strain, SDA 7d, 37℃ [Illumina_KD_yeast_2(KD3Y)]


title: Monocyte derived macrophages (MDM) S3B

description:
Monocyte derived macrophages (MDM)
Sample 4 (S3B)

value: PBMC derived MDM cells


title: PM1 strain, SDA 7d, 37℃ [Illumina_OE_yeast_B(OEEY)]

value: circDS-1 OE


title: Th17_ Control_2_RNA_Select

value: Wild type


title: Integument of EG at 28 DAP Rep2

value: "Egan No.1" ponkan


title: PM1 strain, SDA 7d, 25℃ [Illumina_KD_mycelium_3(KD4M)]

value: cultured at 25degreeC in SDB for 3 d


title: 200d Ctrl Hypothalamus 2

value: Hypothalamus

value: Ctrl


title: Th17_TOFA_1_RNA_Select


title: Freshy isolated HAM cells S1B

description:
Freshy isolated HAM cells
Sample 2 (S1B)

source_name: Human BAL, donor-2

value: AMs collected from BAL


title: Integument of HG at 28 DAP Rep3

value: "Huagan No.4" ponkan


title: 200d KO Hypothalamus 4

value: COX10 KO

value: Male


title: Freshy isolated human alveolar macrophages (HAM)  S1A

description:
Freshy isolated human alveolar macrophages (HAM)
Sample 1 (S1A)

source_name: Human bronchoalveolar lavage (BAL), donor-1


title: PM1 strain, SDA 7d, 25℃ [Illumina_KD_mycelium_1(KD2M)]


title: PM1 strain, SDA 7d, 37℃ [Illumina_OE_yeast_C(OEFY)]

value: cultured at 37degreeC in SDB for 3 d


title: Integument of HG at 32 DAP Rep1

value: 32 day after pollening


title: Integument of HG at 28 DAP Rep2


title: PM1 strain, SDA 7d, 37℃ [Illumina_WT_yeast_03(WTY3)]

value: WT


title: 200d KO Hypothalamus 1


title: Integument of HG at 32 DAP Rep3

value: Ovule


title: Replicate 1 of Small RNA-seq for alfalfa roots under alkaline stress for 4 hours

first: Lin

last: Chen

state: Haidian

address: Beijing, Haidian, West Road 2 yuanmingyuan.

institute: Chinese Academy of Agricultural Sciences

description: Small RNA-seq for 14 days-old alfalfa roots under alkaline stress (50 mmol/L NaHCO3)

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Medicago sativa using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Medicago sativa
Supplementary files format and content: tab-delimited text files include known miRNA values for each Sample(All_samples_known_miRNA.txt)
Supplementary files format and content: tab-delimited text files include novel miRNA values for each Sample(All_samples_novel_miRNA.txt)

organism: Medicago sativa

source_name: roots

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: roots

value: seedling

value: alkaline stress

tag: time


title: Replicate 2 of Small RNA-seq for alfalfa roots under alkaline stress for 8 hours

tag: tissue


title: Replicate 3 of Small RNA-seq for alfalfa roots under alkaline stress for 24 hours


title: PM1 strain, SDA 7d, 37℃ [Illumina_OE_yeast_A(OEDY)]

value: circDS-1 OE


title: Integument of HG at 32 DAP Rep2


title: 200d Ctrl Hypothalamus 4


title: Replicate 1 of Small RNA-seq for alfalfa roots under alkaline stress for 8 hours


title: Integument of HG at 18 DAP Rep3

value: 18 day after pollening


title: Replicate 3 of Small RNA-seq for alfalfa roots under alkaline stress for 8 hours


title: Integument of HG at 18 DAP Rep2


title: PM1 strain, SDA 7d, 25℃ [Illumina_WT_mycelium_03(WTM3)]


title: Replicate 3 of Small RNA-seq for alfalfa roots under alkaline stress for 4 hours


title: 200d Ctrl Hypothalamus 3


title: PM1 strain, SDA 7d, 25℃ [Illumina_OE_mycelium_A(OEDM)]


title: PM1 strain, SDA 7d, 25℃ [Illumina_OE_mycelium_B(OEEM)]


title: 200d Ctrl Hypothalamus 1


title: Replicate 2 of Small RNA-seq for alfalfa roots under alkaline stress for 4 hours


title: 200d KO Muscle 2

source_name: Muscle

value: Muscle

value: Female


title: PM1 strain, SDA 7d, 25℃ [Illumina_WT_mycelium_02(WTM2)]

value: cultured at 25degreeC in SDB for 3 d


title: PM1 strain, SDA 7d, 25℃ [Illumina_WT_mycelium_01(WTM1)]


title: Nucellus of EG at 32 DAP Rep3

source_name: Nucellus

value: "Egan No.1" ponkan


title: PM1 strain, SDA 7d, 25℃ [Illumina_OE_mycelium_C(OEFM)]


title: 200d KO Muscle 6


title: Integument of HG at 28 DAP Rep1

value: 28 day after pollening


title: 200d KO Muscle 1


title: Replicate 2 of Small RNA-seq for alfalfa roots under alkaline stress for 24 hours


title: PM1 strain, SDA 7d, 37℃ [Illumina_WT_yeast_02(WTY2)]


title: Replicate 1 of Small RNA-seq for alfalfa roots under alkaline stress for 24 hours


title: PM1 strain, SDA 7d, 37℃ [Illumina_WT_yeast_01(WTY1)]


title: 200d Ctrl Muscle 6

value: Ctrl


title: Replicate 2 of Small RNA-seq for alfalfa roots under normal conditions

value: CK


title: Replicate 3 of Small RNA-seq for alfalfa roots under alkaline stress for 12 hours


title: 200d KO Muscle 5

value: COX10 KO

value: Male


title: Integument of HG at 18 DAP Rep1

value: "Huagan No.4" ponkan


title: heavy0h_2

city: Palo Alto

first: Maria

last: Barna

state: CA

address: 240 Pasteur Drive, 4500

department: Genetics

institute: Stanford University

data_processing:
QC assessment of raw reads performed with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters were clipped with Trimmomatic-0.36 with the following settings LEADING:5 TRAILING:40 MINLEN:50 and reads with phred quality score > 33 were retained.
A gene index was built with RSEM version 1.2.3076 based on the axolotl transcriptome assembly of Bryant et al. (2017) downloaded from https://data.broadinstitute.org/Trinity/SalamanderWeb/Axolotl.Trinity.CellReports2017.fasta.gz and concatenated to the sequences of ERCC Spike-In mix sequences (Invitrogen, ERCC92.fa).
Paired reads were aligned with Bowtie 2 version 2.2.977 and expression was calculated with RSEM.
473,373 of 1,388,890 gene models in the transcriptome had at least one read across all libraries. This data is in processed data file "10072021_expected_counts_matrix.txt".
Raw read counts in the fraction libraries were normalized by linear scaling against the ERCC Spike-In controls in the heavy polysome libraries at 0 h. For the input libraries, the 24 h samples were normalized to the ERCC in the 0 h samples. This data is saved in file "10072021_ERCC_normalized_counts.txt".
For analysis, data were filtered to retain only genes with > 1 cpm across all input library time-points and replicates and > 10 reads in total across all fraction libraries ("RNP/free", "light" and "heavy" polysome). This resulted in 8139 normalized genes with read counts across all libraries provided in the file "10072021_normalized_and_filtered_for_analysis.txt" that were used for further analysis as reported in our manuscript.
Supplementary_files_format_and_content: Three processed data files are provided as described above: "10072021_expected_counts_matrix.txt" contains raw expected counts for all genes with at least 1 read in any one library. "10072021_ERCC_normalized_counts.txt" contains ERCC normalized counts. "10072021_normalized_and_filtered_for_analysis.txt" contains counts for 8139 genes filtered to have cpm > 1 in input libraries and > 10 reads across all polysome libraries as described above. This data was used for subsequent analysis.

organism: Ambystoma mexicanum

source_name: left forelimb 0h post-amputation

growth_protocol: Axolotls, purchased from the Ambystoma Genetic Stock Center were housed in 40% Holtfreter's Salt Solution, at room temperature, and fed three times per week with salmon pellets. Experiments were performed in compliance with Stanford's IACUC.

extract_protocol:
For each sample we pooled 5 pieces of tissue from 5 wildtype subadult axolotls. The tissues in liquid nitrogen with a mortar and pestle. A small quantity of bulk tissue powder was added to Trizol - this sample is labelled "bulk tissue" in the above data files. The powderized tissue was resuspended in lysis buffer (100 mM Tris pH7.5, 15 mM MgCl2, 150 mM NaCl, 1% Triton X-100, 2 mM DTT, 750U/mL SuperaseIn RNase Inhibitor (Ambion, AM2696), 0.2 mg/mL cycloheximide (Sigma-Aldrich, C7698-1G), 1X Halt Protease and Phosphatase Inhibitor Cocktail (Thermo Fisher, 78442), 25 U/mL Turbo DNase (Thermo Fisher, AM2238), 8% Glycerol, 0.5% DOC, 0.5 mg/mL heparin, 200 U/mL RNaseOUT Recombinant Ribonuclease Inhibitor (Thermo Fisher, 10777019), 400U/mL RNasin (Promega, N2611)) at 500 μL per 70 mg of tissue powder. Samples were incubated on ice for 20 min with sporadic vortexing and dissociated by pipetting and passing through a 16G and 18G needle. The lysates were cleared and 75 μL were removed, combined with 1 mL of Trizol Reagent (Invitrogen, 15596018) and stored at -20°C (this was the "input" sample). The remaining lysate was loaded onto 4 mL sucrose gradients (17.5% - 50%) and underwent centrifugation for 2.5 h at 4°C at 35,000 rpm on Beckman SW60 rotor. Gradients were fractionated using a density gradient fraction system (Brandel, BR-188). Fractions were collected into 100 μL of 10% SDS and subjected to acid-phenol mRNA extraction (for "free/RNP", "light" or "heavy" polysome fraction samples) or Trizol extraction ("input" or "bulk tissue" samples). Pellets were precipitated in isopropanol, washed in 75% ethanol and resuspended in 10 μL (for fractions) or 40 μL (for input) of Ultra Pure DNase/RNase-Free Distilled Water (Invitrogen, 10977-015). The fractions were pooled as follows: : (1) RNP to 40S, (2) “light” polysome containing the monosome and disome fractions, (3) “heavy” polysome containing all fractions with 3+ ribosomes. The total volume of the fraction pools was topped up to 180 μL with Ultra Pure water and 1 μL of 1:200 ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added to each fraction pool. The samples underwent DNase treatment with TURBO DNase (Ambion, AM2238) for 30 min at 37°C in a total volume of 500 μL followed by acid-phenol mRNA extraction. The samples were then resuspended in 30 μL of Ultra Pure DNase/RNase-Free Distilled Water.
Libraries were prepared by the Stanford Genomic Services Center using the TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold Human/Mouse/Rat (Illumina) and sequenced (PEx150) on a HiSeq 4000 (Illumina) following the manufacturer's instructions.

treatment_protocol: Axolotls were anesthetized in 2 g/L Tricaine in 40% Holtfreter's Salt Solution and left forelimbs were amputated at the mid-forearm level. A ~ 2 mm piece of tissue was harvested from the plane of amputation ("0h" samples). Animals recovered in clean 40% Holtfreter's Salt with 0.5 mg/L butorphanol tartrate (analgesic). At 24 h after amputation the animals were euthanized in 5 g/L Tricaine and ~2 mm piece of tissue was harvested from the plane of amputation. Tissues were snap frozen by direct immersion in liquid nitrogen immediately after harvesting and stored at -80°C until use.

value: wildtype subadult (AGSC_100S)

value: left forelimb amputation

value: plane of amputation

tag: time-point (hours post-amputation)

tag: sample type

value: heavy polysome fraction


title: 200d KO Muscle 3

tag: Sex


title: Nucellus of EG at 32 DAP Rep2

value: Ovule

tag: development stage

value: 32 day after pollening

tag: cultivar


title: Replicate 1 of Small RNA-seq for alfalfa roots under normal conditions

value: roots

tag: cell type

value: seedling

value: alkaline stress


title: Replicate 1 of Small RNA-seq for alfalfa roots under alkaline stress for 12 hours


title: Replicate 2 of Small RNA-seq for alfalfa roots under alkaline stress for 12 hours


title: heavy24h_2

source_name: left forelimb 24h post-amputation


title: 200d KO Muscle 4

value: Muscle

tag: genotype


title: 200d Ctrl Muscle 4


title: Nucellus of EG at 28 DAP Rep2

value: "Egan No.1" ponkan


title: Replicate 3 of Small RNA-seq for alfalfa roots under normal conditions

tag: treatment


title: 200d Ctrl Muscle 3

tag: strain

value: Female


title: Nucellus of EG at 32 DAP Rep1


title: Nucellus of EG at 28 DAP Rep1

value: 28 day after pollening


title: 200d Ctrl Muscle 5

value: Ctrl


title: Nucellus of EG at 28 DAP Rep3


title: RNP24h_2

value: free/RNP fraction


title: Replicate 3 of RNA-seq for alfalfa roots under alkaline stress for 8 hours

description: RNA-seq data for alfalfa roots under normal conditions and alkaline (50 mmol/L NaHCO3) stress

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Medicago sativa using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Medicago sativa
Supplementary files format and content: tab-delimited text files include known miRNA values for each Sample(fpkm.txt)


title: light0h_2

value: light polysome fraction


title: Replicate 2 of RNA-seq for alfalfa roots under alkaline stress for 8 hours


title: RNP0h_2


title: Replicate 1 of RNA-seq for alfalfa roots under alkaline stress for 8 hours


title: 200d Ctrl Muscle 2


title: 200d Ctrl Muscle 1


title: input24h_2

value: input lysate


title: Replicate 3 of RNA-seq for alfalfa roots under alkaline stress for 4 hours


title: light24h_2

value: wildtype subadult (AGSC_100S)


title: 200d KO Liver 5

source_name: Liver

value: Liver

value: COX10 KO

value: Male


title: Replicate 2 of RNA-seq for alfalfa roots under alkaline stress for 4 hours


title: 200d KO Liver 6


title: Replicate 1 of RNA-seq for alfalfa roots under alkaline stress for 4 hours


title: Nucellus of EG at 18 DAP Rep2

value: Ovule

value: 18 day after pollening


title: Nucellus of HG at 32 DAP Rep3

value: 32 day after pollening

value: "Huagan No.4" ponkan


title: Nucellus of EG at 18 DAP Rep1


title: Nucellus of HG at 32 DAP Rep1


title: Nucellus of EG at 18 DAP Rep3


title: input0h_2

value: left forelimb amputation

value: plane of amputation


title: Replicate 3 of RNA-seq for alfalfa roots under alkaline stress for 24 hours

value: roots

value: seedling

value: alkaline stress


title: 200d KO Liver 3

value: Female


title: tissue0h_1

description:
tissue0h_161219
Processed data is not provided for the "bulk tissue" samples because they were not analyzed. These samples are included for completion because they were generated at the same time and from the same samples as the other libraries.

value: bulk tissue


title: Nucellus of HG at 28 DAP Rep3

value: 28 day after pollening


title: heavy24h_1

value: heavy polysome fraction


title: Replicate 2 of RNA-seq for alfalfa roots under alkaline stress for 24 hours


title: Nucellus of HG at 28 DAP Rep2


title: 200d KO Liver 1


title: heavy0h_1

value: wildtype subadult (AGSC_100S)


title: Replicate 1 of RNA-seq for alfalfa roots under alkaline stress for 24 hours


title: tissue24h_1

description:
tissue24h_161219
Processed data is not provided for the "bulk tissue" samples because they were not analyzed. These samples are included for completion because they were generated at the same time and from the same samples as the other libraries.


title: light24h_1

value: light polysome fraction


title: Nucellus of HG at 28 DAP Rep1


title: Nucellus of HG at 32 DAP Rep2


title: Replicate 3 of RNA-seq for alfalfa roots under alkaline stress for 12 hours


title: 200d Ctrl Liver 6

value: Liver

value: Ctrl


title: light0h_1


title: Replicate 2 of RNA-seq for alfalfa roots under alkaline stress for 12 hours


title: 200d Ctrl Liver 5

value: Male


title: 200d Ctrl Liver 4


title: Nucellus of HG at 18 DAP Rep3

value: Ovule

value: 18 day after pollening


title: 200d KO Liver 2

value: COX10 KO


title: RNP0h_1

value: left forelimb amputation

value: free/RNP fraction


title: Nucellus of HG at 18 DAP Rep2

value: "Huagan No.4" ponkan


title: Replicate 1 of RNA-seq for alfalfa roots under alkaline stress for 12 hours

value: roots

value: seedling


title: 200d KO Liver 4


title: 200d Ctrl Liver 3

value: Female


title: Nucellus of HG at 18 DAP Rep1


title: Replicate 3 of RNA-seq for alfalfa roots under normal conditions

value: alkaline stress

value: CK


title: input24h_1

value: plane of amputation

value: input lysate


title: Replicate 2 of RNA-seq for alfalfa roots under normal conditions


title: 200d Ctrl Liver 1


title: 200d Ctrl Liver 2


title: input0h_1

value: wildtype subadult (AGSC_100S)


title: 20-case

status: Public on May 07 2023

city: Medellín

first: Gloria

middle: I.

last: Sanchez

state: Antioquia

address: Carrera 51D No 62-29 Lab 219

department: Facultad de Medicina

country: Colombia

institute: Universidad de Antioquia

description:
microRNA
20-57748

data_processing:
BaseCall performed with CASAVA v1.8.2
FASTQ files generated by the MiSeq instrument were uploaded to the Qiagen’s GeneGlobe Data Analysis Center – DAC and analyzed under the Primary QIAseq miRNA Quantification algorithm and the Secondary QIAseq miRNA Analysis
The trimming of the 3’ adapter and low-quality base using cut-adapt (cutadapt.readthedocs.io/en/stable/guide.html), discarding reads with less than 16 bp insert sequences or less than 10 bp sequences (defective reads).
The reads were aligned to the reference transcriptome with up to two mismatches tolerated (miRBase V.21 http://www.mirbase.org/) using Bowtie (bowtie-bio.sourceforge.net/index.shtml)
The raw count were normalized using GLM from DESeq2, the normalized counts were used to determine differential microRNA expression between high-grade cervical lesion (case)and low-grade cervical lesion (control) with DESeq2.
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Genome_build: miRBase V.21
Supplementary_files_format_and_content: Excel files contain raw counts and GLM normalized counts

extract_protocol:
The total RNA was isolated using the miRNeasy FFPE Kit (QIAGEN®) according to the manufacturer’s instructions. Briefly, the paraffin was removed with Xylene and the samples were incubated at 56°C for 15 min, then at 80°C for 15 min in an optimized lysis buffer, which contains proteinase K for RNA release from FFPE sections. Then, the sample was treated with DNase I to eliminate genomic DNA. The lysate was then mixed with guanidine salt-based Buffer to provide appropriate RNA binding conditions   and then ethanol was added, and the samples were transferred to a RNeasy MinElute spin column, where the total RNA binds to the membrane, and contaminants were washed. Finally, the sample containing the total RNA, including miRNA, was eluted in 20 μL of RNase-free water and stored at -80°C.
Library preparation was performed from 1 µg of total RNA using the QIAseq miRNA Library Kit from Qiagen. Briefly, a pre-adenylated adapter was ligated to the 3’ end of the miRNAs while an RNA adapter was ligated to the 5’ of all mature miRNAs. cDNA synthesis was carried out with a reverse transcription primer that binds at the 3’ adapter and incorporates a universal molecular index (UMI). The cDNA was cleaned up  using magnetic beads and the library was amplified by using a universal forward primer and indexing reverse primers. The libraries were  cleaned up with magnetic beads and analyzed on an Agilent 2100 Bioanalyzer using a High Sensitivity DNA 1000 chip, according to the manufacturer’s instructions. The miRNA Library concentration was determined using the Qubit™ dsDNA HS Assay kit (Invitrogen™), on the Qubit 3.0 Fluorometer (Thermo).
The libraries were adjusted to 4nM and pooled (2 10-sample pools) and sequenced at 1 x 75 bp on the MiSeq platform (Illumina) following the instructions of the MiSeq System Denature and Dilute Libraries Guide insert.

value: Cervix

tag: hpv status

value: hr-HPV

tag: disease state

value: HGSIL


title: 18-case

description:
microRNA
18-53558


title: 16-control

description:
microRNA
16-24622

value: LSIL


title: RNP24h_1


title: 17-control

description:
microRNA
17-34369


title: 19-case

description:
microRNA
19-89346


title: 8-control

description:
microRNA
8-20069


title: 7-control

description:
microRNA
7-40871


title: 10-control

description:
microRNA
10-31682


title: 14-control

description:
microRNA
14-82579

source_name: NL

value: No lesion


title: 6-case

description:
microRNA
6-10756


title: 13-case

description:
microRNA
13-73283


title: 5-control

description:
microRNA
5-51828


title: 4-case

description:
microRNA
4-19204


title: 11-control

description:
microRNA
11-54845


title: 15-case

description:
microRNA
15-73026


title: Replicate 1 of RNA-seq for alfalfa roots under normal conditions


title: 1-case

description:
microRNA
1-71278


title: 3-case

description:
microRNA
3-37969


title: 2-case

description:
microRNA
2-62320


title: HSFA3-ACC+56h-R3

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

data_processing:
Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using bwa mem (Li, 2013; http://arxiv.org/abs/1303.3997) version 0.7.12-r1044.
Mappings were sorted and indexed using samtools (Li et al., 2009; http://doi.org/10.1093/bioinformatics/btp352) version 1.3.1.
RPGC normalized coverage tracks were generated using the deepTools (Ramírez et al., 2016; http://doi.org/10.1093/nar/gkw257) version 1.50 bamCoverage function.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Normalized coverage files in bigWig format.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown on GM medium (1 % [w/v] glucose) under a 16 h/8 h light/dark cycle at 23/21°C. pHSFA3::3xFlag-HSFA3 hsfa3 was described previously (Friedrich et al., 2021; https://doi.org/10.1038/s41467-021-23786-6).

extract_protocol:
Cross-linking and immunoprecipitation of samples was performed as described previously (Kaufmann et al., 2010; Friedrich et al., 2021). Briefly, 3xFlag-HSFA2 and 3xFlag-HSFA3 seedlings were harvested at the indicated time points (3 replicates) and immediately cross-linked under vacuum in 25 ml ice-cold MC buffer (1 % (v/v) formaldehyde) for 2 x 10 min. For chromatin extraction, frozen tissue was ground, resuspended in 25 ml M1 buffer, and filtered through Miracloth mesh (Merck), washed five times in 5 ml M2 buffer, and washed once in 5 ml M3 buffer with a 10 min, 4°C, 1,000 g centrifugation step in between each washing step. The chromatin pellet was resuspended in 1 ml Sonication buffer and sonified using a Diagenode Bioruptor (17 cycles of 30 sec on/off at low intensity settings). For 3xFlag-HSFA2/A3 ChIP, chromatin was incubated with anti-DYKDDDDK paramagnetic beads (Miltenyi Biotec) for 1.5 h at 4°C and recovered with DYKDDDDK isolation kit (Miltenyi Biotec).
DNA libraries for each sample were prepared from isolated chromatin using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) in combination with NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer’s instructions. No size selection was performed after adaptor ligation. DNA was amplified by PCR with 11 amplification cycles. Library concentration and fragment size distribution were checked using D1000 ScreenTape with TapeStation bioanalyzer (Agilent). Library quantification was done with the NEBNext Library Quant Kit for Illumina (NEB) according to the manufacturer’s instructions. Pooled libraries were sequenced on a NextSeq 500 (Illumina), 75 bp SE reads.

treatment_protocol: For HS treatments for ChIP-seq, 4 d-old seedlings were exposed to a two-step acclimation (ACC) protocol consisting of 37°C for 1 h, 23°C for 90 min and 44°C for 45 min. Samples for ChIP-seq were harvested 4 h, 28 h, or 52 h after the end of the ACC treatment. Non-heat stressed (NHS) samples were harvested at the same time as the ACC+4h samples. For maintenance of acquired thermotolerance assay, 4 d-old seedlings were exposed to the same ACC protocol as described above and 3 d later, to a triggering heat stress of 44°C of 70-110 min as indicated. Seedlings were imaged 14 d after end of ACC.

value: 6 day old seedling

tag: chip antibody


title: HSFA3-NHS-R3

value: 4 day old seedling

value: NHS

value: DYKDDDDK isolation kit (Miltenyi Biotec)


title: HSFA3-NHS-R2


title: HSFA3-ACC+28h-R3

value: 5 day old seedling


title: HSFA3-ACC+4h-R3

value: 4 day old seedlings


title: HSFA3-ACC+28h-R2


title: HSFA3-ACC+56h-R1


title: HSFA3-NHS-R1


title: HSFA3-ACC+28h-R1


title: 9-control

description:
microRNA
9-34778


title: HSFA3-ACC+4h-R1


title: HSFA2-NHS-R3


title: HSFA2-NHS-R2


title: HSFA2-ACC+4h-R3


title: HSFA2-ACC+28h-R3


title: HSFA2-ACC+56h-R3


title: HSFA2-ACC+28h-R2


title: HSFA2-ACC+4h-R2


title: HSFA2-NHS-R1


title: HSFA2-ACC+56h-R2


title: 12-control

description:
microRNA
12-32386


title: HSFA2-ACC+4h-R1


title: HSFA2-ACC+56h-R1


title: PIX-HALO_37

data_processing:
Library strategy: DAP-seq
Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using bwa mem (Li, 2013; http://arxiv.org/abs/1303.3997) version 0.7.12-r1044.
Mappings were sorted and indexed using samtools (Li et al., 2009; http://doi.org/10.1093/bioinformatics/btp352) version 1.3.1.
RPGC normalized coverage tracks were generated using the deepTools (Ramírez et al., 2016; http://doi.org/10.1093/nar/gkw257) version 1.50 bamCoverage function.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Normalized coverage files in bigWig format.

extract_protocol:
Genomic DNA was isolated from young seedlings of Col-0 using CTAB method, and digested with RNase A and cleaned using phenol: chloroform: isoamylalcohol.
Isolated genomic DNA was sonicated to an average length of 200 bp in Covaris sonicator and quantified. After sonication, fragmented genomic DNA was end prepared and adaptor ligated according to the protocol of  NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645), and purified using NaOAc and ethanol. The DNA was diluted in Elution buffer (10 mM Tris-HCl, pH 8.5) and measured using Qubit dsDNA HS Assay Kit. 200-300 ng prepared DNA was used for each binding reaction. cDNA sequences of HSFA1b, HSFA2 and HSFA3 were subcloned into pIX-HALO. HALO-tagged HSFs were expressed in the TNT wheat germ expression system (Promega). Different combinations of HSFs or HALO (negative control) were incubated with prepared DNA overnight at room temperature, respectively. For 37°C treatment, the samples were treated at 37°C for 45 min before overnight incubation at room temperature. Washing and DNA recovery steps were as described (Bartlett et al., 2017). The recovered DNA was amplified using Q5 Master Mix and different index primers in NEBNext® Ultra™ II DNA Library Prep Kit, then pooled and size selected (200-700 bp) by gel fractionation. 10 nM DNA library was sequenced using NextSeq 500/550 Mid output Kit (300 cycles), 150 bp SE reads.

value: young seedlings

value: 37°C for 45min


title: HSFA3-ACC+56h-R2


title: A2_37


title: HSFA3-ACC+4h-R2


title: A3_37


title: A1b-A2_37


title: PIX-HALO


title: rat ileum, control [C1_I]

city: Kobe

first: Youhei

last: MANTANI

state: Hyogo

address: Rokkodai-cho 1-1, Nada-ku

department: Graduate school of Agricultural Science

institute: Kobe University

data_processing:
We controlled the quality of RNA-seq data using fastp (version 0.20.1) with “-3 -q 30” options to discard reads with low quality.
We aligned the remaining reads to the rat reference genome (rn6) using HISAT2 (version 2.2.1) with the “--no-mixed --dta” options.
For the quantification of gene-level expressions, we counted reads for each transcript using featureCounts (version 1.6.4) with the RefSeq gene annotation (rn6.ncbiRefSeq,gtf) and the “-p -B -t exon -g gene_id” options.
The read count was used in iDEP (version 94), which is a web tool for RNA-seq data analysis, to make dimensionality reduction plots (tSNE) and perform differential expression analysis with the DESeq2 method.
Assembly: rn6
Supplementary files format and content: DESeq2_result.xlsx

source_name: ileum

extract_protocol:
RNA was harvested using Nucleospin RNA plus kit (MACHEREY-NAGEL). 1.7 ug or more of total RNA was used for the construction of sequencing libraries.
We prepared Poly(A) RNA using Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and then RNA libraries using NEBNext® Ultra™II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: We treated rats with a nonabsorbable antibiotics cocktail (vancomycin, polymyxin B and sucrose) for antibiotics-treatment group or sucrose solution for control group in drinking water 1 day before euthanasia.

value: Wistar rat

value: ileum

value: WT

value: sucrose solution


title: rat ileum, control [C3_I]


title: rat ileum, control [C2_I]


title: rat ileal Peyer's patch, control [C3_P]

source_name: ileal Peyer's patch

value: ileal Peyer's patch


title: rat ileal Peyer's patch, antibiotics treatment [A3_P]

value: antibiotics cocktail (vancomycin, polymyxin B and sucrose)


title: rat ileal Peyer's patch, control [C2_P]


title: A2


title: A2-A3


title: rat ileal Peyer's patch, antibiotics treatment [A2_P]


title: HSFA2-ACC+28h-R1


title: rat ileum, antibiotics treatment [A2_I]


title: A3


title: A1b


title: rat ileum, antibiotics treatment [A1_I]


title: Sorted CD8+ T cells, SRT-like (Sample 12)

city: Stanford

first: Juliana

last: Idoyaga

state: California

address: 299 Campus drive, 3RD FLOOR RM D330 & D345

department: Microbiology and Immunology

description: Sorted CD8+ T cells_SRT-like assayed by NanoSTRING and counts were normalized via ROSALIND software

hyb_protocol: According to the manufacturer's instructions

scan_protocol: nCounter analysis system

data_processing: Data was analyzed by ROSALIND® with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Normalization, fold changes and p-values were calculated using criteria provided by NanoSTRING ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual

source_name: Sorted CD8+ T cells, SRT-like

growth_protocol: MC38 tumor cells were implanted into C57BL/6J mice and treated with radiation therapy (20Gy) once the tumor reached 40-100 mm3.

extract_protocol: Cells were washed and resuspended in 1/3 RNeasy Lysis Buffer RLT (Qiagen) at a concentration of 1,000-5,000 cells/μL. Samples were analyzed on the NanoString nCounter® Mouse Immune Exhaustion Panel Standard Platform according to the manufacturer’s instructions.

treatment_protocol: Tumors were digested with collagenase and Dnase into a single cell suspension. Cells were stained with primary antibody, enriched with CD45-biotin and anti-biotin beads, and sorted for CD8+ T cells

value: CD8+ T cells

value: SRT-like


title: rat ileal Peyer's patch, control [C1_P]


title: A1b-A3


title: A1b-A2


title: Sorted CD8+ T cells, SRT-like (Sample 11)


title: LB_FIN_6

city: Irvine

last: Calof

address: Biological Sciences III, 519 Ring Rd

department: Developmental & Cell Biology

institute: University of California, Irvine

data_processing:
Base-calling was performed in Illumina's HCS v3.4.0.
Read filtration, trimming, mapping, and cell calling was performed in 10X Genomics' Cell Ranger v3.0.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz contain list of all cell barcodes in that library; features.tsv.gz contain list of all genes reads were mapped onto in reference genome; matrix.tsv.gz; contain UMI count per gene per cell.

molecule: polyA RNA

source_name: intraembryonic mouse embryo

extract_protocol:
Whole embryos were dissected from pregnant dams in 1X phoshate buffered saline (PBS). Parietal and visceral yolk sacs were removed for DNA extraction and PCR genotyping. Extraembryonic tissue was removed for genotyping by X-gal stain. Intraembryonic tissues from embryos of the same genotype were paired into 1.5 ml DNA LoBind tubes, washed with 1X PBS, incubated in 1X TrypLE Express at 37°C for 5 (early bud), 10 (late bud), or 15 (early head fold) min, dissociated into single cells by passage through pipette, quenched with 1X PBS, underlayed with hanks balanced salt solution + 1% deaceytlated bovine serum albumin, and spun at 1200 rpm for 5 min in a swing bucket centrifuge. The resulting upper supernatant layer was discarded by pipette and the cells were spun again at 1200 rpm for 5 min. The resulting supernatant was again discarded. The cells were washed in 1X PBS by raising them in 1X PBS, spinning them at 1200 rpm for 5 min, and discarding the resulting supernatant.  The cells were then re-suspended in 1X PBS.
Single cell RNA libraries were constructed using 10X Genomics Chromium Single Cell 3' Reagents Kit v2 protocol and paired-end sequenced with single-indexing on the Illumina HiSeq 4000 to a minimum of 50,000 reads per cell using its standard protocol.

value: late bud (7.5 dpc)

value: Nipbl FIN/+


title: rat ileum, antibiotics treatment [A3_I]


title: EHF_FLOX_1

value: early head fold (7.6 dpc)

value: Nipbl Flox/+


title: LB_FIN_5


title: EHF_FLOX_2


title: A1b_37


title: LB_FIN_4


title: Sorted CD8+ T cells, SRT-like (Sample 10)


title: Adult mouse lung Acta2hrGFP+ cells

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

library_source: transcriptomic single cell

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCm38 with GFP and dsRed
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38
Supplementary files format and content: h5 is the standard output from the cell ranger count pipeline

organism: Mus

source_name: Acta2hrGFP/Cspg4dsRed mouse lungs

growth_protocol: Cells were isolated from adult mice and directly submitted for sequencing without culture

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single-Cell 30 Library Kit (10X Genomics) and loaded on a NextSeq500 (Illumina) with a custom sequencing setting to obtain a sequencing depth of ~40k reads/cell

treatment_protocol: Lungs were isolated, digested into a single cell suspension using collagenase and dispase, and treated with red blood cell lysis buffer.

value: Adult

tag: age

value: 3-6 months old

value: lung

value: Acta2-hrGFP+ lung cells

tag: isolation method

value: FACS purification for live, single, GFP+ cells


title: LB_FIN_2

tag: developmental stage


title: Sorted CD8+ T cells, CRT (Sample 9)

description: Sorted CD8+ T cells_CRT assayed by NanoSTRING and counts were normalized via ROSALIND software

source_name: Sorted CD8+ T cells, CRT

value: CRT


title: LB_FIN_3


title: A1b-A2-A3

value: young seedlings


title: rat ileal Peyer's patch, antibiotics treatment [A1_P]

value: Wistar rat

value: WT


title: LB_FLOX_6


title: Sorted CD8+ T cells, SRT (Sample 8)

description: Sorted CD8+ T cells_SRT assayed by NanoSTRING and counts were normalized via ROSALIND software

source_name: Sorted CD8+ T cells, SRT

value: SRT


title: LB_FIN_1


title: LB_FLOX_5


title: LB_FLOX_4


title: Sorted CD8+ T cells, Nontreated (Sample 7)

description: Sorted CD8+ T cells_Nontreated assayed by NanoSTRING and counts were normalized via ROSALIND software

source_name: Sorted CD8+ T cells, Nontreated

value: Nontreated


title: Sorted CD8+ T cells, Nontreated (Sample 6)

value: CD8+ T cells


title: LB_FLOX_3


title: Serum, 3 months post-RT, patient 27

city: Łódź

first: Zuzanna

last: Nowicka

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

institute: Medical University of Łódź

data_processing:
Assayed miRNAs must have been detected with ≥ 5 Cqs less than the negative control, and with Cq < 37 to be included in the data analysis
Cq was calculated as the 2nd derivative. All data were normalized to the average of assayed miRNAs detected in all samples (average–assay Cq)
Fold Change worksheet reports ratios of miRNA expression for comparisons between timepoints

label: SYBR Green

source_name: Serum

label_protocol: 19 μl RNA was reverse transcribed in 95 μl reactions using the miRCURY LNA™ Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). cDNA was diluted 50 x and assayed in 10 μl PCR reactions according to the protocol for miRCURY LNA™ Universal RT microRNA PCR

extract_protocol: Total RNA was extracted from the samples using the miRCURY RNA isolation kit – Biofluids; high-throughput bead-based protocol v.1 (Exiqon, Vedbaek, Denmark) in an automated 96 well format. The purified total RNA was eluted in a final volume of 50 μl.

treatment_protocol:
All patients underwent adjuvant chemotherapy prior to RT, if indicated. Concomitant treatment with systemic therapies other than chemotherapy was allowed, including treatment with trastuzumab, tamoxifen or aromatase inhibitors. From eligible patients, three serum samples were collected: prior to starting RT, 24 hours after receiving the last fraction of RT, and one month after the last fraction of RT, during a routine visit.
The isolated and frozen serum was thawed on ice and centrifuged at 3000 x g for 5 min in a 4°C microcentrifuge. An aliquot of 200 μL per sample was transferred to a FluidX tube and 60 μl of Lysis solution BF containing 1 μg carrier-RNA per 60 μl Lysis solution BF and RNA spike-in template mixture was added to the sample, mixed for 1 min and incubated for 7 min at room temperature, followed by the addition of 20 μL Protein Precipitation solution BF.

tag: time point

value: Timepoint 3

tag: diagnosis

value: Breast cancer


title: EB_FLOX_1

value: early bud (7.4 dpc)


title: Serum, 3 months post-RT, patient 28


title: mock infected, scRNAseq

city: New Haven

first: Holly

last: Steach

state: Connecticut

address: 300 Cedar St.

department: School of Genetics

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38, HSV-2 SD90
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tonsil

extract_protocol:
Human palatine tonsillar tissue was obtained from a patient undergoing elective tonsillectomy, placed immediately into 50ml conical tubes containing 30ml RPMI 1640 supplemented with 10% (v/v) fetal bovine serum; 100U/ml penicillin, 100ug/ml streptomycin, 0.25ug/ml Amphotericin B (Gibco Cat. no. 15240062), and 5ug/ml Gentamicin (Lonza Cat. no. 17-518L) (RPMI-t) and processed within two hours. To isolate CD4+ T cells, tonsillar tissue was cut into small sections using sterile scissors and manually dissociated by passing through a 70mm mesh strainer to form single cell suspensions. The single cell suspensions were then pelleted and washed 2x in ice cold RPMI-t. Cells were resuspended in 45ml RPMI-t and overlayed on 15ml Ficoll and centrifuged at 1200xg for 20 minutes. Cells isolated from the interphase were washed twice with RPMI-t and CD4 T cells were isolated by negative selection using the EasySepTM Human CD4+ T Cell Enrichment Kit (Cat. 19052, STEMCELL Technologies). Cells isolated from tonsil were cultured in RPMI-t,  harvested at 0 (mock), 6 and 24 h post-infection and dead cells were depleted by FACS.
Single cell libraries were prepared at the Yale Center for Genome Analysis. Gel/bead emulsions were prepared by loading single cell suspensions in RT Master Mix on the Single Cell A Chip with a pool of 750,000 barcoded gel beads each containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence. Leftover biochemical reagents and primers were removed using silane magnetic beads. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) was added during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: CD4+ T cells

tag: tissue

value: tonsil


title: 6H post HSV2 infection, scRNAseq

description: 10x Genomics


title: 24H post HSV2 infection, scRNAseq

description: 10x Genomics


title: 9_P_1.tabular

description:
100bp
30M reads

data_processing:
Samples were checked for read quality and adapter contamination using FastQC
transcripts were aligned using the GENCODE transcript sequences (v33) as the reference file with Salmon
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: CD4+ T cells

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (Qiagen Cat. no. 217084) per manufacturer’s instructions
Libraries were prepared at the Yale Center for Genome Analysis. mRNA was purified from 200ng of RNA with oligo-dT beads (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing were performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs were ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Indexed libraries were quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854). Insert size distribution was determined using an Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/l and a size distribution of 150-300bp were used for sequencing.

treatment_protocol: CD4 T cells from 5 healthy donor leukopaks were stimulated with ImmunoCultTM Human CD3/CD28 T Cell Activator (Cat. 10971, STEMCELL Technologies) for 72 h. Stimulated cells were mock infected or infected with HSV-2(333 ZAG) at MOI = 10

tag: patient id

value: HSV-2(333 ZAG) at MOI = 10

tag: time


title: 9_UI_1.tabular

description:
100bp
30M reads

value: mock infected


title: Serum, 3 months post-RT, patient 25


title: EB_FLOX_2

value: Nipbl Flox/+


title: Serum, 3 months post-RT, patient 26


title: LB_FLOX_1

value: late bud (7.5 dpc)


title: Serum, 3 months post-RT, patient 24


title: Sorted CD8+ T cells, CRT (Sample 5)


title: 8_UI_2.tabular

description:
100bp
30M reads


title: Sorted CD8+ T cells, SRT (Sample 3)


title: Sorted CD8+ T cells, SRT (Sample 2)


title: Serum, 3 months post-RT, patient 21


title: Serum, 3 months post-RT, patient 22


title: 9_N_1.tabular

description:
100bp
30M reads


title: 8_UI_1.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 19


title: 8_P_2.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 23


title: Serum, 3 months post-RT, patient 20


title: Serum, 3 months post-RT, patient 14


title: Serum, 3 months post-RT, patient 15


title: Sorted CD8+ T cells, CRT (Sample 4)


title: 8_P_1.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 18


title: 7_UI_2.tabular

description:
100bp
30M reads


title: Sorted CD8+ T cells, Nontreated (Sample 1)


title: 20230111_30102627890622-01_Sample12_12

description: Sorted CD8+ T cells_SRT-like sequenced by NanoSTRING and counts were normalized via ROSALIND software

source_name: Sorted monoACT_CRT

growth_protocol: MC38 tumor cells were implanted into C57BL/6J mice and treated with radiationtherapy (20Gy) once the tumor reached 40-100 mm3.

extract_protocol: Cells were washed and resuspended in 1/3 RNeasy Lysis Buffer RLT (Qiagen) at a concentration of 1,000-5,000 cells/μL. Samples were analyzed on the NanoSting nCounter® Mouse NanoString nCounter® Mouse Myeloid Innate Immunity V2 Panel Standard Platform according to the manufacturer’s instructions.

treatment_protocol: Tumors were digested with collogenase and Dnase into a single cell suspension. Cells were stained with primary antibody, enriched with CD45-biotin and anti-biotin beads, and sorted for CD8+ T cells

value: conformal radiotherapy


title: 20230111_30102627890622-01_Sample11_11


title: Serum, 3 months post-RT, patient 11


title: Serum, 3 months post-RT, patient 17


title: 20230111_30102627890622-01_Sample10_10


title: 8_N_2.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 16


title: 20230111_30102627890622-01_Sample06_06

description: Sorted CD8+ T cells_Nontreated sequenced by NanoSTRING and counts were normalized via ROSALIND software

source_name: Sorted Monocytes_CRT


title: 20230111_30102627890622-01_Sample08_08

description: Sorted CD8+ T cells_SRT sequenced by NanoSTRING and counts were normalized via ROSALIND software

source_name: Sorted monoACT_SRT

value: shield radiotherapy


title: 8_N_1.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 13


title: Serum, 3 months post-RT, patient 12


title: Serum, 3 months post-RT, patient 8


title: 20230111_30102627890622-01_Sample09_09

description: Sorted CD8+ T cells_CRT sequenced by NanoSTRING and counts were normalized via ROSALIND software


title: Serum, 3 months post-RT, patient 5


title: 20230111_30102627890622-01_Sample04_04


title: 7_N_1.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 1


title: 20230111_30102627890622-01_Sample07_07


title: Serum, 3 months post-RT, patient 9


title: 20230111_30102627890622-01_Sample02_02

source_name: Sorted Monocytes_SRT


title: 6_UI_1.tabular

description:
100bp
30M reads


title: 7_P_2.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 3


title: Serum, after RT, patient 26

value: Timepoint 2


title: Serum, 3 months post-RT, patient 6


title: Serum, 3 months post-RT, patient 7


title: Serum, after RT, patient 24


title: 7_N_2.tabular

description:
100bp
30M reads


title: 6_P_2.tabular

description:
100bp
30M reads


title: Serum, 3 months post-RT, patient 4


title: 6_P_1.tabular

description:
100bp
30M reads


title: 7_UI_1.tabular

description:
100bp
30M reads


title: 20230111_30102627890622-01_Sample03_03


title: Serum, after RT, patient 21


title: HL_60_EZH2_3_S60869

city: Graz

first: Armin

last: Zebisch

state: Styria

address: Auenbruggerplatz 38

department: Division of Hematology

country: Austria

institute: Medical University of Graz

description: HL-60 cells with EZH2 knock-down construct

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
On-instrument basecalling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes based on Picard tools 2.18.24 (http://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e96 (April 2019) with STAR 2.5.2b and options suggested be the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Biocoductor 3.9 package DESeq2 1.24.0, running under R 3.6.1.
Genome_build: GRCh38 (hg38) Reference Genome Assembly
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: RAS-mutated acute myeloid leukemia cell line HL-60

growth_protocol: HL-60 cells were cultured in RPMI-1640 media supplemented with 0.05% FBS for 24 hours prior to RNA extraction.

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen), including DNase treatment, following the manufacturer’s instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

treatment_protocol: HL-60 cells with a stable knockdown and a respective control situation were used for this experiment. To create these cells, HL-60 were lentivirally transduced with either an EZH2-shRNA vector, or with a matching scrambled control vector. Stable cells were selected by puromycin. Puromycin was washed away two days before the experiment.

tag: cell line

tag: transfection

value: EZH2 shRNA


title: 6_N_2.tabular

description:
100bp
30M reads

tag: cell type


title: Serum, after RT, patient 28


title: Serum, 3 months post-RT, patient 2


title: Serum, after RT, patient 20


title: 20230111_30102627890622-01_Sample01_01


title: Serum, after RT, patient 19


title: 20230111_30102627890622-01_Sample05_05


title: 7_P_1.tabular

description:
100bp
30M reads


title: Serum, after RT, patient 18


title: Serum, after RT, patient 16


title: Serum, after RT, patient 15


title: Serum, after RT, patient 27


title: HL_60_EZH2_4_S60870

value: RAS-mutated acute myeloid leukemia cell line


title: Serum, after RT, patient 25


title: Serum, after RT, patient 14


title: 5_P_2.tabular

description:
100bp
30M reads


title: 6_UI_2.tabular

description:
100bp
30M reads


title: 5_P_1.tabular

description:
100bp
30M reads


title: Serum, after RT, patient 22


title: Y541S_ML_placebo_sample5

city: South San Francisco

first: Jackson

last: Liang

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

data_processing:
HTSeqGenie pipeline
Genome_build: GRCm38
Supplementary_files_format_and_content: TAB (Raw counts and rpkm per gene)

source_name: Mammary mature luminal cells

growth_protocol: Animals were raised under standard husbandry methods until 8 weeks of age.

extract_protocol:
Mammary glands were dissected from treated animals; mature luminal cells were isolated from tissues by FACS. RNA was isolated from mature luminal cells via Qiagen Rneasy Micro Plus kit.
Libraries were prepared from cDNA using the Nextera XT DNA Sample Preparation kit.

treatment_protocol: Animals were ovariectomized, then implanted with hormone pellets (placebo, E2, or P4). Hormone pellet incubation for 8 days post-implantation, then tissue harvest.

tag: er mutation

value: Placebo

value: Mammary mature luminal cells


title: Serum, after RT, patient 23


title: 6_N_1.tabular

description:
100bp
30M reads

tag: treatment


title: 5_N_2.tabular

description:
100bp
30M reads


title: HL_60_EZH2_1_S60868


title: Serum, 3 months post-RT, patient 10


title: HL_60_CTRL_4_S60872

description: HL-60 cells with control construct

value: scrambled control shRNA


title: Serum, after RT, patient 17


title: HL_60_CTRL_3_S60871

description: HL-60 cells with control construct


title: Serum, after RT, patient 10


title: Serum, after RT, patient 11


title: WT_ER_ML_P_sample4

value: WT


title: 5_UI_2.tabular

description:
100bp
30M reads


title: Serum, after RT, patient 13

value: Breast cancer


title: Psoriasis skin 4

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
After sequencing, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Seurat was then used to analyze the expression matrix. Specifically, the SCTransform function was used to scale the data and find variable genes with default parameters. PCA and UMAP were applied for dimensional reduction. The FindTransferAnchors function was used to find a set of anchors between the scRNA-seq data and spatial-seq data, which were then transferred from the scRNA-seq to the saptial-seq data using the TransferData function. The major cell types obtained in the scRNA-seq data were used to annotate the spatial-seq data. The predicted cell type composition for each spot was then used to cluster the spots by the k-means algorithm. The clusters were annotated based on the average cell type prediction score across all the spots in the cluster. The cluster marker genes were found using the FindAllMarkers function. Differential expression analysis between the NS and PP keratinocytes were performed using the FindMarkers function. The common DEGs comparing NS to PP keratinocytes in both scRNA-seq and spatial-seq were plotted.
Assembly: hg38
Supplementary files format and content: zipped file containing the expression matrix, staining picture, and spatial location

source_name: skin

extract_protocol:
Skin samples were frozen in OCT medium and stored at -80°C until sectioning. Optimization of tissue permeabilization was performed on 20-μm-thick sections using Visium Spatial Tissue Optimization Reagents Kit (10X Genomics, Pleasanton, CA, USA), which established an optimal permeabilization time to be 24 minutes. Samples were mounted onto a Gene Expression slide (10X Genomics), fixed in ice-cold methanol, stained with hematoxylin and eosin, and scanned under a microscope (Keyence, Itasca, IL, USA). Tissue permeabilization was performed to release the poly-A mRNA for capture by the poly(dT) primers that are precoated on the slide and include an Illumina TruSeq Read, spatial barcode, and unique molecular identifier (UMI). Visium Spatial Gene Expression Reagent Kit (10X Genomics) was used for reverse transcription to produce spatially barcoded full-length cDNA and for second strand synthesis followed by denaturation to allow a transfer of the cDNA from the slide into a tube for amplification and library construction.   For Visium for FFPE, the skin samples were formalin-fixed and paraffin-embedded. 5-micron thick sections were mounted onto a Visium Gene Expression slide (10X Genomics), baked at 42°C for 3 hours, and dried in a desiccator at room temperature overnight. For deparaffinization, the slide was incubated at 60°C for 2 hours, immersed in xylene, and rehydrated in an ethanol gradient. H & E staining was then performed using Mayer’s hematoxylin (Millipore Sigma), bluing reagent (Dako, Agilent), and alcoholic eosin (Millipore Sigma). Stained slides were scanned under a microscope, followed by decrosslinking using 0.1 N HCl and TE Buffer (pH 9.0) to release RNA that was sequestered by formalin. Human whole transcriptome probe panel (10x) that consisted of a pair of specific probes (5’ containing Small RNA Read 2S and 3’ containing poly-A) for each gene was hybridized to RNA. Probe pairs were then ligated to seal the junctions between them and to form the single-stranded ligation products. The samples were treated with RNase and permeabilized to release the ligation products. Poly-A portion of the products was then captured by the poly(dT) regions of the capture probes precoated on the Visium slide that also include an Illumina Read 1, spatial barcode, and unique molecular identifier (UMI). Probes were extended to produce spatially barcoded ligated probe products and released from the slide for indexing via Sample Index PCR and final library construction and sequencing.
Visium Spatial Single Cell 3ʹ Gene Expression libraries consisting of Illumina paired-end sequences flanked with P5/P7 were constructed after enzymatic fragmentation, size selection, end repair, A-tailing, adaptor ligation, and PCR. Dual Index Kit TT Set A (10X Genomics) was used to add unique i7 and i5 sample indexes and generate TruSeq Read 1 for sequencing the spatial barcode and UMI and TruSeq Read 2 for sequencing the cDNA insert, respectively.

value: skin

tag: tissue storage

value: FFPE

value: psoriasis


title: 5_UI_1.tabular

description:
100bp
30M reads

value: CD4+ T cells


title: WT_ER_ML_P_sample5


title: Y541S_ML_E2/P_sample1


title: Serum, after RT, patient 5


title: Serum, after RT, patient 12


title: Psoriasis skin 3

value: Frozen


title: Serum, after RT, patient 9


title: Serum, after RT, patient 8


title: Serum, after RT, patient 4


title: HL_60_CTRL_5_S60867

description: HL-60 cells with control construct


title: Serum, after RT, patient 6


title: Psoriasis skin 2


title: Alveolar organoids, BLM, rep2, input

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

institute: Hamamatsu University School of Medicine

data_processing:
Adapter sequences and low-quality bases were removed from the sequencing reads with Trim galore ver. 0.6.7 with '-e 0.1 --nextseq 30' parameters.
The trimmed reads were aligned to the UCSC mm39 genome sequences using Bowtie2 ver. 2.5.1 with default parameters.
Filtering of uniquely mapped reads was performed using -F '[XS] == null and not unmapped and not duplicate' in Sambamba ver. 0.8.2.
Peaks were called using MACS3 ver. 3.0.0b1 with the significance cut-off q-value = 0.01 for each sample.
Identification of peaks that were significantly enriched in the BLM-treated samples was calculated using the DiffBind ver. 3.8.4 with edgeR ver. 3.40.2 and filtered with FDR < 0.05.
To associate peaks with genes, peak positions were converted to mm10 and then analyzed on the GREAT ver. 4.0.4 website.
Assembly: UCSC mm39
Supplementary files format and content: bam, narrowPeak (except for Input sample)

source_name: Alveolar organoids

extract_protocol:
Cells were fixed in a PBS (-) solution containing 1 % formaldehyde and 2 mM DSG for 10 min. ChIP was performed as previously described (Kadota et al, 2017) except that, RIPA buffer was used instead of LB3 lysis buffer at permeabilization and sonication steps. Chromatin lysate from 1-5 × 10^7 organoid cells was prepared using the Covaris S220 sonicator.
Illumina compatible libraries were prepared from 20 ng of input DNA or the 2-4 ng ChIP DNA after size selection for 50-400 bp DNA fragments by AMPure XP beads, using the KAPA LTP Library Preparation kit and TruSeq DNA UD Indexes.

value: Alveolar organoids

tag: genotype

value: Wild-type

value: bleomycin 100μM, 24h


title: Alveolar organoids, BLM, rep2

value: p53 (D2H9O) Rabbit mAb, CST #32532


title: Y541S_ML_E2/P_sample3


title: Serum, after RT, patient 7

value: Timepoint 2


title: Alveolar organoids, BLM, rep1


title: Serum, after RT, patient 3


title: 5_N_1.tabular

description:
100bp
30M reads

value: HSV-2(333 ZAG) at MOI = 10


title: Y541S_ML_E2/P_sample2


title: Y541S_ML_P_sample1


title: Serum, after RT, patient 2


title: Alveolar organoids, CTRL, rep2, input

value: DMSO, 24h


title: Serum, before RT, patient 28

value: Timepoint 1


title: Healthy control skin 1

tag: disease state

value: healthy


title: Y541S_ML_E2_sample2

value: Mammary mature luminal cells


title: Y541S_ML_E2_sample3


title: Y541S_ML_P_sample3


title: Alveolar organoids, BLM, rep1, input

tag: chip antibody


title: Y541S_ML_P_sample2


title: ChIP-seq_D542G_PR_rep2

data_processing:
ENCODE ChIP-seq pipeline
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Whole mammary glands

extract_protocol:
Minced mammary glands were fixed in formalin, then used for chromatin preparation.
Chromatin was isolated by disruption with a Dounce homogenizer in lysis buffer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. 30 µg of chromatin was precleared with protein A agarose beads (Invitrogen), then genomic DNA regions of interest were isolated using 4 µg of antibody against ERα (Santa Cruz, sc-543) or PR (Santa Cruz, 7208). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. IIlumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: Animals were implanted with E2 and P4. At 4 days post-implantation, tissues were harvested.

tag: chip target

value: PR

value: Whole mammary glands

tag: molecule subtype

value: Crosslinked chromatin


title: ChIP-seq_D542G_ER_rep2

value: ER-alpha


title: SC-RTL1 RNA-seq biorep2

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

data_processing:
Sequencing of messenger RNA was performed by BGI Genomics (Hong Kong) using DNBSEQ technology.
High quality raw reads were aligned to the Arabidopsis TAIR10 genome using STAR (Dobin et al., 2013).
Assembly: TAIR10
Supplementary files format and content: txt files showing the number of reads mapped to TAIR10 features

source_name: Pollen

growth_protocol: Plants were grown in greenhouse long-day conditions to complete the life cycle (16h photoperiod).

extract_protocol:
Total RNA was extracted using the Directzol Microprep (Zymo)
Library construction and sequencing was performed at BGI genomics (Hong Kong)

value: Pollen

tag: ecotype


title: Healthy control skin 2

value: skin


title: nrpd1a-3 FTL RNA-seq biorep 1

tag: mutant allele


title: Alveolar organoids, CTRL, rep2


title: Serum, before RT, patient 27

tag: time point

tag: diagnosis

value: Breast cancer


title: ChIP-seq_D542G_ER_rep1

tag: tissue


title: Y541S_ML_E2_sample1


title: Y541S_ML_placebo_sample3

value: Placebo


title: Alveolar organoids, CTRL, rep1

value: Alveolar organoids

value: Wild-type


title: Serum, before RT, patient 26


title: D542G_ML_E2/P_sample1


title: Psoriasis skin 1

value: Frozen

value: psoriasis


title: WT FTL RNA-seq biorep 2


title: Serum, before RT, patient 25


title: Y541S_ML_placebo_sample2


title: WT FTL RNA-seq biorep 1


title: Serum, before RT, patient 23


title: Serum, after RT, patient 1

value: Timepoint 2


title: D542G_ML_E2/P_sample3


title: Serum, before RT, patient 20


title: Serum, before RT, patient 24


title: Alveolar organoids, CTRL, rep1, input

value: DMSO, 24h


title: Serum, before RT, patient 22

value: Timepoint 1


title: SC-RTL1 RNA-seq biorep1


title: Col-0 RNA-seq biorep1


title: Serum, before RT, patient 21


title: ChIP-seq_D542G_PR_rep1


title: ChIP-seq_Y541S_PR_rep2

data_processing:
ENCODE ChIP-seq pipeline
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak (Peaks: chromatin coordinates and signal values)


title: ChIP-seq_Y541S_PR_rep1


title: ChIP-seq_WT_PR_rep2

value: WT


title: Serum, before RT, patient 17


title: D542G_ML_P_sample3

value: Mammary mature luminal cells


title: D542G_ML_E2_sample2


title: VC-RTL1 RNA-seq biorep2


title: nrpd1a-3 FTL small RNA-seq biorep 2

data_processing:
Single-end 50-nt reads were pre-processed by trimming 3' adapter and filtering by length and quality. Filtered and collapsed reads were mapped to the Arabidopsis TAIR10 genome annotation with bowtie, reporting all multi-mappers. Only perfect-match reads were used for all downstream analysis. Reads were normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30 nt) and perfectly mapped reads.
Assembly: TAIR10
Supplementary files format and content: txt files showing the number of reads mapped to TAIR10 features

value: Small RNA


title: nrpd1a-3 FTL RNA-seq biorep 2


title: VC-RTL1 RNA-seq biorep1


title: D542G_ML_P_sample2


title: ChIP-seq_WT_PR_rep1

value: PR

value: Whole mammary glands


title: D542G_ML_E2/P_sample2


title: nrpd1a-3 FTL small RNA-seq biorep 1


title: Serum, before RT, patient 19


title: ChIP-seq_Y541S_ER_rep2

value: ER-alpha

value: Crosslinked chromatin


title: Col-0 RNA-seq biorep2

value: Pollen


title: Serum, before RT, patient 18

value: Breast cancer


title: D542G_ML_E2_sample1


title: ChIP-seq_WT_ER_rep2


title: WT FTL small RNA-seq biorep 2


title: D542G_ML_P_sample1


title: D542G_ML_placebo_sample3

value: Placebo


title: ChIP-seq_Y541S_ER_rep1


title: Serum, before RT, patient 16


title: Serum, before RT, patient 15


title: D542G_ML_E2_sample3


title: ChIP-seq_WT_ER_rep1


title: WT FTL small RNA-seq biorep 1


title: Serum, before RT, patient 14


title: D542G_ML_placebo_sample2


title: SC-RTL1 small RNA-seq biorep2


title: D542G_ML_placebo_sample1


title: Serum, before RT, patient 12


title: WT_ER_ML_E2/P_sample3


title: PreIR-NTN_SMG Replicate 4

city: Bethesda

first: Matthew

middle: P

last: Hoffman

state: MD

address: 30 Convent Dr MSC4370

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Submandibular Gland

extract_protocol:
SMGs were harvested, minced and lyzed in RNA lysis buffer and homogenized using Fastprep-24 instrument with lysing matrix D tubes. RNA was purified using RNAqueous-4PCR kit (Ambion, Houston, TX, USA).
Total RNA per sample was reverse transcribed, and full-length cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA). Libraries for Illumina sequencing were prepared using the Nextera XT kit (Illumina), pooled, and analyzed on four lanes of a NextSeq 500 sequencer (Illumina).

treatment_protocol: Injection of AAV2-GFP or Cere-120 10 days before irradiation of the murine SMGs and tissue harvested after 300 days.

tag: strain

value: SMG

tag: age

value: 1 year old (300 days after treatment)

tag: agent

value: PreIR-NTN


title: SC-RTL1 small RNA-seq biorep1


title: VC-RTL1 small RNA-seq biorep2


title: PreIR-NTN_SMG Replicate 3


title: VC-RTL1 small RNA-seq biorep1


title: WT_ER_ML_E2/P_sample2

tag: cell type


title: WT_ER_ML_E2/P_sample1

tag: er mutation


title: PreIR-NTN_SMG Replicate 2


title: Serum, before RT, patient 10


title: Serum, before RT, patient 11


title: Serum, before RT, patient 9


title: PreIR-GFP_SMG Replicate 5

value: PreIR-GFP


title: WT_ER_ML_P_sample3

tag: treatment


title: PreIR-NTN_SMG Replicate 1


title: Col-0 small RNA-seq biorep1


title: Col-0 small RNA-seq biorep2


title: WT_ER_ML_P_sample2


title: PreIR-GFP_SMG Replicate 4


title: Serum, before RT, patient 7


title: Serum, before RT, patient 13


title: WT_ER_ML_E2_sample3


title: PreIR-NTN_SMG Replicate 5


title: PreIR-GFP_SMG Replicate 3


title: Serum, before RT, patient 6