title: scATACseq_vehicle

data_processing:
Reads were aligned to the hg18 genome assembly using bowtie2 v2.3.5 with the option (--very-sensitive -X 2000 --end-to-end --no-mixed --no-discordant)
peaks were called using Genrich version v0.6
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing chromosome coordinates of peaks

source_name: human GBM TIC GBM#22

extract_protocol:
Cell were lysed with  ATAC-RSB buffer (Tris-HCl pH 7.4 10mM, NaCl 10mM, MgCl2 3mM, NP-40 0.1%, Tween-20 0.1% and Digitonin 0.01%) and underwent transposase reaction. Tagmented DNA was isolated with Zymo DNA Clean and Concentrator-5 kit (Zymo Research).
Tagmented-DNA was amplified and barcoded by PCR to construct DNA library. DNA fragments underwent a doubled-side size selection to remove primer dimers and fragments larger than 1000bp

treatment_protocol: GBM TICs were plated at 125000 cells/ml and treted as indicated in each sample for 24 hours.

value: primary GBM tumor initiating cell line


title: scATACseq_DDP

status: Public on Jan 10 2022

type: SRA

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: GBM TICs  were grown in DMEM/F12 medium supplemented with  B27 supplement (Life Technologies), 20 ng/ml epidermal growth factor, 10 ng/ml basic fibroblast growth factor, 2mM L-Glutamine, penicillin (50 units/ml) and streptomycin (100 mg/ml).

tag: cell line

tag: treatment


title: SK-N-Be2C TWIST1_KO, Xenograft 4 [TBegT4]

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

library_source: transcriptomic

data_processing:
fastq files were mapped with STAR version 2.5.2b on both the Human genome version Hg19 and the Mouse genome version Mm10, simultaneously. The following options were changed from the default parameters: --outSAMmultNmax 50; --outFilterMatchNminOverLread 0.4;   --quantMode TranscriptomeSAM.
Transcriptome annotations in gtf format for both organisms were downloaded from the gencode website (https://www.gencodegenes.org/). Reads mapped on either the Human or the Mouse transcriptome were then parsed and split in one file per organism with an in-house perl script. Reads with matches on both Human and Mouse were discarded from the Mouse file. Per-gene quantification was then calculated independently for each organism using rsem version 1.3.0.
Mouse and Human data were analyzed independently, but following the same protocol. Genes with a log2 (rpkm) value above 1 in at least one sample were kept
Differential analysis was performed using the raw data counts in DESeq2 package version 1.26.0. For each comparison, the cutoffs for fold-change and adjusted p-values to call differentially transcribed genes were set to 1 and 0.05, respectively
Genome_build: Hg19/Mm10
Supplementary_files_format_and_content: The two supplemental tab-delimited text files Hs_GeneMat_raw_counts.txt and Mm_GeneMat_raw_counts.txt contain the rsem raw counts for Homo sapiens and Mus musculus.

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: SK-N-Be2C TWIST1_KO Xenograft

growth_protocol: SK-N-Be2c either WT or TWIST1_KO cells have been cultured at the density of 2x10^5 cells/ml in DMEM containing 1% P/S and 10% FBS. SK-N-Be2c -derived xenograft have been obtained upon orthotopical injection of 5x10^5 cells in the left adrenal gland of mice. Xenograft have been grown since their size reached 1000 mm3.

extract_protocol:
Total RNA from cell lines and tumors was extracted using RNeasy or miRNeasy mini kit (Qiagen, Hilden, Germany), respectively according to manufacturer instructions. RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was verified using the Agilent 2100 Bioanalyzer system (Agilent Technologies).
RNAseq was performed at the iGE3 Genomics platform (University of Geneva). The total RNA ribo-zero gold kit from Illumina was used for the library preparation with 1 µg or 500 ng of total RNA as input for cells (n=3 biological replicates/group) and tumors (n=4/group), respectively. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on 1.5 lanes for cells and 1.5 lanes for tumors of a Single-read Illumina Flow cell. Reads of 100 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: cell-line

tag: genotype

tag: sample type

value: Tumor from Xenograft


title: H3K4me1_LSD1i

data_processing:
Basecalls was performed using CASAVA software v1.8 and quality check  performed with fastqc version 0.10
ChIP-seq reads were aligned to the hg18 genome assembly using bowtie v1.0.1 with the option (-m 1 –v 2)
peaks were called using MACS version 1.4.1 with threshold of 10-5. For LSD1 ChIP the threshold was set to 10-10
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing chromosome coordinates of peaks and MACS score

extract_protocol:
Cells were cross-linked in culture medium with 1% formaldehyde in PBS and the reaction was stopped after 10 min at RT by adding 0.125 M glycine for 5 min at 4°C. The cells were washed twice with PBS and collected by centrifugation. Pellets were stored at -80° in SDS buffer (50 mM Tris•HCl pH 8.1, 0.33% SDS, 150mM NaCl, 5 mM EDTA, and protease inhibitor cocktail). Fixed cells were resuspended in IP buffer (100mM tris ph 8.6 0.3% SDS 1.7% TRITON x-100 and 5mM EDTA). Chromatin was then fragmented to obtain ~200 bp in average size length by using a Branson Sonifier 250. Chromatin pre-clearing was obtained with protein A-sepharose beads (Amersham).  For histone modification 250ug of chromatin were incubated with 2ug of primary antibody; for LSD1, 2mg of chromatin were incubated with 10ug of primary antibody. Before IP 2.5% of input was stored prior to the decrosslinking procedure. After overnight IP,  protein G magnetic beads have been added to the samples and incubated for 4 hours.  Decrosslinking was performed for all the IP samples and corresponding inputs, overnight in 0.1%SDS and 0.1% NaCOH3. The day after, the enriched DNA was treated with proteinase K at 56°C for 40 min and purified with a DNA purification kit (Qiagen).
The obtained DNA was then quantified with Qubit and processed for ChIP-Seq library preparation (as described for the Illumina protocol). For libraries preparation, 2ng of immunoprecipitated DNA was used.

treatment_protocol: NB4 cells were plated at 500000 cells/ml and treted as indicated in each sample for 24 hours.

tag: antibody used


title: small RNA_51ms_3_0mm_2

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description: sRNA-seq, bhlh51-1 sterile anther, 3.0 mm, replicate 2

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 50 nucleotides. RNA-seq reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome
Supplementary_files_format_and_content: Text containing distinct RNAs with their raw abundance after removing the adapter sequences

organism: Zea mays

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ105-2

extract_protocol:
TRI Reagent® (Sigma-Aldrich) follow instruction from manufacturer
For sRNA library preparation, 20- to 30-nt RNAs were excised from a 15% polyacrylamide/urea gel, and ~25 ng of sRNA used for library construction with NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, lnc.) were used for ultra-low amount of total RNA starting from 100 ng. For RNA-seq, 2 µg of total RNA was treated with DNase I (New England BioLabs) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research). The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs) was used for library construction with 500 ng of treated RNA.

tag: tissue

value: Dissected whole anthers

tag: Stage


title: Meningioma 5 Dura (scRNA-seq)

city: San Francisco

first: Abrar

last: Choudhury

state: California

institute: University of California, San Francisco

description:
Sex: 1
Gender: 1

data_processing:
Library demultiplexing, read alignment to the hg38 human reference genome, identification of empty droplets, and UMI quantification was performed using CellRanger v3.0.2
Single cell UMI count data were processed in R v3.6.1 with the Seurat v3.0.1 package using the sctransform workflow, with scaling based on regression of UMI count and percentage of reads attributed to mitochondrial genes per cell.
Genome_build: hg38
Supplementary_files_format_and_content: matrix.mtx.gz (Matrix table with the number of unique molecular identifiers for every feature (gene) by row and every barcode (cell) by column)
Supplementary_files_format_and_content: barcodes.tsv.gz (Sequences corresponding to every barcode in the matrix table)
Supplementary_files_format_and_content: features.tsv.gz (Sequences corresponding to every feature in the matrix table)

molecule: polyA RNA

source_name: Dura

extract_protocol:
Fresh meningiomas were dissociated into single cells by mincing and then treating with collagenase, trypsin, and RBC lysis buffer. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.

value: dura

tag: age


title: SK-N-Be2C TWIST1_KO, Xenograft 2 [TBegT2]


title: small RNA_51ms_3_0mm_1

description: sRNA-seq, bhlh51-1 sterile anther, 3.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-9


title: Meningioma 5 BTI (scRNA-seq)

description:
Sex: 1
Gender: 1

source_name: Meningioma

value: meningioma brain-tumor interface


title: SK-N-Be2C TWIST1_KO, Xenograft 1 [TBegT1]


title: AEC-fAT1D6

city: Los Angeles

first: Evelyn

last: Tran

state: CA

address: 1441 Eastlake Ave

department: Biochemistry/Surgery

institute: University of Southern California

data_processing:
Raw fastq files were imported to Partek Flow using the USC High Performance Computing Commons (HPCC) through the USC Norris Medical Library Bioinformatics Core. Partek Flow was used to process RNA-seq data to obtain raw gene counts.
Unaligned reads were imported to Partek Flow. Pre-alignment QA/QC was performed. Bases were trimmed from both ends using the "Trim bases" option, remaining settings were default.
Trimmed reads were then aligned to the human genome using STAR aligner (v2.6.1d): Homo sapiens - hg 38, GENCODE Genes - release 29.
Aligned reads were assessed for quality using the "Post-alignment QA/QC" option. Aligned reads were quantified to the transcriptome using the annotation model "Partek E/M" and genome version hg38 - GENCODE Genes - release 29  on default settings.
Raw gene counts were saved and imported to R (v3.6.0 "Planting of a Tree") for normalization (default settings) and differential gene expression analyses (LFC shrinkage type 'Normal') using DESeq2.
Genome_build: Homo sapiens, GENCODE Genes, hg38, version 29
Supplementary_files_format_and_content: Matrix table of raw gene counts generated by Partek Flow which were then converted to whole integers to use in DESeq2
Supplementary_files_format_and_content: csv file of FPKM values normalized by Partek Flow

source_name: Lung

growth_protocol: AEC lines were maintained on standard tissue culture dishes in media containing ROCK inhibitor Y-27632. Cells were passaged and re-plated up to Passage 10 when, at subconfluence, cell lines were collected for total RNA extraction. The fibroblast line HLF-133 was briefly cultured on plastic in DMEM plus 10% FBS medium before harvesting. Primary AT2 cells purified from donor lung tissue were collected for RNA extraction immediately after purification. Primary AT2:AT1 intermediate and AT1-like cells resulting from transdifferentiation of purified AT2 cells on Transwell filters were collected after 2, 4, and 6 days in culture.

extract_protocol:
Total RNA was extracted and purified using the Illustra TriplePrep kit (GE Healthcare 28-9425-44)
Purified total RNA was submitted to the USC Molecular Genomics Core facility for library preparation and sequencing. RNA quality was assessed on the Bioanalyzer (Agilent) then rRNA-depleted using Ribo-Zero rRNA Removal kit for human samples (Illumina MRZH11124) before proceeding with library preparation (TruSeq mRNA Stranded Library preparation kit, Illumina 20020594).

treatment_protocol: No treatments.

tag: cell type

value: Primary AEC

value: AT1-like cells (D6)

tag: source tissue/donor

value: Donor Lung f


title: Meningioma 5 (scRNA-seq)

description:
Sex: 1
Gender: 1

value: meningioma


title: AEC-fAT1D4

value: AT1-like cells (D4)


title: Meningioma 4 Dura (scRNA-seq)

description:
Sex: 2
Gender: 2


title: small RNA_51ms_2_0mm_2

description: sRNA-seq, bhlh51-1 sterile anther, 2.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-10


title: SK-N-Be2C WT, Xenograft 4 [TBeC4]

source_name: SK-N-Be2C WT Xenograft

value: wild-type


title: small RNA_51ms_2_0mm_1

description: sRNA-seq, bhlh51-1 sterile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-3


title: Meningioma 4 (scRNA-seq)

description:
Sex: 2
Gender: 2


title: AEC-fAT1D2

value: intermediate AT2:AT1 cells (D2)


title: SK-N-Be2C WT, Xenograft 3 [TBeC3]


title: small RNA_51ms_1_5mm_2

description: sRNA-seq, bhlh51-1 sterile anther, 1.5 mm, replicate 2


title: SK-N-Be2C WT, Xenograft 2 [TBeC2]


title: Meningioma 3 (scRNA-seq)

description:
Sex: 1
Gender: 2


title: small RNA_51ms_1_5mm_1

description: sRNA-seq, bhlh51-1 sterile anther, 1.5 mm, replicate 1


title: AEC-aAT1D6

value: Donor Lung a


title: Meningioma 2 (scRNA-seq)

description:
Sex: 1
Gender: 1


title: small RNA_51ms_1_0mm_2

description: sRNA-seq, bhlh51-1 sterile anther, 1.0 mm, replicate 2


title: Meningioma 1 (scRNA-seq)

description:
Sex: 2
Gender: 2


title: AEC-fAT2

value: Primary AT2 cells


title: small RNA_51ms_1_0mm_1

description: sRNA-seq, bhlh51-1 sterile anther, 1.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-4


title: AEC-aAT1D2


title: SK-N-Be2C WT, Xenograft 1 [TBeC1]


title: AEC-aAT1D4


title: E3-12

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
NovaSeq SPlanepaired-end150bp read length, v1sequencing chemistry
FASTQ were mapped Giardia WB genome using STAR v2.7.0f. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.26.8 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample

organism: Giardia duodenalis

source_name: WB

growth_protocol: Trophozoites were grown in TYi-S33 until 80% confluency after that encystation was induced following the Uppsala encystation protocol reported by Einarsson et al. 2016.

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNA was then treated with Turbo DNase free kit according to manufacturers instructuons
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection.The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: Upon reaching 80% confluence, trophozoites were detached on ice (10m),  pelleted and washed with PBS and after lysed in 1ml of Trizol. Samples were frozen immediatedly in liquid nitrogen and kept at -80 until RNA extraction

value: Trophozoites excysted

tag: time after start of encystation

value: Excysted cells

tag: strain

value: WB


title: HLF-133

value: Lung fibroblast line


title: AEC-ROCKinh

value: alveolar epithelial cell (AEC) line

value: Donor Lung-FT


title: E3-10

value: Encysting trophozoites


title: AEC-aAT2


title: E3-9


title: AEC-CDK4R24C+hTERT


title: E3-8


title: AEC-hTERT


title: E3-7


title: WT_LV_Sham_rep3

type: RNA

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

description: Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). Each labeled cRNA was then fragmented, and the mixture was heated at 60°C for 30min. Lastly, labeled cRNAs were loaded into gasket slides and assembled to microarray slides. The slides were then incubated for 17h at 65°C in the SureHyb Hybridization Chamber (Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

organism: Mus musculus

source_name: LV_Sham_4 week

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit).

extract_protocol: Total RNAs from LVs were prepared using Qiagen RNeasy Plus kit. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: sample type (gender, strain, tissue, age upon harvesting)

value: male, C57BL/6J, LV, 13 week age

value: LV


title: WT_LV_Sham_rep2

value: male, C57BL/6J, LV, 14 week age


title: E3-6


title: WT_LV_MI_rep1

source_name: LV_MI_4 week


title: WT_LV_Sham_rep1


title: WT_LV_MI_rep3


title: AEC-FT_rep2


title: AEC-FT_rep1


title: E3-5


title: WT_LV_MI_rep2


title: E3-4


title: c16

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

description:
SG16_S16
Kidney cell lines *transiently* transfected with AT1R expression plasmid

data_processing:
Files *filtered.fastq.gz result from TrimGalore trimming (service provided by service company who performed the sequencing. Done due to lower sequencing quality for these samples)
For all samples, adaptors were clipped (Cutadapt v1.8.1), read were mapped with Tophat 2.0.14 and counted with featureCounts 1.4.6. Annotation was made with Ensembl assembly v75.
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts

growth_protocol: Cells were cultivated in DMEM/Ham's F-12 medium (Biochrom), supplemented with 10% Fetal calf serum (FCS). Medium was changed to DMEM without FCS prior to addition of stimuli. Stable transfected AT1R-HEK-293 cells were obtained by cotranfection with pBABEpuro, incubation with 2µg/ml puromycin and 10 µmol/l losartan (to prevent AT1R activation by residual AII in serum) and limited dilution cloning.

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Potental gDNA contamination was removed by treatement with DNAse I (New England Biolabs) for 10min at 37°C, followed by enzyme inactivation at 75°C for 10min.
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen). Resulting RNAs were used to generate cDNA libraries using Illumina index adapters.  10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot). Paired end sequencing (2x100bp) was performed on Illumina HiSeq2000.

treatment_protocol: Cells were treated incubated for 6h or 24h with 10 µg/L EGF and/or 1 nM Angiotensin II.

tag: transfection

tag: treatment type

value: EGF+AngII

tag: treatment length


title: c15

description:
SG15_S15
Kidney cell lines *transiently* transfected with AT1R expression plasmid

tag: cell line


title: E3-3


title: E3-2


title: c14

description:
SG14_S14
Kidney cell lines *transiently* transfected with AT1R expression plasmid

value: AngII


title: E3-11

value: Cysts

value: Cyst


title: E3-1

value: Trophozoites


title: c13

description:
SG13_S13
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: AEC-CDK4R24C


title: WT RNA-seq rep1

city: Norfolk

first: Sanjeeva

middle: Reddy

last: Dodlapati

state: VA

address: E&CS, odu

department: Computer Science

institute: old dominion university

data_processing:
RNA-seq reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore-0.6.
The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (MM10) by STAR (2.5.3a) with default parameters.
Individual mapped reads were adjusted to provide TPM (transcripts per million) values with mouse genome as the reference
Genome_build: MM10
Supplementary_files_format_and_content: csv

source_name: Heart

growth_protocol: In vivo

extract_protocol:
Cardiac fibroblasts isolated from WT and Acta2fl/fl mice were transduced with Adeno-Cre, treated with TGFβ for 2 days, and then subjected to RNA isolation using a Direct-zol RNA Microprep Kit (Zymo). cDNA libraries were constructed using the NEBNext single cell/low input RNA library prep kit for Illumina (E6420) from New England BioLabs. The cDNA libraries were sequenced on the Illumina Hi-seq platform using 150 bp paired-end sequencing. RNA-seq reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore-0.6. The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (MM10) by STAR (2.5.3a) with default parameters. Individual mapped reads were adjusted to provide TPM (transcripts per million) values with mouse genome as the reference.
Heart tissue samples were minced and digested in DMEM containing 0.75U/ml Collagenase D (Roche 11088866001), 1.0U/ml Dispase II (Roche 10165859001), and 1 mM CaCl2 at 37oC for 40 min. The slurry was then passed through a 100-μm cell strainer and then a 40-μm cell strainer. Cells were collected by centrifugation at 350 × g for 10 min. The cell pellet was then resuspended in PBS. Tcf21 lineage-traced eGFP+ cardiac fibroblasts were sorted on FACSaria II (BD Biosciences). Gates were made based on WT eGFP- control. Sorted eGFP+ cardiac fibroblasts were used for RNA-seq and ATAC-seq analyses

treatment_protocol: To induce the activity of the MerCreMer, mice were treated with tamoxifen (Sigma T5648) dissolved in corn oil through intraperitoneal (IP) injections at a dosage of 75 mg/kg body weight/day for 5 days starting at 6 weeks of age. Mice were subjected to permanent surgical ligation of the left coronary artery to induce MI at 9 weeks of age. Briefly, mice were anesthetized using isoflurane and a left lateral thoracotomy was performed. The left coronary artery was identified and ligated just below the left atrium. To ensure the efficient deletion of Acta2, mice were given another course of tamoxifen treatment from 1 day before MI to 5 days after MI.  Echocardiography was performed in M-mode using a Toshiba Aplio SSA-770a ultrasound system and a 12-MHz transducer as previously described. For pain management related to surgical procedures, mice were given a dose of Carprofen (5 mg/kg body weight) before the surgery followed by a second dose 12 hours after the surgery.

value: Cardiac fibroblasts

value: WT


title: WT RNA-seq rep2


title: MIATKO_LV_Sham_rep3

value: male, C57BL/6J, LV, 15 week age


title: MIATKO_LV_MI_rep3

value: male, C57BL/6J, LV, 16 week age


title: MIATKO_LV_Sham_rep1


title: MIAT KO_LV_MI_rep1


title: MIATKO_LV_MI_rep2


title: c12

description:
SG12_S12
Kidney cell lines *transiently* transfected with AT1R expression plasmid

value: EGF


title: E2-11

value: WB


title: MIATKO_LV_Sham_rep2


title: E2-10


title: KO RNA-seq rep1

value: Acta2 KO


title: E2-9


title: KO ATAC-seq rep1

data_processing:
ATAC-seq reads of all samples underwent adapter removal using TrimGalore-0.6, followed by quality assessment using FastQC. Reads were then aligned to the mouse reference genome MM10 using Bowtie 2.3 with the following options: – very-sensitive -X 2000 – no-mixed – no- discordant. Only unique alignments within each sample were retained in subsequent analysis. Macs2 was used to call peaks with following options: --nolambda --nomodel.
Genome_build: MM10
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
ATACseq was performed as previously described. Briefly, cardiac fibroblasts isolated from WT and Acta2fl/fl mice were transduced with Adeno-Cre, treated with TGFβ for 2 days, and then 10,000 cells were lysed on ice for 20 minutes to isolate the nuclei. Isolated nuclei were then incubated with the Tn5 transposase (TDE1, Illumina) and tagmentation buffer at 37°C for 30 minutes with shaking on a thermomixer at 700 rpm. Tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen). PCR was performed to amplify the ATACseq libraries using Illumina TrueSeq primers and multiplex by indexes primers. After the PCR reaction, libraries were purified with the 1.1X AMPure beads (Beckman). The ATACseq libraries were sequenced on the Illumina Hi-seq platform using 150 bp paired-end sequencing. Sequencing reads of all samples underwent adapter removal using TrimGalore-0.6, followed by quality assessment using FastQC. Reads were then aligned to the mouse reference genome MM10 using Bowtie 2.3 with the following options: – very-sensitive -X 2000 – no-mixed – no-discordant. Only unique alignments within each sample were retained in subsequent analysis. Moreover, alignments resulting from PCR duplicates or located in mitochondria were excluded. The mouse genome was tiled with consecutive non-overlapping 300bp bins. The accessibility of each of the 300bp bins was assessed by the number of fragments per million mapped (FPM) that was aligned to the bin. ATAC-seq peaks were called separately for each sample by MACS2 (48) with the following options: – keep-dup all – nolambda – nomodel. The identification of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/).
Heart tissue samples were minced and digested in DMEM containing 0.75U/ml Collagenase D (Roche 11088866001), 1.0U/ml Dispase II (Roche 10165859001), and 1 mM CaCl2 at 37oC for 40 min. The slurry was then passed through a 100-μm cell strainer and then a 40-μm cell strainer. Cells were collected by centrifugation at 350 × g for 10 min. The cell pellet was then resuspended in PBS. Tcf21 lineage-traced eGFP+ cardiac fibroblasts were sorted on FACSaria II (BD Biosciences). Gates were made based on WT eGFP- control. Sorted eGFP+ cardiac fibroblasts were used for RNA-seq and ATAC-seq analyses


title: c10

description:
SG10_S10
Kidney cell lines *transiently* transfected with AT1R expression plasmid

value: Control


title: WT ATAC-seq rep1


title: KO RNA-seq rep2


title: E2-8

value: Encysting trophozoites


title: E2-7


title: hiPSC-derived lacrimal glands (Day 10)

city: Osaka

first: Ryuhei

last: Hayashi

state: US and Canada only

address: 2-2 Yamadaoka, Suita

department: Graduate School of Medicine

country: Japan

institute: Osaka University

data_processing:
cellranger-5.0.1 processed the raw fastq data and generated BAM file.
The processed data files included averaged gene expression in each cell population after filtering and processing with DropletUtils and Seurat3.
Genome_build: hg38
Supplementary_files_format_and_content: text files

source_name: 201B7 hiPSCs

growth_protocol: Human iPSCs were differentiated in the culture medium for 10 weeks and then the lacrimal gland-like progenitors were isolated by FACS. The lacrimal gland-like cells were cultivated in Matrigel to make organoids

extract_protocol:
total RNA
10X Chromium

value: lacrimal gland

value: 3D culture day 10


title: c11

description:
SG11_S11
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: hiPSC-derived lacrimal glands (Day 0)

value: 3D culture day 0


title: a48

description: Kidney cell lines *stably* transfected with AT1R expression plasmid

data_processing:
Alignment (HISAT2 2.1.0), Counting (featureCounts - 2.0.0)
Annotation with Ensembl v100.
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing raw counts obtained after counting with featureCounts

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
mRNA were enriched using oligo(dT) beads and then fragmented randomly by adding fragmentation buffer. cDNA synthesis is done with random hexamers primers and is followed by second strand synthesis after sequencing adaptor ligation. Double-stranded cDNA libraries are then subjected to size selection (250-300bp) and PCR enrichment. Libraries were pooled before clustering on flowcell for sequencing.

value: EGF+AngII


title: hiPSC-derived lacrimal glands (Day 20)

value: 3D culture day 20


title: 10550Kid

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

data_processing:
iIllumina multiplex analysis -> fastq
hisat2 alignment -> BAM
featurecounts -> DE table
edgeR normalization filtering statistical analysis -> fitted table (CPM)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...

source_name: kidney

extract_protocol:
Kidney were removed, preserved in RNAlater in -80C, and total RNA was harvested using the Rneasy kit (qiagen). Sequencing results (fastq files) were provided by Novogene (Sacramento, CA) using Illumina Hiseq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: no


title: c07

description:
SG07_S7
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: c09

description:
SG09_S9
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: c08

description:
SG08_S8
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: a47

value: AngII


title: E2-6


title: E2-5


title: a46


title: c06

description:
SG06_S6
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: 10459Kid


title: 10104Kid

value: yes


title: E2-4


title: 10548Kid


title: c05

description:
SG05_S5
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: c04

description:
SG04_S4
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: 10056Kid


title: 10057Kid


title: c03

description:
SG03_S3
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: E2-3


title: c01

description:
SG01_S1
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: a42


title: E1-11

value: Cysts

value: Cyst


title: E2-1

value: Trophozoites


title: 10022Kid


title: E1-12

value: Trophozoites excysted

value: Excysted cells


title: b15

description:
SG_23
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: 10021Kid


title: 10024Kid


title: a41

value: CON


title: a44


title: a40


title: a45


title: a43


title: a38

value: EGF


title: 24_S24_RNA-Seq

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ATAC-Seq reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
ATAC-Seq peak calling was performed using MACS
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw), Count Tables (.txt)

source_name: Ring1 mutant lumbar motor neurons replicate4

extract_protocol: RNA was extracted from FACS purified MNs dissected from E12.5 mouse embryo (10-20,000 cells/segment), using the Arcturus Picopure RNA isolation kit. For on-column DNase treatment, Turbo DNase was used (ambion, AM2238). Each sample used separated bar code for libraries. RNA quality and quantity were measured with an Agilent Picochip using a Bioanalyzer, all samples had quality scores between 9-10 RIN. For library preparation 10ng of total RNA was used to generate cDNA, which was amplified with SMARTer Stranded RNA-Seq kit. 100ng of cDNA were used as input to prepare the libraries (Takara, #634837), and amplified by 10 PCR cycles. Samples were run in four 50-nucleotide paired-end read rapid run flow cell lanes with the Illumina HiSeq 4000 sequencer.

value: lumbar motor neurons

value: Ring1 mutant


title: a39


title: E1-8

value: Encysting trophozoites

value: WB


title: E1-10


title: E1-9


title: b14

description:
SG_22
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: 23_S23_RNA-Seq

source_name: Ring1 mutant thoracic motor neurons replicate 4

value: thoracic motor neurons


title: b16

description:
SG_24
Kidney cell lines *transiently* transfected with AT1R expression plasmid

value: EGF+AngII


title: c02

description:
SG02_S2
Kidney cell lines *transiently* transfected with AT1R expression plasmid

value: Control


title: E2-2


title: E1-7


title: a37


title: b12

description:
SG_20
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: a36


title: 22_S22_RNA-Seq

source_name: Ring1 mutant brachial motor neurons replicate 4

value: brachial motor neurons


title: b13

description:
SG_21
Kidney cell lines *transiently* transfected with AT1R expression plasmid

value: AngII


title: E1-5


title: a34


title: b11

description:
SG_19
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: E1-4


title: 21_S21_RNA-Seq

source_name: Ring1 mutant lumbar motor neurons replicate 3


title: b10

description:
SG_18
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: 20_S20_RNA-Seq

source_name: Ring1 mutant thoracic motor neurons replicate 3


title: a33

description: Kidney cell lines *stably* transfected with AT1R expression plasmid


title: 18_S18_RNA-Seq

source_name: Ring1 mutant lumbar motor neurons replicate 2


title: a35


title: b08

description:
SG_8
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: E1-3


title: a32


title: 19_S19_RNA-Seq

source_name: Ring1 mutant brachial motor neurons replicate 3


title: 17_S17_RNA-Seq

source_name: Ring1 mutant thoracic motor neurons replicate 2


title: a31


title: b07

description:
SG_07
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: E1-2


title: 16_S16_RNA-Seq

source_name: Ring1 mutant brachial motor neurons replicate 2


title: b06

description:
SG_06
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: E1-1


title: a30


title: b05

description:
SG_05
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: a29


title: a28


title: RNA-seq_ms32_2_0mm_2

description: RNA-seq, ms32-ref sterile anther, 2.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP109-6

value: Dissected whole anthers


title: b04

description:
SG_04
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: b09

description:
SG_17
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: RNA-seq_ms32_2_0mm_1

description: RNA-seq, ms32-ref sterile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP109-4


title: b02

description:
SG_02
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: a27


title: RNA-seq_ms32_1_5mm_3

description: RNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP112-5


title: 11_S11_RNA-Seq

source_name: control thoracic motor neurons replicate 4

value: control


title: b01

description:
SG_01
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: 13_S13_RNA-Seq

source_name: Ring1 mutant brachial motor neurons replicate 1


title: 12_S12_RNA-Seq

source_name: control lumbar motor neurons replicate4


title: a25


title: 10_S10_RNA-Seq

source_name: control brachial motor neurons replicate 4


title: a24


title: RNA-seq_ms32_1_5mm_1

description: RNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 1


title: a26


title: a23


title: 9_S9_RNA-Seq

source_name: control lumbar motor neurons replicate 3


title: E1-6

source_name: WB


title: RNA-seq_ms32_1_0mm_3

description: RNA-seq, ms32-ref sterile anther, 1.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP111-5


title: 8_S8_RNA-Seq

source_name: control thoracic motor neurons replicate 3


title: 15_S15_RNA-Seq

source_name: Ring1 mutant lumbar motor neurons replicate 1


title: RNA-seq_ms32_2_0mm_3

description: RNA-seq, ms32-ref sterile anther, 2.0 mm, replicate 3


title: 14_S14_RNA-Seq

source_name: Ring1 mutant thoracic motor neurons replicate 1


title: RNA-seq_ms32_1_0mm_2

description: RNA-seq, ms32-ref sterile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP111-3


title: RNA-seq_ms32_1_0mm_1

description: RNA-seq, ms32-ref sterile anther, 1.0 mm, replicate 1


title: b03

description:
SG_03
Kidney cell lines *transiently* transfected with AT1R expression plasmid


title: ON cultured for 3DIV with 0,5uM LY294002;_3

city: Padova

first: Andrea

middle: Domenico

last: Rivera

address: Via Gabelli 67

department: Neuroscience

institute: University of Padova

description: Gene expression data for P35-45 Optic nerves cultured for 3DIV with 0,5uM LY294002

hyb_protocol: 10 µg of each biotinylated cRNA sample was hybridised on an Affymetrix GeneChip Mouse Genome 430 2.0 for 16 h at 45 °C, using the Affymetrix GeneChip Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Quality control analysis and data analysis produced.CEL image and.CHP image files for analysis using Affymetrix GeneChip Operating Software. data normalisation was carried out using the MAS-5 algorithm

label: Biotin

source_name: Cultured Optic Nerve with LY295002 0.5uM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol following manufacturer instructions

growth_protocol: Adult murine optic nerves cultured for 3 days in vitro (DIV) ex-vivo in organotypic media containing different concentrations of LY294002 or saline.

extract_protocol: Trizol extraction followed with QIAGEN RNAeasy kit following manufacturer instructions.

treatment_protocol: Optic nerves were cultured for 3DIV with either 0,5uM; 50uM LY294002 or saline

value: Organotypic culture of P35-45 Optic nerve

tag: treatment


title: a22

description: Kidney cell lines *stably* transfected with AT1R expression plasmid


title: a21


title: RNA-seq_ms32_1_5mm_2

description: RNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 2


title: 6_S6_RNA-Seq

source_name: control lumbar motor neurons replicate 2


title: RNA-seq_ms32F_2_0mm_3

description: RNA-seq, ms32-ref//Ms32 fertile anther, 2.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP112-8


title: a20


title: ON cultured for 3DIV with 0,5uM LY294002;_2


title: 5_S5_RNA-Seq

source_name: control thoracic motor neurons replicate 2


title: RNA-seq_ms32F_2_0mm_2

description: RNA-seq, ms32-ref//Ms32 fertile anther, 2.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP111-11


title: a19


title: Treg treated with TNFR2 agonist antibody_3

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

description: MR2-1 rep 3

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.10.1).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_21K_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.10.1.2).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.10.1.2).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

growth_protocol: CD4+CD25+ Tregs were isolated using a Dynabeads Regulatory CD4+CD25+T Cell (Thermo Fisher Scientific) following the manufacturer’s instructions. Treg were seeded into a round-bottom 96-well plate and cultured in RPMI1640 (FUJIFILM Wako Pure Chemical) containing 10% fetal bovine serum (FBS) and 500 IU/mL interleukin-2 (IL-2) (R&D Systems) in a humidified CO2 incubator at 37⁰C. Dynabeads Treg expander (Invitrogen) was added to culture medium.

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, QIAGEN)
10 ng of total RNA was reverse-transcribed using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific) followed by library generation using the Ion AmpliSeq Transcriptome Human Gene Expression Kit. Libraries were diluted to 45 pM and pooled equally, with 5 samples per pool.

treatment_protocol: Tregs were cultured in the presence of MR2-1 TNFR2 agonist antibody (Hycult Biotech) or mouse IgG1 (R&D Systems) for 7 days.

value: Treg

value: TNFR2 agonist antibody


title: RNA-seq_ms32F_2_0mm_1

description: RNA-seq, ms32-ref//Ms32 fertile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP109-5


title: Treg treated with TNFR2 agonist antibody_2

description: MR2-1 rep 2


title: 4_S4_RNA-Seq

source_name: control brachial motor neurons replicate 2


title: a18


title: ON cultured for 3DIV with 50uM LY294002;_2

description: Gene expression data for P35-45 Optic nerves cultured for 3DIV with 50uM LY294002

source_name: Cultured Optic Nerve with LY295002 50uM


title: Treg treated with TNFR2 agonist antibody_1

description: MR2-1 rep 1


title: RNA-seq_ms32F_1_5mm_3

description: RNA-seq, ms32-ref//Ms32 fertile anther, 1.5 mm, replicate 3


title: a17


title: ON cultured for 3DIV with 0,5uM LY294002;_1


title: Treg treated with control IgG_2

description: Control rep 2

source_name: Treg treated with control IgG

value: Control IgG


title: 2_S2_RNA-Seq

source_name: control thoracic motor neurons replicate 1


title: 7_S7_RNA-Seq

source_name: control brachial motor neurons replicate 3


title: a16


title: 1_S1_RNA-Seq

source_name: control brachial motor neurons replicate 1


title: RNA-seq_ms32F_1_5mm_2

description: RNA-seq, ms32-ref//Ms32 fertile anther, 1.5 mm, replicate 2


title: RNA-seq_ms32F_1_5mm_1

description: RNA-seq, ms32-ref//Ms32 fertile anther, 1.5 mm, replicate 1


title: Treg treated with control IgG_1

description: Control rep 1


title: RNA-seq_ms32F_1_0mm_3

description: RNA-seq, ms32-ref//Ms32 fertile anther, 1.0 mm, replicate 3


title: a15


title: a14


title: RNA-Post-meiosis-KO-rep2

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

description: Post-meiotic cell fraction

data_processing:
The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-end 50 base reads following Illumina's instructions. Image analysis and base calling were performed using RTA 2.7.3 and and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover. (https://sourceforge.net/projects/dimerremover/). Reads were mapped onto the mm9 assembly of the mouse genome by using Tophat version : tophat-2.0.14 and the bowtie version bowtie-2-2.1.0.
Gene expression analysis. Quantification of gene expression has been performed using HTSeq-0.6.1 (http://www-huber.embl.de/users/anders/HTSeq) and gene annotations from Ensembl release 67. Read counts were normalized across libraries with the method proposed by Anders and Huber. Comparisons of interest were performed using the method proposed by (Love et al. 2014) implemented in the DESeq2 Bioconductor library (DESeq2 v1.14.1). Resulting p-values were adjusted for multiple testing using the Benjamini and Hochberg method. The following thresholds have been used to select significantly differentially expressed genes: p-value adjusted for multiple testing < 0.01 and |log2 Fold-Change| > 1.
piRNA cluster expression analysis. Using IntersectBed from BEDTools release v2.26.0, split-mapped reads and reads that overlap genes annotated by Ensembl were removed (IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, Mt_rRNA, Mt_tRNA, polymorphic_ pseudogene, protein_coding, pseudogene, rRNA). The region corresponding to those genes was extended to 3kb upstream of the transcription start site and 10kb downstream of the transcript end site, in order to minimize signal from polymerase read-through from genic transcripts. The overlap was performed on the opposite strand as the library preparation protocol used to construct these RNA-seq libraries leads to sequence the strand generated during first strand cDNA synthesis. Quantification of piRNA cluster expression has been performed using IntersectBed from BEDTools release v2.26.0q. piRNA read counts were added to those of gene expression’s and used as follows: read counts were normalized across libraries with the method proposed by Anders and Huber [Anders, 2010 #1539]. Comparisons of interest were performed using the method proposed by (Love et al. 2014) implemented in the DESeq2 Bioconductor library (DESeq2 v1.14.1). The following thresholds have been used to select significantly differentially expressed piRNA clusters: p-value adjusted for multiple testing < 0.01 and |log2 Fold-Change| > 0.5.
DNA repeat expression analysis. Repeat analysis was performed following the methodology described in (Papin et al. 2017). Data were normalized based upon library size. Significance of the difference of repeat read counts between RNA samples was assessed using the Bionconductor package DESeq. To avoid over- or underestimating fold enrichments due to low sequence representation, repeat families with less than 5 RPM (reads per million mapped reads) per RNA sample were excluded from further analysis. The following thresholds have been used to select significantly differentially expressed DNA repeats: p-value adjusted for multiple testing < 0.01 and |log2 Fold-Change| > 0.5.
Genome_build: mm9
Supplementary_files_format_and_content: A multiple spreadsheets excel file contains processed data for gene, piRNA cluster and DNA repeat expression analyses.

source_name: Fractionated spermatogenic cells

growth_protocol: The mice was born in the plateforme de hautes technologies animales (Agreement: C 38 516 10 006) in Grenoble France. After weaning, mice were transferred to the pet shop in the institute for advanced biosciences Grenoble France (Agreement: C 38 516 10 001).

extract_protocol:
Total RNA was isolated from one single mouse seminiferous tubules usingTRIzol (Invitrogen) according to the manufacturer’s instructions.
After isolation of total cellular RNA from H3.3WT and H3.3BKO meiotic and post-meiotic cells, libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA Sample Preparation Guide” (PN 15031048).

treatment_protocol: Male mice were euthanized and testes were recovered. After the removal of albuginae, seminiferous tubules were incubated in a 1 mg/ml collagenase solution for 15 min at 35°C. After centrifugation, collagenase-treated cells were suspended in 0.5% BSA-DMEM medium, 10 mM sodium butyrate. The aggregates cells were dissociated by rapid pipetting for 10 min and filtered through a 100 μm filter. The fractionation of the spermatogenic cells was carried out essentially by using the available protocol (Bellvé et al., 1993; Buchou et al., 2017). Briefly, the total germ cell suspension was loaded on the top of a 2%–4% BSA gradient. The cells were let to sediment for 70 min. Cell fractions were collected and processed for examination with a phase contrast microscope. Meiotic and post-meiotic cell fractions (mainly round spermatids) were pooled and used for further analysis. The post-meiotic fraction contains only small contaminations of elongated spermatids.

tag: genotype/variation

value: H3.3BKO/KO :Actin Cre WT

value: Between 3 and 6 months


title: RNA-Post-meiosis-KO-rep1

description: Post-meiotic cell fraction


title: RNA-seq_ms32F_1_0mm_2

description: RNA-seq, ms32-ref//Ms32 fertile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP112-4

tag: genotype


title: RNA-seq_ms32F_1_0mm_1

description: RNA-seq, ms32-ref//Ms32 fertile anther, 1.0 mm, replicate 1


title: KC_Control [DMSO]

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

institute: UKE Hamburg-Eppendorf

description: bulk RNA-seq

data_processing:
Quality control was done with FastQC (Barbraham Bioinformatics). Raw reads were trimmed using TrimGalore! (Barbraham Bioinformatics) and mapped with RNA Star to mm9 using Galaxy Freiburg.
Read counts extracted with htseq-count.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene from every sample

source_name: kidney

growth_protocol: E12.5 embryonic kidneys were grown in DMEM medium with 10% fetal bovine serum, 100 µg/ml of penicillin, 100µg/ml of streptomycin.

extract_protocol:
Total RNA of kidney cultures was isolated using the Qiagen RNeasy Micro Kit
All steps were performed according to standard protocol of Ilumina/BGI library preparation.
RNA sequencing was performed by GATC, Germany (single-end) or BGI, Hongkong (paired-end)

treatment_protocol: Cultures were treated for 24 h with either DMSO or JQ1.

value: kidney cultures

tag: time point

value: DMSO

tag: strain background


title: KC_JQ1 [JQ1]

description: bulk RNA-seq

tag: tissue


title: M3_Proximal_H2O

city: Cambridge

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq pipeline made available by CellRanger v2.2 software (10x Genomics)
FASTQ reads were aligned to the mm10 mouse transcriptome, to extract cell barcodes and UMI barcodes using the cellranger count function. A digital gene expression (DGE) matrix for each sample was processed further
Cells that satisfied any one of the following criteria were removed: (1) < 300 detected genes; 2) outlier number of Unique Molecular Identifiers (UMIs); 3) outlier proportion of mitochondrial gene expression were excluded. Outlier cutoffs for each batch of samples were determined empirically based on the distribution of UMI and proportion of mitochondrial gene expression per cell; or 4) doublets identified by the python package Scrublet
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx:  gene expression UMI count matrix of all intron and exon spanning transcripts are in sparse matrix format. Can be read using the Read10x function in Seurat R package
barcodes.tsv: cell barcodes for each single cell corresponding to each column in the count matrix
genes.tsv: Gene symbols corresponding to each row in the count matrix
metadata.tsv: additional collected attributes for each cell barcode in count matrix. Contains informations on final annotated cell types, mouse sample, treatment, tissue site

source_name: Mouse proximal colon

extract_protocol:
To obtain a stromal single cell suspension for single cell RNA-seq we collected colons from water- and chronic DSS-treated C57BL6J mice and flushed them with ice cold washing buffer (2% FBS in 1X PBS (Sigma-Aldrich, calcium and magnesium free)). After removing fat and any connective tissue, colons were flipped inside out using forceps and cut into 2 cm chunks. Each colon was then incubated with 25 mL epithelial strip buffer (5 mM EDTA (Invitrogen), 1 mM DTT (Sigma Aldrich), 2.5 mM HEPES (Gibco), and 5% FBS in HBSS (GE Healthcare, calcium and magnesium free)) for 30 minutes at 37ºC with stirring. Tissues were collected, rinsed with ice cold washing buffer, minced using scissors and razor blades, and transferred into 50 mL conicals containing 5 mL enzyme digest buffer (0.2 mg/mL Collagenase P (Roche), 0.2 mg/mL Dispase II (Gibco), 0.1 mg/mL DNase I (Roche) in full media (CO2 independent media (Gibco), 2% FBS, 1X GlutaMAX (Gibco), 1X MEM NEAA (Gibco))) and placed into a bead bath at 40ºC. The conicals were vortexed every 5 minutes for 10 minutes, tissue chunks were allowed to settle for 5 minutes, and the supernatants were collected into ice cold collection media (full media with 10% FBS and 10 mM EDTA) that was kept on ice. Next, 5 mL enzyme digest media was added to the remaining colon fragments, the conicals were vortexed every 5 minutes for 5 minutes, tissue chunks were allowed to settle for 5 minutes, and the supernatants were added to previously collected fraction. Then, 3 mL enzyme digest media was added to the remaining tissue fragments, pipetted up and down for 2 minutes, allowed to settle for 3 minutes, and supernatants were collected and added to the previously collected fraction; this process was repeated for ~45 minutes until no colon fragments remained. The collection buffer and its contents were filtered using a 100μm cell strainer (Falcon), centrifuged (10 minutes, 450g, 4ºC), and resuspended in full media (2% FBS, 10 mM EDTA). Lamina propria single cell suspensions obtained as above were blocked with FcR blocking reagent (Miltenyi Biotec) for 10 minutes on ice, stained with primary antibodies previously listed for 20 minutes on ice, and cells were sorted using the Beckman Coulter MoFlo Astrios EQ (100 μm nozzle, 25 psi). For all steps, cells were kept in full media (2% FBS, 10 mM EDTA). Stromal cells that were sorted were defined as Ter119-CD45-EpCAM-, and dead cells were excluded using NucBlue (1 drop/500 μL cells). Cells were collected in full media, and purity was assessed by taking a fraction of sorted cells and re-analyzing them immediately on the MoFlo Astrios EQ. All samples were analyzed using FlowJo (Tree Star).
Single cell suspensions were processed using the Chromium Single Cell 3’ Gene Expression kit (v2, 10x Genomics) per manufacturer’s instructions.
Libraries were sequenced on the Illumina instruments per manufacturer’s instructions.

value: 12 weeks

tag: tissue site

value: proximal colon

value: Water

tag: Sex

value: female

tag: mouse


title: RNA-Meiosis-KO-rep1

description: Meiotic cell fraction

tag: age


title: 3_S3_RNA-Seq

source_name: control lumbar motor neurons replicate 1

value: lumbar motor neurons


title: small RNA_ms32_2_0mm_r3

description: sRNA-seq, ms32-ref sterile anther, 2.0 mm, replicate 3

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 50 nucleotides. RNA-seq reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome
Supplementary_files_format_and_content: Text containing distinct RNAs with their raw abundance after removing the adapter sequences

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP111-5

extract_protocol:
TRI Reagent® (Sigma-Aldrich) follow instruction from manufacturer
For sRNA library preparation, 20- to 30-nt RNAs were excised from a 15% polyacrylamide/urea gel, and ~25 ng of sRNA used for library construction with NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, lnc.) were used for ultra-low amount of total RNA starting from 100 ng. For RNA-seq, 2 µg of total RNA was treated with DNase I (New England BioLabs) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research). The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs) was used for library construction with 500 ng of treated RNA.

tag: Stage


title: a11

value: EGF


title: a12


title: M3_Proximal_DSS

tag: strain

value: DSS


title: ON cultured for 3DIV with 50uM LY294002;_1


title: small RNA_ms32_2_0mm_r2

description: sRNA-seq, ms32-ref sterile anther, 2.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP109-6

value: Dissected whole anthers


title: a10

value: CON


title: a9


title: RNA-Post-meiosis-WT-rep1

description: Post-meiotic cell fraction

value: H3.3BWT/WT :Actin Cre WT


title: small RNA_ms32_2_0mm_r1

description: sRNA-seq, ms32-ref sterile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP109-4


title: small RNA_ms32_1_5mm_r3

description: sRNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP112-5


title: RNA-Meiosis-WT-rep2

description: Meiotic cell fraction


title: a8

value: EGF+AngII


title: RNA-Meiosis-WT-rep1

description: Meiotic cell fraction


title: small RNA_ms32_1_5mm_r2

description: sRNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 2


title: M2_Proximal_H2O


title: M3_Distal_DSS

source_name: Mouse distal colon

value: distal colon


title: a13

description: Kidney cell lines *stably* transfected with AT1R expression plasmid

value: AngII


title: RNA-Meiosis-KO-rep2

description: Meiotic cell fraction

value: H3.3BKO/KO :Actin Cre WT


title: small RNA_ms32_1_5mm_r1

description: sRNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 1


title: a6


title: M2_Distal_H2O


title: M2_Distal_DSS


title: FH-Meiosis

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and and bcl2fastq 2.17.1.14. Adapter dimer reads were removed using DimerRemover v0.9.2 (https://sourceforge.net/projects/dimerremover/).
Reads were mapped to the mouse genome (mm9) using Bowtie v1.0.0 with the following arguments: -m 1 --strata --best -y -S –l 40 -p 8.
Heatmaps and quantifications of the ChIP-seq data were performed running seqMINER, using datasets normalized to 10 million uniquely mapped reads. As reference coordinates, we used the Ensembl 67 database (for coding genes) of the mouse genome (mm9) and the piRNA cluster database generated by the small RNA group Mainz University (http://www.smallrnagroup.uni-mainz.de/piRNAclusterDB.html) after having translated mm10 coordinates to mm9 using liftOver (UCSC: https://genome.ucsc.edu/cgi-bin/ hgLiftOver). For chromosome coverage analysis, the number of reads for each non-overlapping 40Kb windows of the Mouse genome (mm9/NCBI37) was computed for each sample using BEDtools v2.26. Then, data were normalized to 10 million reads and plots were generated using custom R scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b). Scores represent tag numbers per total uniquely mapped reads.

growth_protocol: The mice was born in the plateforme de hautes technologies animales (Agreement: C 38 516 10 006) in Grenoble France. After weaning, mice were transferred to the pet shop in the institute for advenced biosciences Grenoble France (Agreement: C 38 516 10 001).

extract_protocol:
Meiotic and post-meiotic cells expressing FLAG-HA tagged endogenous H3.3 were lysed in hypotonic buffer (10 mM Tris-HCl at pH 7.65, 1.5 mM MgCl2, 10 mM KCl) and disrupted by Dounce homogenizer. The cytosolic fraction was separated from the nuclei by centrifugation at 4°C. Nuclei were re-suspended in sucrose buffer (20 mM Tris-HCl at pH 7.65, 15 mM KCl 60 mM NaCl, 0.15 mM spermine, 0.5 mM spermidine) adjusted with high-salt buffer (20 mM Tris-HCl at pH 7.65, 25 % glycerol, 1.5 mM MgCl2, 0.2 mM EDTA, 900 mM NaCl) to get a final NaCl concentration of 300 mM. The nuclear-soluble fraction was recovered by centrifugation at 4°C. The pellet containing chromatin fraction was incubated in sucrose buffer containing 1mM CaCl2, and MNase (2.5U/g of cells) 10 min at 37°C. Digestion was stopped with 4 mM EDTA and mononucleosomes were recovered by centrifugation at 4°C. Tagged nucleosomes were immunoprecipitated with anti-FLAG M2-agarose (Sigma), eluted with FLAG peptide (0.5 mg/mL), further affinity-purified with anti-HA antibody-conjugated agarose, and eluted with HA peptide (1 mg/mL). The HA and FLAG peptides were first buffered with 50 mM Tris-Cl (pH 8.5), then diluted to 4 mg/mL in TGEN 150 buffer (20 mM Tris at pH 7.65, 150 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, 10% glycerol, 0 0.01% NP40), and stored at −20°C until use. Between each step, beads were washed in TGEN 150 buffer. Nucleosomes were submitted to RNase and proteinase K digestion, and DNA was extracted by phenolchloroform.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit version v.2 02.15, and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

tag: antibody

value: FLAG-HA

value: Between 3 and 6 months


title: FH-Post-meiosis


title: RNA-Post-meiosis-WT-rep2

description: Post-meiotic cell fraction


title: M1_Proximal_H2O


title: Input-Post-meiosis

value: input, none


title: a4

tag: transfection


title: a5

tag: treatment type


title: M3_Distal_H2O

value: 12 weeks


title: small RNA_ms32_1_0mm_r3

description: sRNA-seq, ms32-ref sterile anther, 1.0 mm, replicate 3


title: Input-Meiosis


title: small RNA_ms32_1_0mm_r1

description: sRNA-seq, ms32-ref sterile anther, 1.0 mm, replicate 1


title: small RNA_ms32_1_0mm_r2

description: sRNA-seq, ms32-ref sterile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP111-3


title: GM01393_paternal_fibroblast

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

data_processing:
Obtained reads were processed to remove any read duplicates by the default parameters set in the IonTorrent Suite.
The reads were quality filtered for a minimum of Q20 and trimmed using fastQValidator v0.1. The reads were mapped to hg38 (repeat-unmasked) using bowtie2 v2.3.5.1. Samtools v1.12 was used for manipulation of the alignment files. Bedtools v2.30.0 was used to generate genomic coordinates and interconversion of BAM and BED files. Samtools v1.12 was used to manipulate FASTA files.
Base composition and cytosine context identification were done using EMBOSS toolkit v6.5.7.
Genome_build: hg38 (UCSC; unmasked)

source_name: Primary fibroblast

growth_protocol: Human primary fibroblasts (GM01391, GM01392 and GM01393) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution.

extract_protocol:
For each sample, three T75 flasks were harvested of cells for genomic DNA isolation. The genomic DNA extraction was according to the standard phenol:chloroform:isoamyl alcohol method followed by ethanol precipitation and dissolution in nuclease-free water. For GM01391-CT and GM01391-KD samples, the isolated genomic DNA were sonicated and subjected to immunoprecipitaion for methylcytosine as mentioned in PMID: 32727353
The sequencing libraries for all the samples were generated as per the protocol mentioned in PMID: 31547883
Unpaired single-end sequencing on Ion Torrent S5 sequencing platform.

treatment_protocol: GM01391 fibroblasts were either transfected with non-targeting siRNA (GM01391-CT) or CGGBP1-targting siRNA (GM01391-KD) in three sucessions with 24h intervals. The siRNA (ThermoFisher) transfection was carried out using Oligofectamine transfection reagent (ThermoFisher) for a transient depletion of endogenous CGGBP1. The other fibroblasts, GM01392 and GM01393, were not provided any treatment.

value: GM01393 (Coriell Repository)


title: small RNA_ms32F_2_0mm_r3

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 2.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP112-8


title: M1_Proximal_DSS

value: proximal colon


title: GM01392_maternal_fibroblast

value: GM01392 (Coriell Repository)


title: M1_Distal_H2O

value: Water

value: female


title: a2

tag: treatment length


title: small RNA_ms32F_2_0mm_r2

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 2.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP111-11


title: M2_Proximal_DSS

value: DSS


title: M1_Distal_DSS


title: small RNA_ms32F_2_0mm_r1

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, fromms32-ref//Ms32 fertile sibling ZPP109-5

value: Dissected whole anthers


title: a7

tag: cell line


title: GM01391-KD_daughter_fibroblast

description: Methylcytosine immunoprecipated genomic DNA (MeDIP)

data_processing:
Library strategy: MeDIP-seq
Obtained reads were processed to remove any read duplicates by the default parameters set in the IonTorrent Suite.
The reads were quality filtered for a minimum of Q20 and trimmed using fastQValidator v0.1. The reads were mapped to hg38 (repeat-unmasked) using bowtie2 v2.3.5.1. Samtools v1.12 was used for manipulation of the alignment files. Bedtools v2.30.0 was used to generate genomic coordinates and interconversion of BAM and BED files. Samtools v1.12 was used to manipulate FASTA files.
Base composition and cytosine context identification were done using EMBOSS toolkit v6.5.7.
Genome_build: hg38 (UCSC; unmasked)

source_name: Primary fibroblast; CGGBP1-targeting siRNA

value: GM01391 (Coriell Repository)

value: CGGBP1-targeting siRNA

value: Anti-5-methylcytosine antibody cocktail (MABE146, SAB2702243; Sigma and NBP2–42813; Novus Biologicals)


title: do_Naive_rep2

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

data_processing:
Adapter Trimming using first "bbduk.sh -Xmx1g threads=7 in1=<<Sample.R1.fastq>> in2=<<Sample.R2.fastq>> out1=<<Sample.trim.R1.fastq>> out2=<<Sample.trim.R2.fastq>> ref=<<adapters.fa>> ktrim=r k=28 mink=13 hdist=1 tbo tpe" and then Trimmomatic with parameters: "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25"
Mapping to reference hg38 genome using bowtie2 in pair-end mode: "bowtie2 --very-sensitive -k 2 -t --phred33 -p 4 -q"
Filtering reads using samtools: i) removing reads mapping to mitochondrial and EBV chromosomes, ii) selection of reads mapping in proper pair satifying mappability of both mates and quality e.g. "samtools view -b -f 3 -F 524"
Reads mapping to black list regions (Boyle lab: https://github.com/Boyle-Lab/Blacklist) have been removed using pairToBed with -type set to neither
Duplicated reads have been removed using samtools, following step reported in samtools manual e.g. a) samtools fixmate -m; b) samtools sort -o; c) samtools markdup -r
ATACseq 5' end was shifted using alignmentSieve -p 4 --ATACshift
ATACseq peaks were called using MACS2 in pair end mode e.g. --format=BAMPE
Peaks have been filters using R/GRanges functionalities by replicates selecting those with associate significance <= 10^-10 and with overlapping area gretaer or equal to 50%. Resulting peak lists by condition (selected by replicates) were merged.
Reads counts were scalled relative to a quasi-normally distributed sub-set of peaks (see Gualdrini et al. 2016 PMCID: PMC5179500 , Esnault 2014 PMCID: PMC4018493)
bamCoverage was then used to create scaled bigWig tracks using computed scaling factors
Genome_build: hg38
Supplementary_files_format_and_content: .bw are BigWig normalised files

source_name: primary cells

growth_protocol: 100000 primary human CD4+ T memory and CD4+ T naive cells either freshly stored (day 0) or supplemneted with RPMI (day 1 and day 3).

extract_protocol:
cells were resuspended in 50 µL of lysis buffer (Niccolò, please insert the lysis buffer that you used) and incubated on ice for 3 minutes followed by centrifugation (500 g, 4°C, 20 mins). Cells were resuspended in 50 µL of tagmentation buffer (10 mm Tris-HCl, 25 mM MgCl2 and 1 µL of adaptor-loaded Tn5 transposase (produced in-house)) and incubated for 1 hour at 37°C. Subsequently tagmented DNA cleanup was performed by the addition of 10 μl of clean-up buffer (900 mM NaCl, 300 mM EDTA), 2 μl of 10% SDS, 6 μl of milliQ water and 2 μl of Proteinase K (20 μg/μl) followed by incubation at 40°C for 30 minutes.
Tagmented DNA was isolated using 2× AMPure XP beads and amplified by PCR with barcoded primers using 14 cycles of PCR. Finally, fragments smaller than 500 bp were purified with 0,65x AMPure XP beads and primers removed by purification with 1,8x AMPure XP beads. Libraries were sequenced paired-end on an Illumina NextSeq500 platform.

treatment_protocol: Cells were either processed for ATACseq directly (day 0) or stimulated for either 1 or 3 days with anti-CD3 and anti-CD28

tag: cell type

value: CD4+ T naive Cell

tag: treatment

value: untreated (day 0)


title: IRG1_KO-12h

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
Raw reads were trimmed to 36 bp and aligned to the mouse genome build mm9 using bowtie2 (version 2.3.4.1) with default parameters. All unmapped reads and PCR duplicates were removed. Peaks were called using MACS2 (version 2.1.1.20160309) with the parameters “-q 0.05 --nomodel --nolambda --broad --extsize 300 -B --SPMR -g mm” and signal tracks for each sample were generated with wigToBigWig tool from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: mouse bone marrow-derived macrophages (BMDMs)

growth_protocol: Mice were euthanized in a CO2 chamber and death was confirmed by cervical dislocation. Bone marrow cells were harvested from the femur and the tibia and differentiated in DMEM (containing 10% fetal calf serum, 1% penicillin/streptomycin and 20% and 20 ng/mL M-CSF) for 6 days.

extract_protocol:
Genomic DNA was extracted from BMDMs by the phenol-chloroform method followed by library construction.
5 µg of sonicated and adaptor ligated genomic DNA was used as input, and 5 µL of 5hmC antibody (Active Motif,39791) was used to immunoprecipitate modified DNA. Immunoprecipitated DNA was amplified for Illumina sequencing.

treatment_protocol: 1 × 10^6 BMDMs per milliliter were used for LPS and/or OI treatments. Unless otherwise stated, the cells were pre-treated with OI (250 μM) for 12 hrs and then stimulated with LPS (100 ng/ml). Moreover, the unmodified itaconic acid was adjusted to pH 7.0 with NaOH. Cells were pretreated with unmodified ITA for 12 hs using indicated dose.

tag: dip antibody

value: Treated with LPS for 12 hrs


title: TP53BP1 KD

data_processing:
The ChIP DNA libraries were sequenced on Ion Torrent S5 platform. The quality attribution for base call was done as per the IonTorrent suite default of Q20 or more.
TP53BP1 signals exclusive to CT or KD with a minimum read coverage of 5 reads in genomic bins of 0.2kb were generated and used to compare TP53BP1 occupancy difference between the two samples using frequency plots for read densities and pileups across the 0.2kb bins genome-wide.
Genome_build: hg38

source_name: HEK293T (stable cell line; CGGBP1-targetting shRNA)

growth_protocol: Human primary fibroblasts [Coriell Cell Repository GM02639] and HEK293T CT and KD [lentivirally transduced shRNA system as described in PMID 31547883] were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution.

extract_protocol:
Human primary fibroblasts [Coriell Cell Repository GM02639] were harvested from two T25 flasks for each sample. HEK293T CT and KD cells were harvested from two 10cm dishes for each sample. Genomic DNA was extracted using standard phenol:chloroform:isoamyl alcohol extraction method followed by ethanol precipitation and dissolution in nuclease-free water. For TP53BP1 ChIP-seq was performed as described elsewhere [PMID 31547883] except for the following modifications: The antibody used was NB100-304 (Novus Biologicals) against TP53BP1.
Ion Express Plus Fragment Library kit (Cat. No. 4471269) from ThermoFisher Scientific

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) [Origene Lentiviral system TL313955V]. For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin. Human primary fibroblast (GM02639) cells were cultured at 37°C, heat stressed at 40°C for 24h with 1°C increment per day and recovered at 37°C post-heat stress for 24 h. The CT and KD cells were cultured at 37°C, heat stressed at 42°C for 24h and recovered at 37°C post-heat stress for 24h.

tag: transduction

value: CGGBP1-targetting shRNA

value: NB100-304 (Novus Biologicals)


title: do_Naive_rep1


title: IRG1_KO-0h

value: mouse bone marrow-derived macrophages (BMDMs)


title: TP53BP1 CT

source_name: HEK293T (stable cell line; non-targetting shRNA)

value: non-targetting shRNA


title: IRG1_WT-12h


title: a3

value: EGF


title: small RNA_ms32F_1_5mm_r3

city: St. Louis

first: Blake

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 1.5 mm, replicate 3

tag: genotype


title: do_Mem_rep2

value: CD4+ T memory Cell


title: small RNA_ms32F_1_0mm_r3

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 1.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, from ms32-ref//Ms32 fertile sibling ZPP112-8

tag: tissue


title: small RNA_ms32F_1_5mm_r1

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 1.5 mm, replicate 1


title: pIXHALO_PN94-B_r2

city: New York

first: Shao-shan

middle: Carol

last: Huang

address: 12 Waverly Pl

department: Biology

institute: New York University

data_processing:
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using TrimGalore 0.4.4 wrapper for Cutadapt 1.16 with the following parameter: "-q 20".
Trimmed reads were aligned by bowtie2 version 2.3.2 against the Vitis vinifera genome assembly PN40024_12X.2 with default parameters, and additionally filter for alignments with MAPQ score of at least 30.
Peaks were called using GEM peak caller version 3.4 with the default version read distribution, PN40024_12X.2 genome sequences, in multi-replicate mode with the pIXHALO samples as control, and parameters " --q 1 --t 1 --f BAM --outNP --outBED --outJASPAR --outMEME --outHOMER --k_min 6 --k_max 20 --k_seqs 600 --k_neg_dinu_shuffle".
Genome_build: Vitis vinifera genome assembly PN40024_12X.2
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.

organism: Vitis vinifera

source_name: young leaf

growth_protocol: Leaf material (1-2 in) was collected from a single plant of cv. ‘Pinot Noir’ clone PN94 located in the Foundation Plant Services Facility-UCDavis, California.

extract_protocol:
Genomic DNA was extracted following procedure described in Chin et al., 2016 (Chin, CS., Peluso, P., Sedlazeck, F. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13, 1050–1054 (2016). https://doi.org/10.1038/nmeth.4035). DAP-seq experiment was performed as described in Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055).  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing a HALO-tagged transcription factor is translated by in vitro (rabbit reticulocyte) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina NextSeq 500.
DAP-Seq

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior gDNA isolation.

tag: cultivar

value: Pinot Noir (clone PN-94)

tag: protein

value: pIXHALO

tag: protein affinity tag

value: HALO

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source

tag: replicate


title: do_Mem_rep1


title: IRG1_WT-4h

tag: strain

value: Treated with LPS for 4 hrs


title: d3_Naive_rep2

value: 3 days anti-CD3 and and-CD28 treatment


title: VvMYB15_PN94-B_q2

description: DAPSeq-MYB_rr-VvMYB15_PN94-B-pn_GEM_events.narrowPeak

tag: gene id vcost

tag: gene id v1

tag: protein family

value: MYB

tag: protein source

value: Vitis vinifera


title: pIXHALO_PN94-B_r1


title: a1

tag: cell line

tag: transfection

tag: treatment type

value: CON

tag: treatment length


title: d3_Naive_rep1

tag: cell type

value: CD4+ T naive Cell

tag: treatment


title: d3_Mem_rep2


title: small RNA_ms32F_1_0mm_r1

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 1.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, from ms32-ref//Ms32 fertile sibling ZPP109-5

tag: tissue

value: Dissected whole anthers

tag: genotype

tag: Stage


title: IRG1_WT-0h

tag: dip antibody


title: VvMYB15_PN94-B_q1

tag: cultivar

tag: protein

tag: protein affinity tag

tag: expression system

tag: dna source


title: GM01391-CT_daughter_fibroblast

source_name: Primary fibroblast; Non-targeting siRNA

value: GM01391 (Coriell Repository)

value: non-targeting siRNA

tag: antibody

value: Anti-5-methylcytosine antibody cocktail (MABE146, SAB2702243; Sigma and NBP2–42813; Novus Biologicals)


title: LnCaP_OSMI2_AT7519_Replicate2

city: Helsinki

first: Harri

last: Itkonen

address: Room B125b / B129b

department: Department of Biochemistry and Developmental Biology

country: Finland

institute: University of Helsinki

data_processing:
Two biological replicates of each condition were used for the assay
Samples were multiplexed and paired-end sequenced with 150bp read length
Sequencing reads were aligned to Hg19 (GRCh37) using STAR
Raw counts of reads were mapped to genes using HTSeq counts
Normalised counts were generated using DESeq2
Genome_build: Genome_build: Hg19 (GRCh37)
Supplementary_files_format_and_content: normalied counts for each condition (title).  Txt tab-limited format.  Ensembl gene ids.
Supplementary_files_format_and_content: raw counts for each condition (title).  Txt tab-limited format.  Ensembl gene ids.

source_name: LnCaP

extract_protocol:
RNA was isolated with Illustra RNAspin Minikit (GE healthcare, cat num. 25-0500-72)
Libraries for sequencing were prepared by the Norwegian High Throughput Sequencing Centre using Strand-specific TruSeq RNA-seq library prep kit

treatment_protocol: Knockdown of OGT for 48 hours and treated with either DMSO or CDK inhibitor (0.5μM AT7519) for 4 hours prior to harvesting

value: LnCaP

tag: sirna

tag: agent


title: IRG1_KO-4h

value: mouse bone marrow-derived macrophages (BMDMs)

tag: strain


title: DMSO-DIP

value: Treated with DMSO for 8 hrs


title: LnCaP_OSMI2_Replicate2

tag: cell line

value: DMSO


title: LnCaP_siOGT2_AT7519_Replicate2


title: VvMYB14_PN94-B_q1

description: DAPSeq-MYB_rr-VvMYB14_PN94-B-pn_GEM_events.narrowPeak

value: Pinot Noir (clone PN-94)

tag: gene id vcost

tag: gene id v1

tag: protein family

tag: protein source

tag: replicate


title: small RNA_ms32F_1_5mm_r2

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 1.5 mm, replicate 2

tag: tissue

tag: genotype

tag: Stage


title: VvMYB14_PN94-B_q2

tag: cultivar

tag: protein

value: HALO


title: d1_Mem_rep2

tag: cell type

value: CD4+ T memory Cell

tag: treatment

value: 1 day anti-CD3 and and-CD28 treatment


title: d1_Naive_rep2


title: d1_Naive_rep1


title: LnCaP_siOGT1_AT7519_Replicate2


title: VvMYB13_PN94-B_r1

description: DAPSeq-MYB_rr-VvMYB13_PN94-B-pn_GEM_events.narrowPeak

tag: protein affinity tag

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source


title: DIP_5hmC_WT

data_processing:
Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2. Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Tag densities were calculated in 100 bp sliding windows spanning +/- 2 kb of gene bodies running seqMINER (http://bips.u-strasbg.fr/seqminer/), using datasets normalized to the total number of uniquely mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: To visualize tag densities in a genome browser, wig track files were generated for each dataset using WigMaker.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were grown in glutamine and pyruvate containing DMEM (4.5g/L D-glucose), supplemented with 10% serum, 1% penicillin-streptomycin.

extract_protocol:
Lysates clarified from sonicated nuclei were treated with RNAse and proteinase K. Genomic DNA was purified by phenol extraction and ethanol precipitation.
Libraries were prepared according to Illumina's instructions. The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.

tag: strain

tag: genotype/variation

value: MBD4 WT

tag: age

value: Embryos were isolated from the uteri of day 12.5 postcoitus pregnant mice

tag: fraction

value: anti-5hmC immunoprecipitation


title: DIP_Input_WT

value: Input fraction


title: Octyl-ITA-DIP

tag: dip antibody

value: Pre-treated with 0.5 mM OI for 8 hrs


title: small RNA_ms32F_1_0mm_r2

description: sRNA-seq, ms32-ref//Ms32 fertile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, from ms32-ref//Ms32 fertile sibling ZPP112-4

value: Dissected whole anthers


title: LNCaP_Scr_AT7519_Replicate2

tag: cell line

tag: sirna

value: Scr

tag: agent


title: DIP_5mC_WT

value: anti-5mC immunoprecipitation


title: VvMYB13_PN94-B_r2

tag: gene id vcost

tag: gene id v1

tag: protein family

value: MYB

tag: protein source

value: Vitis vinifera

tag: replicate


title: DIP_5hmC_KO

value: MBD4 KO


title: KrrA-FLAG+205#2

city: Nashville

first: Hualiang

last: Pi

state: TN

address: 1161 21st Avenue South

institute: VUMC

description:
RIPed RNA
KrrA-FLAG+205
4590-HP-16

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 20.0.1) platform for analysis. The Illumina paired reads option was chosen for import.
Imported reads were trimmed to remove adapters using CLC Genomics Workbench
To remove rRNA reads, all paired reads were aligned to a sequence list containing all rRNA sequences for each corresponding bacterial strain. Unmapped (non-rRNA) reads were collected and used for subsequent analysis. Steps were performed using CLC Genomics Workbench. The refrence genome NC_005945 was used for mapping.
Expression values (as RPKM) for Gene Tracks were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench. For cross-comparison between strain a 'consensus genome' was generated by BLASTing every CD630 gene agains each CD196 gene and generating a gene track of the resulting consensus sequences.
Comparison of samples was performed using the "Differential Expression in Two Groups" function in CLC Genomics Workbench
Output was exported to MS Excel and manually curated if neccesary

organism: Bacillus anthracis

source_name: Bacterial cells, pelleted

growth_protocol: Bacteria were grown in LB medium overnight and subcultured at a 1:100 ratio into fresh LB medium. After 6 h of growth at 37°C in the presence or absence of 50 µM ‘205,

extract_protocol:
The cell lysates (supernatants) were collected after centrifugation. Aliquots of 1% lysates were diluted with buffer A and kept at −80°C to serve as the input control (1% of input RNA). The remaining lysates were incubated with α-FLAG M2 magnetic agarose beads (Sigma, Cat# M8823) on a rotating wheel for 2 h at 4°C for immunoprecipitation. The bead slurry was recovered using a magnetic stand, washed twice with 1ml of high-salt wash buffer (50mM Tris pH7.4, 1 M NaCl, and 1mM EDTA), then washed once with 1 ml of IP wash buffer (50mM Tris pH7.4, 10mM MgCl2, and 0.2% Tween-20). Aliquots of 5% beads were saved for immunoblotting to examine the immunoprecipitation efficiency. The remaining beads were subjected to DNAase treatment and the protein–RNA complexes were eluted with 3X FLAG peptide according to the manufacturer’s protocol. All samples including 1% input RNA samples were incubated in buffer B (50mM Tris pH7.4, 10mM DTT, 1% SDS, 1 mg ml-1 protease K, and 5mM EDTA) at 70oC for 45 min to reverse crosslinking. Enriched RNAs were extracted using Trizol, precipitated using isopropyl alcohol with linear acrylamide, washed twice with 75% ethanol, and quantified using a NanoDrop spectrophotometer.
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina

treatment_protocol: Bacterial cells were harvested by centrifugation, washed with PBS, subjected to crosslinking using formaldehyde (0.75% final) at room temperature for 10 min, then treated with glycine (125 mM final, pH7.5) at room temperature for 5 min to quench the crosslinking reaction. The cells were subsequently harvested by centrifugation, washed twice with buffer A (50 mM Tris pH 7.4, 150 mM NaCl and 1 mM EDTA), and resuspended in 0.5 ml buffer A amended with 1mM PMSF and 2µl RNase inhibitor followed by sonication for cell lysis and DNA fragmentation.

value: Sterne

tag: genotype

value: {delta}krrA pOS1.PlgtkrrA-FLAG

tag: growth media

tag: atomosphere

value: aerobic

tag: growth temperature


title: LnCaP_siOGT2_Replicate2

value: LnCaP

value: DMSO


title: d1_Mem_rep1

tag: cell type

value: CD4+ T memory Cell

tag: treatment

value: 1 day anti-CD3 and and-CD28 treatment


title: DIP_5mC_KO

tag: strain

tag: genotype/variation

tag: age

value: Embryos were isolated from the uteri of day 12.5 postcoitus pregnant mice


title: LnCaP_siOGT1_Replicate2

tag: cell line


title: KrrA-FLAG+205#1

description:
RIPed RNA
KrrA-FLAG+205
4590-HP-15


title: DIP_Input_KO

tag: fraction


title: d3_Mem_rep1

value: 3 days anti-CD3 and and-CD28 treatment


title: Donor4 PDCTRL L2

description:
Activated T cells
Total RNA

data_processing:
Quality control with Fastqc
Trimming overrepresented sequences with cutadapt
Mapping to human genome assembly GRCh37 - hg19
Counts generation by feature counts
DE analysis DESeq2
Genome_build: GRCh37 - hg19

source_name: CD4+ human total memory

extract_protocol: Extraction was performed using TRI reagent RT by MRC directly on agarose-streptavidin beads, followed by RNA column purification with Zymo spin kit from Zymo research.

tag: experimental

value: control

tag: activation state

value: day 5 post-activation

value: Primary T cells


title: Donor4 PDCTRL L1

description:
Activated T cells
Total RNA


title: KrrA-FLAG#2

description:
RIPed RNA
KrrA-FLAG
4590-HP-14

value: LB


title: RNA_WT_2

description: library strategy: Ribo-Zero RNA-seq

data_processing:
Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7 pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions. Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2. Reads were mapped onto the mm9 assembly of the mouse genome by using Tophat2 and the bowtie aligner3. Quantification of gene expression was performed using HTSeq-0.5.4p3 (http://www-huber.embl.de/users/anders/HTSeq) and gene annotations from Ensembl release 67. Read counts have been normalized across librairies with the statistical method proposed by Anders and Huber4 and implemented in the DESeq Bioconductor library.
Genome_build: mm9
Supplementary_files_format_and_content: Processed expression data were summarized in a single tab-delimited text file containing the following informations: gene name (c1), Gene description (c2), Ensemble_gene_id (c3), MBD4_KO1 raw read count (c4), MBD4_KO2 raw read count (c5), MBD4_WT1 raw read count (c6), MBD4_WT2 raw read count (c7), MBD4_KO1 normalized read count (c8), MBD4_KO2 normalized read count (c9), MBD4_WT1 normalized read count (c10), MBD4_WT2 normalized read count (c11), log2foldchange (c12), p-value (c13), p-value adjusted for multi-testing (c14).

extract_protocol:
RNA samples were purified using standard methods from subconfluent MEFs cultures.
Libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” .

value: Mouse embryonic fibroblasts

value: MBD4 WT


title: KrrA-FLAG#1

description:
RIPed RNA
KrrA-FLAG
4590-HP-13


title: LnCaP_Scr_Control Sample_Replicate2

description: LnCaP_Scr_Control Sample_Replicate2

tag: sirna

value: Scr

tag: agent


title: Donor4 PD146a L2

description:
Activated T cells
Total RNA

value: miR-146a pulldown


title: LnCaP_OSMI2_AT7519_Replicate1


title: RNA_WT_1

description: library strategy: Ribo-Zero RNA-seq


title: LnCaP_OSMI2_Replicate1


title: Donor3 PDCTRL L2

description:
Activated T cells
Total RNA


title: RNA_KO_2

description: library strategy: Ribo-Zero RNA-seq

value: MBD4 KO


title: RNA_KO_1

description: library strategy: Ribo-Zero RNA-seq


title: Donor4 PD146a L1

description:
Activated T cells
Total RNA


title: Donor3 PDCTRL L1

description:
Activated T cells
Total RNA


title: LnCaP_siOGT2_AT7519_Replicate1


title: LnCaP_siOGT1_AT7519_Replicate1


title: WT#1

description:
RIPed RNA
WT
4590-HP-11

value: Sterne

value: Wild-type


title: WT#2

description:
RIPed RNA
WT
4590-HP-12

value: aerobic


title: Input#2

description:
total RNA
Input
4590-HP-10


title: LnCaP_siOGT2_Replicate1

value: LnCaP

value: DMSO


title: DM RPTECs_miRNA

city: Kaohsiung

first: Yi-Chun

last: Tsai

address: No.100 , Tzyou 1st Road

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
For small RNA sequencing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
Supplementary_files_format_and_content: excel files include miRNA, raw read counts and normalized values for samples 1 and 2.

source_name: renal proximal tubular epithelial cells

growth_protocol: RPTECs were grown under normoxia and hypoxia conditions and maintained in 37 °C incubator containing 5% CO2 until confluence.

extract_protocol:
total RNAs from RPTECs were extracted by Trizol Reagent according to the manufacturer’s instructions.
Small RNA/mRNA library construction and deep sequencing was carried out using Illumina sample preparation kit, according to the TruSeq Small RNA Sample Preparation Guide.

tag: tissue

value: Kidney

value: renal proximal tubular epithelial cells


title: LNCaP_Scr_AT7519_Replicate1


title: Input#1

description:
total RNA
Input
4590-HP-9


title: Donor3 PD146a L2

description:
Activated T cells
Total RNA


title: Donor3 PD146a L1

description:
Activated T cells
Total RNA


title: Donor2 PDCTRL L2

description:
Activated T cells
Total RNA


title: krrA 205-3

description:
krrA 205
5425-HP-51

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 20.0.1) platform for analysis. The Illumina paired reads option was chosen for import.
Imported reads were trimmed to remove adapters using CLC Genomics Workbench
To remove rRNA reads, all paired reads were aligned to a sequence list containing all rRNA sequences for each corresponding bacterial strain. Unmapped (non-rRNA) reads were collected and used for subsequent analysis. Steps were performed using CLC Genomics Workbench. Refrence genomes NC_009089 and  NC_013315 were used for CD630 and CD196, respectively.
Expression values (as RPKM) for Gene Tracks were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench. For cross-comparison between strain a 'consensus genome' was generated by BLASTing every CD630 gene agains each CD196 gene and generating a gene track of the resulting consensus sequences.
Comparison of samples was performed using the "Differential Expression in Two Groups" function in CLC Genomics Workbench
Output was exported to MS Excel and manually curated if neccesary

growth_protocol: Bacteria were grown in BHIS medium at 37°C anaerobically or with 1.5% oxygen

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit. DNA was removed by treatment with Invitrogen  TURBO Dna-free kit and rRNA was depleted using the Invitrogen RiboMinus Transcriptome Isolation kit (bacteria) and the RiboMinus Concentration Module
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: {delta}krrA


title: Donor1 PDCTRL L1

description:
Activated T cells
Total RNA

value: control


title: normal individual RPTECs_mRNA


title: LnCaP_siOGT1_Replicate1


title: Donor3 Input CTRL

description:
Activated T cells
Total RNA

value: control input

value: day 5 post-activation


title: krrA vehicle3

description:
krrA vehicle
5425-HP-42

value: LB


title: WT 205-1

description:
WT 205
5425-HP-46


title: krrA 205-2

description:
krrA 205
5425-HP-50


title: Donor2 PDCTRL L1

description:
Activated T cells
Total RNA

value: Primary T cells