title: Noise trauma specimen 8 [8_S42]

value: Left cochlea


title: testis - region R3 - 5'end-triphosphate_rep1

status: Public on Dec 15 2021

type: SRA

city: Knoxville

first: Maxim

middle: Vladimirovich

last: Zagoskin

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

country: USA

institute: The University of Tennessee, Knoxville

description:
Testis_R3_tri_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

library_source: transcriptomic

data_processing:
Adapters were clipped and artifacts removed with FASTX Toolkit 0.0.13 (fastx_clipper and fastx_artifacts_filter).
18-30nt were filtered.
Annotated against local databases of rRNA, tRNA, mtRNA, miRNAs, repeats and transcripts with bowtie with following parameters: -f -v 1 --best.
Reads were mapped to Ascaris genome with bowtie2 with following parameters: -f -x
Genome_build: WGS Project JACCHR01 (assembly ASM1343314v1)
Supplementary_files_format_and_content: Nonredundant reads (nr) of processed fasta files: ids >1_23421, where 1 is order number of the read and 23421 is number of reads.

molecule: total RNA

organism: Ascaris suum

source_name: total male germline

growth_protocol: Ascaris 4-cell embryos were developed in incubator at 30 C shaking at 100 rpm for 64hr.

extract_protocol:
Male and female germline tissues were extracted from worms and washed in PBS, frozen whole or following dissection in liquid nitrogen, and stored at -80°C. Argonaute IPs were carried out using affinity purified rabbit antibodies pre-bound to Protein A Dynabeads (Fisher Scientific) (5-10 ug of antibody per 100 ul of beads). Germline or embryo whole cell lysates were mixed with Protein A Dynabeads and rotated overnight at 4°C. Protein A Dynabeads were recovered and washed with high-salt buffer (50 mM Tris–HCl, pH 7.4, 1M NaCl, 1mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate) three times. The beads were resuspended in 250 ul of Proteinase K buffer containing 200 µg/ml Proteinase K and incubated for 1 hr at 37°C. RNA was extracted using Trizol LS (Invitrogen) adapted for small RNA recovery by precipitation using 2 volumes of isopropanol, 15 µg of GlycoBlue (Invitrogen), and 30 minutes incubation at -80°C followed by centrifugation at 18,500 x g for 35 minutes at 4°C. The RNA was treated with RppH (25 units, New England Biolabs) in Thermopol buffer for 5’ independent cloning. Both untreated and RppH-treated samples were done for AsALG-1 and AsALG-4 samples. Following RppH treatment, samples were repurified with Trizol LS (Invitrogen) (adopted for small RNAs extraction) and stored at -80°C. RNA was isolated using Trizol or LS Trizol (Invitrogen). Total RNA samples were fractionated into small RNA (< 200 nt) and long RNA (>200nt) using the Monarch RNA cleaner (New England Biolabs).
Small RNA libraries were prepared using the Small RNA-Seq Library Prep Kit (Lexogen). Both 5’-phosphate and 5’-phosphate independent libraries (RppH-treated) were prepared. Libraries from 4-cell embryos were also prepared using 18-30 nt gel purified RNA using the SMARTer smRNA-Seq Kit (Clontech) and NEXTflex-Small-RNA-Seq (New England Biolabs) with similar results. RNA >200 nt was treated with TURBO DNase (Ambion) and rRNA depletion carried out using RiboCop rRNA Depletion Kit for Human/Mouse/Rat (Lexogen). Long RNA (>200 nt) libraries were made using CORALL Total RNA-Seq Library Prep Kit (Lexogen). Both small and long RNA libraries were sequenced 150 nt from both ends using the Illumina NovaSeq 6000 System.

tag: tissue

value: total male germline

tag: 5'-end modification

value: mono- and triphosphate

tag: argonaute ip antibody

tag: treatment

value: RNA 5' Pyrophosphohydrolase


title: testis - region R2 - 5'end-triphosphate_rep1

description:
Testis_R2_tri_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: testis - region R1 - 5'end-triphosphate_rep1

description:
Testis_R1_tri_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: CLIP1_IP_2 (RIP-Seq)

city: Wuhan

first: Shiyong

last: Liu

country: China

institute: Huazhong University of Science and Technology

description:
iRIP-seq
1 end reads

data_processing:
remove adapter sequences with cutadapt and set the parameter as “cutadapt -a AGATCGGAAGAGC -u 3 -m 16”.
remove bases with quality below 20, and retain reads longer than 16 bases with FASTX-Toolkit package by setting parameter “fastq_quality_trimmer -t 20 -l 16 -Q 33”
remove reads if it has more than 30% base with quality below 20 (“fastq_quality_filter -q 20 -p 70 -Q 33”)
discard NN, polyG and polyA, retention reads longer than 16 bases(cutadapt -a N -m 16 -O 1 -N - | cutadapt -a GGGGGGGGGGGGGG -O 4 -e 0.1 -n 5 - | cutadapt -a AAAAAAAAAAAAAAA -m 16 --label clean -O 4 -e 0.1)
end2 in the double-ended sequencing data performs reverse complementation by fastx_reverse_complement of FASTX-Toolkit package and then cats to end1 to form single-ended data
Peaks called by Piranha or CIMS software.
Genome_build: GRCH38
Supplementary_files_format_and_content: bed files are all included in a tar archive available on the series record.

organism: Homo sapiens

source_name: HeLa cell

extract_protocol:
For iRIP-seq, the libraries were prepared following the manufacturer's instructions and applied to Illumina Nextseq500 system for 150 nt paired-end sequencing by Ablife. For CLIP-seq, the libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).
For iRIP-seq, the cDNA libraries used the Illumina ScriptSeq? v2 RNA-Seq Library Preparation Kit(Epicentre).The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing. For CLIP-seq, the recovered RNA was used to generate paired-end sequencing library with Balancer NGS Library Preparation Kit for small/microRNA (Gnomegen) following the manufacture instructions. Libraries corresponding to 150-250 bps were purified, quantified and stored at -80C until used for sequencing. The libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).

tag: cell line

value: HeLa

tag: rip target


title: sample_9_Male B6 mice (<1yr)

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma.
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include gene raw counts and normalized CPM (counts per million reads) values for each sample.

organism: Mus musculus

source_name: brain

extract_protocol:
Brain tissue samples were collected and snap frozen using liquid nitrogen. The extraction of the total RNA from was performed by using kits from Applied Biosystems.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Adropin transgenic mice (AdrTG) were crossed with LDLR-deficient C57BL/6J mouse model (LDLRKO). Male and female progeny were fed a high fat diet for 3-months. Male chow-fed wild type (WT) mice were used as controls. Brain tissue samples were collected and snap frozen using liquid nitrogen and subsequently used for RNA-Seq.

tag: strain

tag: Sex

value: male

value: brain

value: Male B6 mice (<1yr)

tag: diet

value: regular chow


title: Sperm Con-2 rep2

city: wuhan

first: ping

last: su

state: hubei

address: qiaokou district hankong road 13

department: Institute of Reproductive Health, Tongji Medical College

institute: huazhong university of science and technology

data_processing:
The raw sequencing data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality are examined by FastQC software (v0.11.7) and 5’, 3’-adaptor bases were trimmed by cutadapt software (1.17).
The trimmed reads are aligned allowing for 1 mismatch only to the mature tRNA sequences, and then reads that do not map were aligned to precursor tRNA sequences with bowtie software (v1.2.2).
The remaining reads were aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2 (2.0.0.8)
Genome_build: GtRNAdb
Supplementary_files_format_and_content: Matrix table with CPM for every gene and every sample

source_name: Sperm

extract_protocol:
The total RNA was isolated using TRIzol LS Reagent (Invitrogen Corp., Carlsbad, CA)  based on the manufacturer’s instructions. Before the sequencing experiment, agarose gel electrophoresis was used to check the integrality of total RNA samples, and then the samples were quantified on the NanoDrop ND-1000 instrument.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter.The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

tag: cell type

value: Sperm

value: 0.9% NaCl

tag: molecule type

value: small non-coding RNA


title: Sperm Con-1 rep1


title: Sperm Con-3 rep3


title: Sperm Cd-2 rep2

value: cadmium


title: Sperm Cd-3 rep3


title: testis - region R3 - 5'end-monophosphate_rep3

description:
Testis_R3_mono_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: monophosphate


title: sample_8_Male B6 mice (<1yr)


title: sample_733_AdrTG;Ldlr-/-

value: AdrTG;Ldlr-/-

value: high fat diet


title: testis - region R2 - 5'end-monophosphate_rep3

description:
Testis_R2_mono_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: Sperm Cd-1 rep1


title: 4cell embryo - INPUT_rep1

description:
INPUT_4cell_rep1
small RNA
Library made with NEB kit

source_name: 4 cells embryos

value: 4 cells embryos


title: 4cell embryo - WAGO1_rep1

description:
WAGO1_4cell_rep1
small RNA
Library made with NEB kit
WAGO1_64hr.nr.fa.gz


title: Noise trauma specimen 6 [6_S40]

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas

data_processing:
Data processing carried out by commercial service (sequentiabiotech.com)
Reference Genome C67Bl/6
Processing using Noiseq protocol
Supplementary_files_format_and_content: Upregulated and down regulated genes provieded in .cvs format; raw counts in txt format

source_name: Left cochlea_Noise trauma

extract_protocol:
Trizol and phase lock heacy gel (Tiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: animals subjected to 16 kHz narrow band noise or noise and mesenchymal stem cells.  RNA extracted 2 days post treatement

value: Noise trauma

value: Left cochlea


title: testis - region R1 - 5'end-monophosphate_rep3

description:
Testis_R1_mono_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline


title: 210303_B: Barcode dataset of TrackerSeq-E12

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Neurobiology.

description: Barcode dataset of TrackerSeq-E12

data_processing:
- Transcritpomic dataset: Sequencing reads in FASTQ files were aligned to a reference transcriptome (mm10-2.1.0) and collapsed into unique molecular identifier counts using the 10x Genomics Cell Ranger software (version 3.0.2 and 5.0.1).Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome (applied cut-offs see Supplementary Data 1, Bandler et al. 2021).
- Barcode dataset STICR: First, BBMap (BBMap – Bushnell B. – sourceforge.net/projects/bbmap/) was used to remove low quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments which were then aligned to our pre-defined fragment reference sets using Bowtie (v5.2.1), allowing for up to 2 mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using Awk. Finally, UMI-tools (v.0.5.1) was used to remove duplicate STICR barcode/cell barcode reads by UMI, allowing for 1 bp mismatch in the UMI. STICR barcodes/CBC pairings with at least 5 distinct UMIs were retained for clonal analysis. Among cells with multiple STICR barcodes passing these criteria, we attempted to find a “dominant” STICR barcode that we defined as containing greater than or equal to 5 times the number of UMI counts compared to the next most abundance STICR barcode. “Dominant” STICR barcodes meeting these criteria were considered to be the clonal barcode of their respective cells and retained for further analysis. Finally, we applied an additional UMI threshold to STICR barcodes, requiring that all STICR barcode/CBC pairings used for clonal analysis have at least 9 distinct UMIs.
- Barcode dataset TrackerSeq: R2 FASTQ files were pre-processed using BBduk; the sequences to the left and right of the lineage barcodes were trimmed so that only the lineage barcode (BC) remained. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from corresponding Seurat object of the dataset to generate a cell barcode whitelist. The extracted cell barcodes and UMIs were added to the read names of the lineage barcode FASTQ files. The resulting FASTQ files were processed by clonal_annotation.ipynb from LARRY (Klein lab), to output a sparse matrix in csv format, where rows were cells identified by individual cell barcodes and columns were lineage barcode, with 1 indicating its presence and 0 its absence. Only (Cell,UMI,BC) triples supported by at least 10 reads and (Cell,BC) pairs with at least 6 UMI were considered for further analyses. A CloneIDs were assigned to cell barcodes. The distance between the cell barcodes in the matrix could be determined by clustering the matrix using Jaccard similarity and average linkage, as demonstrated by Wagner et al. This could be accomplished by using the R function distance(method = ‘jaccard’) and hclust(method = ‘average’). The resulting dendrogram was cut at a height of 0.999 using cutree(hclust_avg, h = 0.999) to obtain the clonal groupings.
Genome_build: mm10-2.1.0
Supplementary_files_format_and_content: - Processed_Transcript: Filtered count matrix
Supplementary_files_format_and_content: - Processed_LBC STICR: Csv files with columns for "CBC", "VBC_Count", "Tier", "Sequence", "UMI", "Final.VBC.call", and "Library"
Supplementary_files_format_and_content: - Processed_LBC TRACKERseq: Csv files with columns for "CBC" and "Lineage-Barcode"

source_name: Forebrain

extract_protocol:
embryonic tissue was collected in ice-cold Leibowitz medium  and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custumed primers with standard Illumina adapters.

value: Forebrain

value: FACSorted for GFP

tag: age


title: testis - ALG1

description:
ALG1_testis
small RNA
Library made with NEB kit

value: mono- and triphosphate

value: RNA 5' Pyrophosphohydrolase


title: tumor-control-6

type: RNA

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.

data_processing: Transcriptome Analysis Console Software v 4.0 was used for basic data analysis and quality control.

label: biotin

source_name: tumor from vector treated control

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridized onto the Affymetrix Clariom S peg plate. The Affymetrix GeneChip® WT PLUS Reagent Kit Manual was followed to prepare the samples. the GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the kit. Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays

extract_protocol: total RNA was isolated from tumor tissue by homogenization in trisol reagent, followed by purification with E.Z.N.A. RNA isolation (omega biotek)

value: vector


title: tumor-control-3

scan_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.


title: tumor-control-4


title: tumor-control-2


title: H37Rv_T72_POA_3100_C

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample

organism: Mycobacterium tuberculosis H37Rv

source_name: bacterial culture

growth_protocol: Samples grown in 7H9-rich media  at 37 degrees C with shaking

extract_protocol:
In three biological replicates, M. tuberculosis cultures with or without drug treatment were harvested at 4, 24  or 72 h. Cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centPOAuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment with no drug or Pyrazinoic acid  at 3100 μg/mL for 4, 24 or 72 h

tag: drug treatment

tag: treatment time

value: 72 hour


title: 4cell embryo - INPUT_rep2

description:
INPUT_4cell_rep2
small RNA
Library made with NEB kit


title: sample_732_Ldlr-/-

value: male

value: brain

value: Ldlr-/-


title: 4cell embryo - WAGO1_rep2

description:
WAGO1_4cell_rep2
small RNA
Library made with NEB kit
WAGO1_64hr.nr.fa.gz


title: sample_731_Ldlr-/-


title: DI_T_199: Barcode dataset of STICR-E12 #1

description: Barcode dataset of STICR-E12 #1

value: SW


title: testis - region R3 - 5'end-monophosphate_rep2

description:
Testis_R3_mono_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: monophosphate


title: tumor-control-5


title: sample_730_Ldlr-/-


title: testis - region R2 - 5'end-monophosphate_rep2

description:
Testis_R2_mono_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: testis - region R1 - 5'end-monophosphate_rep2

description:
Testis_R1_mono_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: H37Rv_T72_POA_3100_A


title: H37Rv_T72_POA_3100_B


title: tumor-control-1


title: DI_T_211: Barcode dataset of STICR-E13 #1

description: Barcode dataset of STICR-E13 #1


title: DI_T_238: Barcode dataset of STICR-E12 #2

description: Barcode dataset of STICR-E12 #2


title: sample_728_AdrTG;Ldlr-/-

value: AdrTG;Ldlr-/-


title: H37Rv_T24_POA_3100_C

value: 24 hour


title: sample_727_AdrTG;Ldlr-/-

value: high fat diet


title: H37Rv_T24_POA_3100_B


title: testis - region R2 - 5'end-monophosphate_rep1

description:
Testis_R2_mono_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: DI_T_239: Barcode dataset of STICR-E13 #2

description: Barcode dataset of STICR-E13 #2


title: DI_T_240: Barcode dataset of STICR-E13 #3

description: Barcode dataset of STICR-E13 #3


title: sample_726_AdrTG;Ldlr-/-


title: sample_636_Ldlr-/-


title: testis - region R1 - 5'end-monophosphate_rep1

description:
Testis_R1_mono_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: DI_T_241: Barcode dataset of STICR-E13 #4

description: Barcode dataset of STICR-E13 #4


title: Male germline region M8 - INPUT

description:
Sperm_M8
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M8

value: male germline region M8


title: sample_635_AdrTG;Ldlr-/-


title: DI_T_242: Barcode dataset of STICR-E14 #1

description: Barcode dataset of STICR-E14 #1


title: H37Rv_T4_POA_3100_C

value: 4 hour


title: 4cell embryo - INPUT_rep3

description:
INPUT_4cell_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: 4 cells embryos


title: H37Rv_T4_POA_3100_B


title: sample_634_Ldlr-/-


title: H37Rv_T4_POA_3100_A


title: ovary - INPUT_rep6

description:
INPUT_ovary_rep6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total female germline

value: total female germline


title: sample_6_Male B6 mice (<1yr)

value: Male B6 mice (<1yr)

value: regular chow


title: ovary - INPUT_rep5

description:
INPUT_ovary_rep5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: mono- and triphosphate

value: RNA 5' Pyrophosphohydrolase


title: H37Rv_T72_POA_0x_F

value: no drug

value: 72 hour


title: testis - region R3 - 5'end-monophosphate_rep1

description:
Testis_R3_mono_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline


title: DI_T_222: Barcode dataset of STICR-E13 #5

description: Barcode dataset of STICR-E13 #5

value: Forebrain

value: FACSorted for GFP


title: sample_592_Ldlr-/-

value: male

value: brain

value: Ldlr-/-


title: sample_591_AdrTG;Ldlr-/-

value: AdrTG;Ldlr-/-

value: high fat diet


title: DI_T_233: Barcode dataset of STICR-E14 #3

description: Barcode dataset of STICR-E14 #3

value: SW


title: H37Rv_T72_POA_0x_E


title: H37Rv_T72_POA_0x_D


title: H37Rv_T24_POA_3100_A

value: 24 hour


title: ovary - INPUT_rep3

description:
INPUT_ovary_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline


title: DI_T_289: Barcode dataset of STICR-E12 #3

description: Barcode dataset of STICR-E12 #3


title: H37Rv_T24_POA_0x_F


title: ovary - INPUT_rep4

description:
INPUT_ovary_rep4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: sample_589_AdrTG;Ldlr-/-


title: ovary - INPUT_rep2

description:
INPUT_ovary_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: sample_583_AdrTG;Ldlr-/-


title: ovary - INPUT_rep1

description:
INPUT_ovary_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: H37Rv_T24_POA_0x_E


title: DI_T_203: Barcode dataset of STICR-E14 #2

description: Barcode dataset of STICR-E14 #2


title: testis - INPUT_rep6

description:
INPUT_testis_rep6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: H37Rv_T24_POA_0x_D


title: H37Rv_T4_POA_0x_F

value: 4 hour


title: sample_5_Male B6 mice (<1yr)

value: Male B6 mice (<1yr)

value: regular chow


title: sample_4_Male B6 mice (<1yr)


title: LV_4b: Barcode dataset of STICR-E10 #3

description: Barcode dataset of STICR-E10 #3


title: LV_3b: Barcode dataset of STICR-E10 #2

description: Barcode dataset of STICR-E10 #2


title: H37Rv_T4_POA_0x_E


title: sample_3_Male B6 mice (<1yr)


title: LV_7b: Barcode dataset of STICR-E10 #4

description: Barcode dataset of STICR-E10 #4


title: sample_590_Ldlr-/-


title: H37Rv_T4_POA_0x_D


title: testis - INPUT_rep4

description:
INPUT_testis_rep4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: mono- and triphosphate

value: RNA 5' Pyrophosphohydrolase


title: CA199: Barcode dataset of STICR-E12 #1

description: Barcode dataset of STICR-E12 #1


title: DI_T_287: Barcode dataset of STICR-E13 #6

description: Barcode dataset of STICR-E13 #6


title: DI_T_304: Barcode dataset of STICR-E14 #4

description: Barcode dataset of STICR-E14 #4


title: zzjB-3

city: Zhengzhou

first: zijing

last: zhang

state: Henan

address: NO:116 road

department: Institute of Animal Husbandry and Veterinary Scienc

institute: Henan Academy of Agricultural Sciences

library_source: genomic

data_processing:
Library quantification was performed by Agilent 2100/LabChip GX Touch to detect the fragment length distribution of the library.
Single-cell libraries were tested, and the sequencing program was run on the Hiseq X-ten sequencing platform
High-quality clean reads were selected after quality-filtering by Trimmomatic software (v.0.36).
After the data were filtered, bisulfite-converted alignment method was used to align the sheep genome (Oar_v.4.0) by Bismark software
Using Bismark Methylation Extractor  and method of lambda DNA spike-in, methylation coverage for every single C was extracted and BS conversion rate was evaluated.
Genome_build: Oar_v3.1

molecule: genomic DNA

organism: Ovis aries

source_name: ovary

growth_protocol: Cumulus–oocyte complexes (COCs) were collected from healthy sheep ovary tissues (n=3) using a cutting method.

extract_protocol:
lysed using 20 mg/mL proteinase K (19131, QIAGEN) for 1 h at 37°. To determine the methylation levels after lysis, bisulfite conversion of single-cell, genome-wide, DNA samples was performed using the EZ DNA Methylation-Gold™ Kit (D5006, Zymo, Irvine, CA, USA).
Bisulfite treatment converts non-methylated, but not methylated, cytosines to uracil (Docherty et al., 2010). The first strand was synthesized using an oligo1 primer with a biotin marker, and streptavidin magnetic beads were used for ‘fishing’. Klenow fragment (3'→5' exo-) (50 U/μL; NEB, M0212M) was used to construct the first strand, and the subsequent steps were performed according to Smallwood et al. (2014). DNA was purified using 0.8X Agencourt Ampure XP beads and M-280 streptavidin Dynabeads (Life Technologies, Carlsbad, CA, USA). The oligo2 primer with a linker sequence for two-strand synthesis was added and the purified DNA was then used for polymerase chain reaction (PCR) amplification, following the manufacturer's instructions. Amplicons were purified using 0.8X Agencourt Ampure XP beads. Then, automated selection of fragments between 300 and 800 bp long was carried out on a Sage Science Pippin HT platform.

treatment_protocol: intracytoplasmic sperm injection (ICSI) was used for the fertilization of preimplantation embryos.

tag: breed

value: Small-tailed Han sheep

tag: developmental stage

value: blastocyst stage

tag: tissues

value: embryos


title: LV_1b: Barcode dataset of STICR-E10 #1

description: Barcode dataset of STICR-E10 #1

tag: tissue

value: Forebrain

value: FACSorted for GFP


title: CA203: Barcode dataset of STICR-E13 #1

description: Barcode dataset of STICR-E13 #1


title: CA211: Barcode dataset of STICR-E12 #2

description: Barcode dataset of STICR-E12 #2


title: testis - INPUT_rep3

description:
INPUT_testis_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline

tag: 5'-end modification


title: testis - INPUT_rep1

description:
INPUT_testis_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

tag: argonaute ip antibody


title: sample_10_Male B6 mice (<1yr)

value: male

value: brain

tag: treatment


title: testis - INPUT_rep5

description:
INPUT_testis_rep5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: Male germline region M7 - INPUT

description:
INPUT_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M7

value: male germline region M7


title: Stimulated CD4+ T cell - 4-MU C3

city: Syracuse

first: Auyon

middle: J

last: Ghosh

address: 750 E Adams St

institute: SUNY Upstate Medical University

description:
Stimulated CD4+ T cell - 4-MU
C3

data_processing:
cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and quantified using Qubit
Libraries were constructed using the Covaris system and quantified using Qubit 2.0 fluorometer
Libraries were pooled and sequenced using Illumina Novaseq 6000 (Mus musculus)
FASTQ files were aligned to BAM files using the Rsubread package
Genome_build: GENCODE release M27/GRCm39
Supplementary_files_format_and_content: counts

source_name: CD4+ T cell

extract_protocol: none provided by the submtter


title: zzjB-2


title: zzjB-1


title: Male germline region M6 - INPUT

description:
INPUT_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M6

value: male germline region M6


title: testis - INPUT_rep2

description:
INPUT_testis_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: Stimulated CD4+ T cell - vehicle C2

description:
Stimulated CD4+ T cell - vehicle
C2

value: Vehicle


title: zzjM-3

value: morula stage


title: zzjM-2


title: sample_12_Male B6 mice (<1yr)


title: CA233: Barcode dataset of STICR-E13 #3

description: Barcode dataset of STICR-E13 #3

value: SW


title: Male germline region M5 - INPUT

description:
INPUT_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M5

value: male germline region M5


title: zzjM-1


title: CA239: Barcode dataset of STICR-E14 #1

description: Barcode dataset of STICR-E14 #1


title: Male germline region M4 - INPUT

description:
INPUT_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M4

value: male germline region M4


title: Naïve CD4+ T cell - control C1

description:
Naïve CD4+ T cell - control
C1

value: Control


title: Stimulated CD4+ T cell - 4-MU B3

description:
Stimulated CD4+ T cell - 4-MU
B3


title: CA238: Barcode dataset of STICR-E13 #4

description: Barcode dataset of STICR-E13 #4


title: zzj16C-3

value: 16-cell stage


title: sample_11_Male B6 mice (<1yr)

value: Male B6 mice (<1yr)

value: regular chow


title: Stimulated CD4+ T cell - vehicle B2

description:
Stimulated CD4+ T cell - vehicle
B2


title: Male germline region M3 - INPUT

description:
INPUT_M3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M3

value: male germline region M3

value: mono- and triphosphate

value: RNA 5' Pyrophosphohydrolase


title: CA240: Barcode dataset of STICR-E14 #2

description: Barcode dataset of STICR-E14 #2

value: Forebrain

value: FACSorted for GFP


title: zzj16C-2

value: Small-tailed Han sheep

value: embryos


title: Naive CD4+ T cell - control B1

description:
Naive CD4+ T cell - control
B1


title: Male germline region M2 - INPUT

description:
INPUT_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M2

value: male germline region M2


title: CA222: Barcode dataset of STICR-E13 #2

description: Barcode dataset of STICR-E13 #2


title: Male germline region M1 - INPUT_rep2

description:
INPUT_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M1

value: male germline region M1


title: CA242: Barcode dataset of STICR-E14 #3

description: Barcode dataset of STICR-E14 #3


title: Stimulated CD4+ T cell - vehicle A2

description:
Stimulated CD4+ T cell - vehicle
A2

value: Vehicle


title: zzj8C-3

value: 8-cell stage


title: Naïve CD4+ T cell - control A1

description:
Naïve CD4+ T cell - control
A1


title: Male germline region M1 - INPUT_rep1

description:
INPUT_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: CA287: Barcode dataset of STICR-E13 #6

description: Barcode dataset of STICR-E13 #6

value: SW


title: CA289: Barcode dataset of STICR-E12 #3

description: Barcode dataset of STICR-E12 #3


title: SE2

city: Minneapolis

first: Sunny

middle: SK

last: Chan

state: MN

department: Pediatrics

institute: University of Minnesota

description: expanded satellite cells

data_processing:
Illumina Casava software were used for basecalling.
Reads were aligned to Mus musculus reference transcriptome (GRCm38/mm10) using Kallisto (v0.44.0).
Transcript abundance was quantified and summarized into gene level as read counts values using the R package tximport (v1.10.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample.

source_name: Myogenic progenitor cells

growth_protocol: Myogenic progenitor cells were plated on 0.1% gelatin-coated wells and cultured in myogenic expansion medium. Cells were passaged every 4-5 days.

extract_protocol:
Qiagen RNeasy Mini Kit with in-column genomic DNA removal
Libraries generation using SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian Kit

value: endogenous satellite cells

tag: passage

value: passage 8


title: 4cell embryo - NRDE3

description:
NRDE3_4cell
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: 4 cells embryos

value: 4 cells embryos


title: zzj8C-2


title: zzj8C-1


title: SE1

description: expanded satellite cells


title: zzjO-3

value: oocyte


title: LV12_b: Barcode dataset of STICR-E12 #4

description: Barcode dataset of STICR-E12 #4


title: SF2

description: fresh satellite cells

value: freshly-isolated


title: zzjO-2


title: ovary - NRDE3_rep2

description:
NRDE3_ovary_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline


title: ovary - NRDE3_rep1

description:
NRDE3_ovary_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: mono- and triphosphate


title: CA304: Barcode dataset of STICR-E14 #4

description: Barcode dataset of STICR-E14 #4


title: TE2

description: expanded teratoma-derived

value: ESC-derived myogenic progenitor cells via teratoma formation


title: zzj16C-1

value: 16-cell stage


title: testis - NRDE3_rep2

description:
NRDE3_testis_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total male germline

value: total male germline

value: RNA 5' Pyrophosphohydrolase


title: CA241: Barcode dataset of STICR-E13 #5

description: Barcode dataset of STICR-E13 #5

source_name: Forebrain

value: Forebrain

value: FACSorted for GFP


title: testis - NRDE3_rep1

description:
NRDE3_testis_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: zzjO-1

value: Small-tailed Han sheep

value: embryos


title: CA199_t: Transcriptomic dataset of STICR-E12 #1

description: Transcriptomic dataset of STICR-E12 #1


title: Male germline region M7 - NRDE3

description:
NRDE3_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M7


title: CA203_t: Transcriptomic dataset of STICR-E13 #1

description: Transcriptomic dataset of STICR-E13 #1

value: SW


title: TE1

description: expanded teratoma-derived


title: Male germline region M6 - NRDE3

description:
NRDE3_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M6


title: CA222_t: Transcriptomic dataset of STICR-E13 #2

description: Transcriptomic dataset of STICR-E13 #2


title: CA211_t: Transcriptomic dataset of STICR-E12 #2

description: Transcriptomic dataset of STICR-E12 #2


title: TF1

description: fresh teratoma-derived


title: Male germline region M4 - NRDE3

description:
NRDE3_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M4


title: SF1

description: fresh satellite cells

value: endogenous satellite cells


title: 912N

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

data_processing:
RNA-seq fragments were aligned by STAR (version 2.5.2b) to the mouse genome (mm10) with basic GENCODE gene annotations (version M22)
Gene expression levels were quantified by RSEM (version 1.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: TSV: RSEM quantification results at the gene level

source_name: bone marrow derived LT-HSC_CH mutant

growth_protocol: 8-16 weeks old mice were maintained according to institutional protocols

extract_protocol:
Qiagen RNeasy Micro Kit (74004)
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

treatment_protocol: Bone marrow was dissociated and resuspended in IMDM with 10% FBS and passed through 25 μm cell strainers to obtain single-cell suspensions prior to antibody staining.

value: bone marrow derived LT-HSC

tag: gender

value: female

tag: genotype

value: CH


title: 930D

tag: strain

value: male


title: Male germline region M5 - NRDE3

description:
NRDE3_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M5

value: mono- and triphosphate


title: 901A


title: Male germline region M3 - NRDE3

description:
NRDE3_M3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M3


title: CA240_t: Transcriptomic dataset of STICR-E14 #2

description: Transcriptomic dataset of STICR-E14 #2


title: Male germline region M2 - NRDE3

description:
NRDE3_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M2

value: RNA 5' Pyrophosphohydrolase


title: 718B


title: CA241_t: Transcriptomic dataset of STICR-E13 #5

description: Transcriptomic dataset of STICR-E13 #5

value: Forebrain

value: FACSorted for GFP


title: TF2

description: fresh teratoma-derived

value: ESC-derived myogenic progenitor cells via teratoma formation

value: freshly-isolated


title: 527F


title: CA242_t: Transcriptomic dataset of STICR-E14 #3

description: Transcriptomic dataset of STICR-E14 #3

value: SW


title: CA233_t: Transcriptomic dataset of STICR-E13 #3

description: Transcriptomic dataset of STICR-E13 #3


title: CA238_t: Transcriptomic dataset of STICR-E13 #4

description: Transcriptomic dataset of STICR-E13 #4


title: 712D

source_name: bone marrow derived LT-HSC_WT

value: WT


title: CA239_t: Transcriptomic dataset of STICR-E14 #1

description: Transcriptomic dataset of STICR-E14 #1


title: CA287_t: Transcriptomic dataset of STICR-E13 #6

description: Transcriptomic dataset of STICR-E13 #6


title: 714E


title: CA289_t: Transcriptomic dataset of STICR-E12 #3

description: Transcriptomic dataset of STICR-E12 #3


title: Male germline region M1 - NRDE3_rep2

description:
NRDE3_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M1


title: 714D


title: 721B


title: testis - WAGO3_rep2

description:
WAGO3_testis_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline


title: Male germline region M1 - NRDE3_rep1

description:
NRDE3_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: ovary - WAGO3_rep1

description:
WAGO3_ovary_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline


title: 4cell embryo - WAGO3

description:
WAGO3_4cell
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: 4 cells embryos


title: ovary - WAGO3_rep2

description:
WAGO3_ovary_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: LV12_t: Transcritpomic dataset of STICR-E12 #4

description: Transcritpomic dataset of STICR-E12 #4


title: testis - WAGO3_rep1

description:
WAGO3_testis_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: CA304_t: Transcritpomic dataset of STICR-E14 #4

description: Transcritpomic dataset of STICR-E14 #4


title: 712F

value: bone marrow derived LT-HSC


title: RNA_WT

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0 and Cellranger mkfastq 3.0.01
Sequencing reads were aligned using CellRanger-ATAC count and CellRanger count to the mm10 reference genome
Protein abundance tag libraries were computed using kallisto | bustools v0.44
Genome_build: mm10
Supplementary_files_format_and_content: Accessible chromatin fragments per ATAC library (tsv), protein abundances per ASAP library (csv), and scRNA-seq gene expression counts (h5)

source_name: Immune cells

extract_protocol:
Digitonin lysis for ASAP-seq and standard 10x Genomics protocol for scRNA-seq
10x Genomics scATAC-seq and v3 scRNA-seq
Customized scATAC-seq (ASAP-seq) workflow as described in https://www.biorxiv.org/content/10.1101/2020.09.08.286914v1 and regular scRNA-seq v3 chemistry from 10x Genomics

tag: magnetic depletion

value: TCRb, B220, Ter199

tag: sorting conditions

value: all live

value: Wildtype


title: Periphery_2

city: Boston

first: Ryoji

last: Amamoto

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Quality control of RNA-seq reads were performed using fastqc version 0.10.1
RNA-seq reads were clipped and mapped onto onto the either the mouse genome (Ensembl GRCm38.90)  using STAR version 2.5.2b. Parameters used were as follows: --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --clip3pAdapterSeq  --quantMode TranscriptomeSAM GeneCounts
Read counts were generated by HT-seq version 0.9.1. Sample parameters used were as follows: -i gene_name -s no
Genome_build: Ensembl GRCm38.90
Supplementary_files_format_and_content: Text files with the read counts for every gene for each sample.

source_name: Mouse peripheral retinas

extract_protocol:
The tissue was dissociated fresh, and cells were, fixed, and labeled with CAR antibody. Specific cellular or nuclear populations were FACS isolated and the RNA was extracted from the cells or nuclei using the RecoverAll Kit.
cDNA was generated using the SMART-Seq v.4 kit. The indices were added using the Nextera XT Kit.

value: peripheral retinas

tag: rna marker

value: CAR+


title: Male germline region M7 - WAGO3

description:
WAGO3_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M7

value: mono- and triphosphate

value: RNA 5' Pyrophosphohydrolase


title: CAL62 cells_U0126-treated_Rep2

city: Madrid

first: Miguel

middle: Angel

last: Zaballos

state: Madrid

address: Arturo Duperier, 4

country: Spain

institute: IIBm-CSIC

data_processing:
Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA v3.4.4) and followed by generation of FASTQ sequence files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Anaplastic thyroid carcinoma-derived cell line

growth_protocol: Cell lines were grown for 24h in 10%FBS-DMEM

extract_protocol:
RNA was extracted using the PureLink™ RNA Mini Kit (Thermo Fisher Scientific)
Total RNA was assayed for quantity and quality using the Qubit RNA BR Assay Kit on the Qubit 2.0 Fluorometer (Life Technologies), and the RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent). The RNASeq libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit protocol (Illumina). The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp following the manufacturer’s protocol for dual indexing.

treatment_protocol: Cell lines were treated for 24h with DMSO (Vehicle), 1mM DEL-22379, 10mM DEL-22379 or 10mM U0126.

value: Thyroid


title: RNA_GFP

value: TCRb, B220, Ter199, CD3

value: GFP+ and live

value: Adig


title: Male germline region M5 - WAGO3

description:
WAGO3_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M5


title: Center_4

source_name: Mouse central retinas

tag: age

value: central retinas


title: Male germline region M6 - WAGO3

description:
WAGO3_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M6


title: Center_2


title: CAL62 cells_1mM-DEL-22379-treated_Rep2


title: Center_3


title: Male germline region M4 - WAGO3

description:
WAGO3_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M4


title: Periphery_3


title: CAL62 cells_10mM-DEL-22379-treated_Rep2


title: ATAC_WT


title: CAL62 cells_DMSO-treated_Rep2

value: 24h DMSO


title: Male germline region M3 - WAGO3

description:
WAGO3_M3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M3


title: 8505c cells_U0126-treated_Rep2


title: Male germline region M2 - WAGO3

description:
WAGO3_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M2


title: ATAC_GFP


title: Small intestine cells, NI_Rep2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description:
processed data file:  NormalizedCounts.txt
N2I_S2_R1_001.fastq.gz.ReadsPerGene.out.tab

data_processing:
basecalling with Illumina
demultiplexing using bcl2fastqv2.20
alignment to mm10 using STAR aligner v2.7
Differential expression was evaluated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts from DESeq2

source_name: Small intestine cells

extract_protocol:
Small intestines sections were harvested from uninfected, PB1- or Δfur-infected HH mice  and stored in RNAlater at -80 °C. Total RNA was extracted from frozen intestine sections using an RNAeasy mini kit (Qiagen, USA).   DNase treatment was performed using RNase-free DNase according to the manufacturer’s instructions.
The quality of total RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). A complementary DNA library was prepared using an NEB Ultra II Directional kit, and sequencing was performed on the Nextseq500 system according to Illumina’s standard protocol

tag: cell type

value: Small intestine cells

value: HH B6.129S6-Hfetm2Nca/J 398 mice in the B6 background

tag: infection

value: Uninfected

tag: time

value: 3 days post infection


title: 8505c cells_10mM-DEL-22379-treated_Rep2


title: TAG_ATAC_WT

value: TCRb, B220, Ter199

value: all live

value: Wildtype


title: 8505c cells_1mM-DEL-22379-treated_Rep2

value: Thyroid


title: 96h_M2

city: Jette

first: Vincent

last: De Smet

state: Brussels

address: Laarbeeklaan, 103 D022

department: Liver Cell Biology Research Group

country: Belgium

institute: Vrije Universiteit Brussel

description: iso20200206_M2_mHSC2D_4D_10pctDMEM_S29_good.fq.gzAligned.out.bam

data_processing:
Trimming FastQ files (polyA, rRNA, adaptors)
Mapping using STAR
Assembly using StringTie
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatic Stellate Cell

growth_protocol: Mouse hepatic stellate cells were isolated by ultraviolet positivity-based sorting from healthy male Balb/c mice aged 23-24weeks and sorted directly into collagen coated 24well plates containing Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 1% Penicillin-Streptomycine and 1% glutamine at 37 °C in a humidified atmosphere with 5% CO2. Culture medium was changed after 3h and 24h and cells were collected for RNA analysis after 3h, 6h, 12h, 18h, 24h and 96h. Every single sample represents 2 technical repeats. A fraction of the cells was immediately collected for RNA analysis without culturing.

extract_protocol:
Hepatic stellate cells were collected for RNA analysis. Total RNA was extracted from cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, USA) according to supplier protocol.
RNA libraries were prepared for sequencing using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Greenland, USA) for Illumina according to supplier protocol.

value: Balb/c

value: Hepatic Stellate Cell

tag: culture time


title: Male germline region M1 - WAGO3_rep1

city: Knoxville

first: Maxim

last: Zagoskin

institute: The University of Tennessee, Knoxville

description:
WAGO3_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

data_processing:
Adapters were clipped and artifacts removed with FASTX Toolkit 0.0.13 (fastx_clipper and fastx_artifacts_filter).
18-30nt were filtered.
Annotated against local databases of rRNA, tRNA, mtRNA, miRNAs, repeats and transcripts with bowtie with following parameters: -f -v 1 --best.
Reads were mapped to Ascaris genome with bowtie2 with following parameters: -f -x
Genome_build: WGS Project JACCHR01 (assembly ASM1343314v1)
Supplementary_files_format_and_content: Nonredundant reads (nr) of processed fasta files: ids >1_23421, where 1 is order number of the read and 23421 is number of reads.

extract_protocol:
Male and female germline tissues were extracted from worms and washed in PBS, frozen whole or following dissection in liquid nitrogen, and stored at -80°C. Argonaute IPs were carried out using affinity purified rabbit antibodies pre-bound to Protein A Dynabeads (Fisher Scientific) (5-10 ug of antibody per 100 ul of beads). Germline or embryo whole cell lysates were mixed with Protein A Dynabeads and rotated overnight at 4°C. Protein A Dynabeads were recovered and washed with high-salt buffer (50 mM Tris–HCl, pH 7.4, 1M NaCl, 1mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate) three times. The beads were resuspended in 250 ul of Proteinase K buffer containing 200 µg/ml Proteinase K and incubated for 1 hr at 37°C. RNA was extracted using Trizol LS (Invitrogen) adapted for small RNA recovery by precipitation using 2 volumes of isopropanol, 15 µg of GlycoBlue (Invitrogen), and 30 minutes incubation at -80°C followed by centrifugation at 18,500 x g for 35 minutes at 4°C. The RNA was treated with RppH (25 units, New England Biolabs) in Thermopol buffer for 5’ independent cloning. Both untreated and RppH-treated samples were done for AsALG-1 and AsALG-4 samples. Following RppH treatment, samples were repurified with Trizol LS (Invitrogen) (adopted for small RNAs extraction) and stored at -80°C. RNA was isolated using Trizol or LS Trizol (Invitrogen). Total RNA samples were fractionated into small RNA (< 200 nt) and long RNA (>200nt) using the Monarch RNA cleaner (New England Biolabs).
Small RNA libraries were prepared using the Small RNA-Seq Library Prep Kit (Lexogen). Both 5’-phosphate and 5’-phosphate independent libraries (RppH-treated) were prepared. Libraries from 4-cell embryos were also prepared using 18-30 nt gel purified RNA using the SMARTer smRNA-Seq Kit (Clontech) and NEXTflex-Small-RNA-Seq (New England Biolabs) with similar results. RNA >200 nt was treated with TURBO DNase (Ambion) and rRNA depletion carried out using RiboCop rRNA Depletion Kit for Human/Mouse/Rat (Lexogen). Long RNA (>200 nt) libraries were made using CORALL Total RNA-Seq Library Prep Kit (Lexogen). Both small and long RNA libraries were sequenced 150 nt from both ends using the Illumina NovaSeq 6000 System.

value: male germline region M1

value: mono- and triphosphate

value: RNA 5' Pyrophosphohydrolase


title: Male germline region M1 - WAGO3_rep2

description:
WAGO3_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 96h_M3

description: iso20200116_M3_mHSC2D_4D_10pctDMEM_S22_good.fq.gzAligned.out.bam


title: Small intestine cells, PI_Rep3

description:
processed data file:  NormalizedCounts.txt
12_PI4_S12_R1_001.fastq.gz.ReadsPerGene.out.tab

value: Y. pseudotuberculosis PB1


title: Small intestine cells, NI_Rep1

description:
processed data file:  NormalizedCounts.txt
N1I_S1_R1_001.fastq.gz.ReadsPerGene.out.tab


title: 8505c cells_DMSO-treated_Rep2

value: 24h DMSO


title: 4cell embryo - CSR1_rep3

description:
CSR1_4cell_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: 4 cells embryos


title: 96h_M1

description: iso20200116_M1_mHSC2D_4D_10pctDMEM_S15_good.fq.gzAligned.out.bam


title: CAL62 cells_U0126-treated_Rep1


title: Small intestine cells, PI_Rep2

description:
processed data file:  NormalizedCounts.txt
11_PI3_S11_R1_001.fastq.gz.ReadsPerGene.out.tab


title: 24h_M2

description: iso20200206_M2_mHSC2D_24h_10pctDMEM_S28_good.fq.gzAligned.out.bam


title: Small intestine cells, PI_Rep1

description:
processed data file:  NormalizedCounts.txt
10_PI2_S10_R1_001.fastq.gz.ReadsPerGene.out.tab


title: 4cell embryo - CSR1_rep2

description:
CSR1_4cell_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 4cell embryo - CSR1_rep1

description:
CSR1_4cell_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 24h_M1

description: iso20200116_M1_mHSC2D_24h_10pctDMEM_S14_good.fq.gzAligned.out.bam


title: Small intestine cells, FI_Rep3

description:
processed data file:  NormalizedCounts.txt
09_FI3_S9_R1_001.fastq.gz.ReadsPerGene.out.tab

value: Y. pseudotuberculosis Dfur


title: CAL62 cells_1mM-DEL-22379-treated_Rep1


title: Small intestine cells, NI_Rep3

description:
processed data file:  NormalizedCounts.txt
N3I_S3_R1_001.fastq.gz.ReadsPerGene.out.tab

value: Small intestine cells


title: ovary - CSR1_rep2

description:
CSR1_ovary_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total female germline

value: total female germline


title: TAG_ATAC_GFP

value: TCRb, B220, Ter199, CD3

value: GFP+ and live

value: Adig


title: Small intestine cells, FI_Rep2

description:
processed data file:  NormalizedCounts.txt
08_FI2_S8_R1_001.fastq.gz.ReadsPerGene.out.tab

value: HH B6.129S6-Hfetm2Nca/J 398 mice in the B6 background

value: 3 days post infection


title: 8505c cells_U0126-treated_Rep1

value: Thyroid


title: CAL62 cells_DMSO-treated_Rep1


title: 18h_M1

description: iso20200116_M1_mHSC2D_18h_10pctDMEM_S13_good.fq.gzAligned.out.bam

value: Balb/c


title: testis - CSR1_rep3

description:
CSR1_testis_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline


title: Small intestine cells, FI_Rep1

description:
processed data file:  NormalizedCounts.txt
07_FI1_S7_R1_001.fastq.gz.ReadsPerGene.out.tab


title: testis - CSR1_rep2

description:
CSR1_testis_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 12h_M2

description: iso20200206_M2_mHSC2D_12h_10pctDMEM_S26_good.fq.gzAligned.out.bam

value: Hepatic Stellate Cell


title: cHSC_2w_3

data_processing:
Trimming FastQ files (polyA, rRNA, barcodes)
Mapping using STAR
Assembly using StringTie
Genome_build: Mus_musculus.GRCm38.94
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Isolated hepatic stellate cells were immediately collected for RNA analysis without culturing. Total RNA was extracted from cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, USA) according to supplier protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male Balb/c mice were subjected to either acute or chronic hepatotoxic liver injury. For acute liver injury, mice aged 10-12 weeks were injected once with carbon tetrachloride (CCl4) and livers collected for further analysis after 24h, 72h and 7days. For chronic liver injury, mice aged 8-10weeks were injected with CCl4 on a semi-weekly basis for a total duration of 4 weeks. At three timepoints after this regimen (i.e. 24h, 72h and 14 days), mice were sacrificed and livers collected for further analysis. All mice were injected intraperitoneally with CCl4 diluted in mineral oil at a dosage of 0.5µL per gram body weight. As control, non-treated (i.e. healthy) mice aging 10-12 weeks were used. Hepatic stellate cell isolation was performed through liver perfusion followed by ultraviolet positivity-based sorting.

value: chronic CCl4 injection

tag: time point


title: 8505c cells_1mM-DEL-22379-treated_Rep1

tag: tissue


title: 18h_M3

description: iso20200116_M3_mHSC2D_18h_10pctDMEM_S20_good.fq.gzAligned.out.bam


title: cHSC_2w_4


title: WBC_sample11

type: genomic

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

department: Department of Biomedical Sciences

country: Italy

institute: Humanitas University

description:
white blood cell methylation status
SAMPLE_11

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: Data were processed using minfi  to obtain DMPs. First, a quality control was performed to evaluate sample-specific methylation parameters. Then, the mean detection p-value was evaluated across all samples, and those probes with a p-value > 0.01 in one or more samples were discarded from the dataset. We also removed those probes where SNPs may affect the CpG, and underperforming probes. Finally, we also filtered out probes localized on the X and Y chromosome, to avoid sex-specific effects.  Finally, data were normalized using the minfi quantile normalization algorithm

label: Cy5 and Cy3

source_name: white blood cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from whole blood using an automated DNA extractor (Chemagic Star workstation; Hamilton, ON, Canada), following manufacturer’s instructions

value: white blood cells

tag: disease state

value: not affected


title: 18h_M2

description: iso20200206_M2_mHSC2D_18h_10pctDMEM_S27_good.fq.gzAligned.out.bam


title: testis - CSR1_rep1

description:
CSR1_testis_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

tag: 5'-end modification

value: mono- and triphosphate

tag: argonaute ip antibody

value: RNA 5' Pyrophosphohydrolase


title: WBC_sample9

description:
white blood cell methylation status
SAMPLE_9

value: affected


title: 12h_M3

description: iso20200116_M3_mHSC2D_12h_10pctDMEM_S19_good.fq.gzAligned.out.bam

tag: treatment


title: WBC_sample13

description:
white blood cell methylation status
SAMPLE_13


title: cHSC_2w_2


title: 8505c cells_10mM-DEL-22379-treated_Rep1


title: WBC_sample14

description:
white blood cell methylation status
SAMPLE_14


title: Male germline region M7 - CSR1

description:
CSR1_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M7

value: male germline region M7


title: Male germline region M5 - CSR1

description:
CSR1_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M5

value: male germline region M5


title: 12h_M1

description: iso20200116_M1_mHSC2D_12h_10pctDMEM_S12_good.fq.gzAligned.out.bam


title: WBC_sample1

description:
white blood cell methylation status
SAMPLE_1


title: ovary - CSR1_rep1

description:
CSR1_ovary_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline


title: Male germline region M6 - CSR1

description:
CSR1_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M6

value: male germline region M6


title: RBFOX2 CLIP-seq, 293T, bio rep 3

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
STAR (Love et al., 2014) (v. 2.7.1a) was used to map raw, paired-end, fastq files to the rDNA locus, then to a genome of repetitive elements, then to the genome.
Custom scripts were used for read processing (https://github.com/dfporter/easyclip-snakemake).
Reads were assigned to genes, separating exons and introns, using HTSeq (v. 0.13.5).
Genome_build: GRCh38 Gencode release 29
Supplementary_files_format_and_content: Unnormalized reads per gene or element.

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) media (Thermo Fisher, #11995-065) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37°C with 5% CO2.

extract_protocol:
Cells were harvested according to the easyCLIP protocol (PMID: 33692367) - lysis buffer was added to the plate, cell scraped into an eppendorf tube, and further lyzed by sonication.
Libraries were created using the easyCLIP protocol (PMID: 33692367), with modifications.
OTHER: CLIP-seq (easyCLIP)

treatment_protocol: Cells washed once with PBS on the petri dish, then UV cross-linked in a Stratalinker at 0.3 mJ/cm2.

tag: antibody

value: Bethyl A300-864AM


title: WBC_sample8

description:
white blood cell methylation status
SAMPLE_8


title: 8505c cells_DMSO-treated_Rep1

value: 24h DMSO


title: cHSC_72h_4


title: 6h_M3

description: iso20200116_M3_mHSC2D_6h_10pctDMEM_S18_good.fq.gzAligned.out.bam


title: cHSC_72h_3


title: cHSC_2w_1


title: WBC_sample12

description:
white blood cell methylation status
SAMPLE_12


title: RBFOX2 CLIP-seq, 293T, bio rep 1


title: cHSC_72h_2


title: WBC_sample5

description:
white blood cell methylation status
SAMPLE_5


title: WBC_sample10

description:
white blood cell methylation status
SAMPLE_10


title: WBC_sample6

description:
white blood cell methylation status
SAMPLE_6


title: 3h_M2

description: iso20200206_M2_mHSC2D_3h_10pctDMEM_S24_good.fq.gzAligned.out.bam


title: Male germline region M3 - CSR1_rep2

address: 1311 Cumberland Avenue

description:
CSR1_M3_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M3

value: male germline region M3


title: WBC_sample7

description:
white blood cell methylation status
SAMPLE_7


title: WBC_sample2

description:
white blood cell methylation status
SAMPLE_2


title: cHSC_72h_1


title: WBC_sample3

description:
white blood cell methylation status
SAMPLE_3


title: WBC_sample4

description:
white blood cell methylation status
SAMPLE_4


title: CAL62 cells_10mM-DEL-22379-treated_Rep1

value: Thyroid


title: 6h_M1

description: iso20200116_M1_mHSC2D_6h_10pctDMEM_S11_good.fq.gzAligned.out.bam

value: Balb/c


title: UTD_donor3

city: BALTIMORE

first: ILIAS

last: CHRISTODOULOU

state: MARYLAND

address: 1650 ORLEANS ST, CRB1

department: ONCOLOGY

institute: JOHNS HOPKINS UNIVERSITY

data_processing:
Reads were aligned to GRCh38 using rsem version 1.3.0 with the following options–star-calc-ci-star-output-genome-bam-forward-prob 0.5.
Differential expression analysis and statistical testing was performed using DESeq2 software
Genome_build: hg38
Supplementary_files_format_and_content: csv format. DEseq2 normalized counts

molecule: polyA RNA

source_name: NK cells

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany; cat. 74104). RNA preparation included an on-column RNase-Free DNase digestion (Qiagen, Hilden, Germany;cat. 79254).
RNA samples were converted to double stranded cDNA using the Ovation RNA-Seq System v2.0 kit (Tecan Cat. No. / ID: 7102-32), which utilizes a proprietary strand displacement technology for linear amplification of mRNA without rRNA/tRNA depletion as per the manufacturer’s recommendations.  This approach does not retain strand specific information. Quality and quantity of the resulting cDNA was monitored using the Bioanalyzer High Sensitivity kit (Agilent Cat. No. / ID: 5067-4626) which yielded a characteristic smear of cDNA molecules ranging in size from 500 to 2000 nucleotides in length.  After shearing 500 nanograms of cDNA to an average size of 250 nucleotides with the Covaris S4 (Covaris Inc. Woburn, MA) library construction was completed with the Illumina Truseq Nano kit (Cat. No. / ID:   20015964) according to the manufacturer’s instructions. mRNA libraries were sequenced on an Illumina Novaseq 6000 instrument using 150bp paired-end dual indexed reads and 1% of PhiX control.

tag: donor disease status

value: healthy

tag: donor number

tag: engineered transgenes

value: none (untransduced)

value: NK


title: UTD_donor2


title: 6h_M2

description: iso20200206_M2_mHSC2D_6h_10pctDMEM_S25_good.fq.gzAligned.out.bam

tag: strain

value: Hepatic Stellate Cell


title: RBFOX2 CLIP-seq, 293T, bio rep 2


title: 3h_M1

description: iso20200116_M1_mHSC2D_3h_10pctDMEM_S10_good.fq.gzAligned.out.bam


title: Male germline region M3 - CSR1_rep1

description:
CSR1_M3_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 3h_M3

description: iso20200116_M3_mHSC2D_3h_10pctDMEM_S17_good.fq.gzAligned.out.bam


title: cHSC_24h_3

value: chronic CCl4 injection


title: UTD_donor1


title: Male germline region M1 - CSR1_rep2

description:
CSR1_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M1

value: male germline region M1

value: mono- and triphosphate


title: secrIL15_donor2

value: secreted IL15


title: cHSC_24h_4


title: Male germline region M2 - CSR1

description:
CSR1_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M2

value: male germline region M2

value: RNA 5' Pyrophosphohydrolase


title: Male germline region M1 - CSR1_rep1

description:
CSR1_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 4cell embryo - WAGO2

description:
WAGO2_4cell
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: 4 cells embryos

value: 4 cells embryos


title: 0h_M2

description: iso20200206_M2_mHSC2D_0h_10pctDMEM_S23_good.fq.gzAligned.out.bam


title: secrIL15_donor3


title: Male germline region M4 - CSR1

description:
CSR1_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M4

value: male germline region M4


title: cHSC_24h_1


title: aHSC_1w_4

value: single CCl4 injection


title: aHSC_1w_3


title: 0h_M3

description: iso20200116_M3_mHSC2D_0h_10pctDMEM_S16_good.fq.gzAligned.out.bam


title: ovary - WAGO2_rep1

description:
WAGO2_ovary_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline


title: MyoD F/R/C 3

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
bcl2fastq v2.19 software used for demultiplexing + basecalling
Trimmomatic v0.36 used for trimming adapter sequences and low quality reads
Kallisto v0.44 used for mapping reads and quantifying gene expression
edgeR v3.28 used for differential gene expression analysis
WebGestalt used for pathway enrichment analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited raw counts

source_name: Embryonal tissue

extract_protocol:
RNA was isolated using Qiagen RNeasy kit (Cat. #74104, Qiagen) and treated with RNase-Free DNase (Cat. #79254, Qiagen).
TruSeq Stranded mRNA protocol (Illumina, Inc, California, USA).

value: Mouse embryonic fibroblasts

tag: genotype

value: Dmdmdx

value: +MyoD+F/R/C


title: secrIL15_donor1

value: healthy


title: 2B4zIsecrIL15_donor1

value: 2B4.zeta CAR and secreted IL15


title: 2B4zIsecrIL15_donor3

value: NK


title: 2B4zIsecrIL15_donor2


title: MyoD F/R/C 2


title: ovary - WAGO2_rep2

description:
WAGO2_ovary_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: MyoD 3

value: +MyoD


title: aHSC_1w_2

value: Balb/c

value: Hepatic Stellate Cell


title: testis - WAGO2_rep2

description:
WAGO2_testis_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total male germline

value: total male germline

value: mono- and triphosphate


title: aHSC_1w_1


title: 2B4z_donor3

value: 2B4.zeta CAR


title: MyoD 2


title: 2B4z_donor2


title: MyoD 1


title: cHSC_24h_2

value: chronic CCl4 injection


title: MyoD F/R/C 1


title: Male germline region M7 - WAGO2

description:
WAGO2_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M7

value: RNA 5' Pyrophosphohydrolase


title: aHSC_72h_4

value: single CCl4 injection


title: 2B4z_donor1


title: Dmdmdx MEF 3


title: Male germline region M6 - WAGO2

description:
WAGO2_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M6


title: aHSC_72h_3


title: aHSC_72h_2


title: aHSC_72h_1


title: Male germline region M5 - WAGO2

description:
WAGO2_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M5


title: Caucasian nasal polyp 7

first: Tsuguhisa

last: Nakayama

address: 801 Welch Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Stanford University

data_processing:
Base calling performed using CASAVA base recognition.
RAW data are stored in FASTQ format files and filtered by removing reads with adaptor contamination, reads when certain nucleotides constitute more than 10 percent of either read, and reads when low quality nucleotides constitute more than 50 percent of the read.
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Nasal polyp

extract_protocol:
Nasal polyp tissues from CRSwNP, and uncinate process tissues from control patients, were collected, placed in RNALater solution (Ambion, Austin, TX). RNA was extracted using NucleoSpin RNA (Macherey-Nagel, Duren, Germany). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Beverly, MA).
RNA libraries were prepared for sequencing using standard protocols

value: Caucasian chronic rhinosinusitis with nasal polyp


title: Male germline region M4 - WAGO2

description:
WAGO2_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M4


title: Dmdmdx MEF 2

value: Mouse embryonic fibroblasts

value: Dmdmdx


title: Caucasian nasal polyp 6


title: aHSC_24h_3


title: Dmdmdx MEF 1


title: β8ITGcKO 24 hr PCS rep3

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

description:
β8ITGcKO 24 hr PCS rep3
B80vsB824.txt
WT24vsB824.txt

data_processing:
Analysis was performed by DNA Link USA, Inc
Sequence quality was assessed using FASTQC
Sequences were  trimmed 5'  8bp and 3' 2bp and filtered 35bp minimum length after trimming using Cutadapt v 1.12
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Pairwise differential expression analysis was performed using Cuffdiff v2.2.1
Genome_build: Mus musculus mm10 (UCSC downlad GRCm38 and gff from NCBI/RefSeq GRCm38.p5 vertion)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: test_id, gene_id, gene locus, sample_1, sample_2, status, Sample1_Rep_1, Sample1_Rep_2, Sample1_Rep_3, Sample1_AVE, Sample2_Rep_1, Sample2_Rep_2, Sample2_Rep_3, Sample2_AVE, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant

source_name: Lens

extract_protocol:
By using an in vivo mouse model of cataract surgery, fiber cells were removed from wild type (WT) and β8 integrin conditional knockout (β8ITGcKO) lenses via a central corneal incision, leaving behind the lens capsule and attached LECs. Samples were harvested at 0 hour and 24 hours PCS, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104).
RNA libraries were prepared for sequencing using standard Clonthech protocols for  SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian

value: 24 hr

tag: surgery

value: cataract surgery

value: Lens capsule and attached LECs

tag: age

value: Adult 2 month old

value: beta8 integrin conditional knockout


title: Male germline region M3 - WAGO2

state: TN

description:
WAGO2_M3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M3

value: mono- and triphosphate


title: testis - WAGO2_rep1

description:
WAGO2_testis_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline


title: Caucasian nasal polyp 5


title: β8ITGcKO 24 hr PCS rep2

description:
β8ITGcKO 24 hr PCS rep2
B80vsB824.txt
WT24vsB824.txt


title: aHSC_24h_1

value: Balb/c

tag: cell type

value: Hepatic Stellate Cell


title: Male germline region M1 - WAGO2_rep2

description:
WAGO2_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO2_maleR1a.nr.fa.gz

value: male germline region M1

value: RNA 5' Pyrophosphohydrolase


title: Caucasian nasal polyp 4


title: β8ITGcKO 24 hr PCS rep1

description:
β8ITGcKO 24 hr PCS rep1
B80vsB824.txt
WT24vsB824.txt


title: β8ITGcKO 0 hr PCS rep3

description:
β8ITGcKO 0 hr PCS rep3
B80vsB824.txt
WT0vsBT80.txt

value: 0 hr


title: Caucasian nasal polyp 3

value: Caucasian chronic rhinosinusitis with nasal polyp


title: Male germline region M1 - WAGO2_rep1

description:
WAGO2_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO2_maleR1a.nr.fa.gz


title: Caucasian nasal polyp 8


title: healthy_4

value: Healthy


title: healthy_3


title: ovary - WAGO1_rep2

description:
WAGO1_ovary_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_female.nr.fa.gz

value: total female germline


title: Caucasian nasal polyp 2


title: β8ITGcKO 0 hr PCS rep2

description:
β8ITGcKO 0 hr PCS rep2
B80vsB824.txt
WT0vsBT80.txt


title: aHSC_24h_2

value: single CCl4 injection


title: healthy_2


title: healthy_1


title: Caucasian nasal polyp 1


title: β8ITGcKO 0 hr PCS rep1

description:
β8ITGcKO 0 hr PCS rep1
B80vsB824.txt
WT0vsBT80.txt


title: testis - WAGO1_rep2

description:
WAGO1_testis_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_male.nr.fa.gz


title: Japanese nasal polyp 8

value: Japanese chronic rhinosinusitis with nasal polyp


title: Male germline region M2 - WAGO2

description:
WAGO2_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M2


title: ovary - WAGO1_rep1

description:
WAGO1_ovary_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_female.nr.fa.gz


title: testis - WAGO1_rep1

description:
WAGO1_testis_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_male.nr.fa.gz


title: Japanese nasal polyp 7


title: WT 24 hr PCS rep2

description:
WT 24 hr PCS rep2
WT0vsBT80.txt
WT24vsB824.txt

value: 24 hr

value: cataract surgery

value: Lens capsule and attached LECs

value: wild type


title: Male germline region M7 - WAGO1

description:
WAGO1_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M7

value: mono- and triphosphate


title: Mlkl-/- BMDMs rep 3

first: Isabella

last: Kong

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The single-end 75 bp were demultiplexed using Casavav1.8.2 and Cutadapt (v1.9) was used for read trimming.
The trimmed reads were subsequently mapped to the mouse genome (mm10) using HISAT2.
FeatureCounts was used for read counting after which differential gene expression analysis was performed using Voom-LIMMA packages.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: BMDM

growth_protocol: Bone marrow cells harvested from femoral, tibial and pelvic bones were cultured on 15-cm non-treated dishes for 6 days (37°C, 10% CO2) in 25 ml Dulbecco’s modified essential medium (DMEM) containing 10% foetal bovine serum (FBS, Sigma), 50 U/ml penicillin and 50 µg/ml streptomycin and supplemented with 15-20% L929 cell conditioned medium. Differentiated BMDMs were harvested and replated in sterile 24-well non-treated plates at 6x105 cells/well in a final volume of 600 µl DMEM/FCS supplemented with 20% L929 conditioned medium.

extract_protocol:
Total RNA was extracted using the ISOLATE II RNA Mini Kit (Meridian Bioscience).
3’mRNA-sequencing libraries were prepared using 100 ng of total RNA using the QuantSeq 3’mRNA-Seq Library Prep (Lexogen) according to the manufacturer’s instructions and sequenced on the NextSeq 500 (Illumina).

treatment_protocol: BMDMs were primed overnight with IFNγ and stimulated with LPS for 7hr.

value: Mlkl-/-

value: overnight IFNgamma priming and 7hr LPS stimulation


title: Mlkl-/- BMDMs rep 2


title: WT 24 hr PCS rep1

description:
WT 24 hr PCS rep1
WT0vsBT80.txt
WT24vsB824.txt

value: Adult 2 month old


title: WT 0 hr PCS rep3

description:
WT 0 hr PCS rep3
WT0vsBT80.txt
WT0vsBT80.txt

value: Lens capsule and attached LECscataract surgery


title: Mlkl-/- BMDMs rep 1


title: Japanese nasal polyp 5


title: Male germline region M6 - WAGO1

description:
WAGO1_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M6

value: RNA 5' Pyrophosphohydrolase


title: Male germline region M5 - WAGO1

description:
WAGO1_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M5


title: WT 0 hr PCS rep2

description:
WT 0 hr PCS rep2
WT0vsBT80.txt
WT0vsBT80.txt

value: 0 hr


title: WT 24 hr PCS rep3

description:
WT 24 hr PCS rep3
WT0vsBT80.txt
WT24vsB824.txt


title: Caspase-8-/-Mlkl-/- BMDMs rep 1


title: Japanese nasal polyp 4


title: Japanese nasal polyp 3


title: WT 0 hr PCS rep1

description:
WT 0 hr PCS rep1
WT0vsBT80.txt
WT0vsBT80.txt


title: Male germline region M3 - WAGO1_rep2

description:
WAGO1_M3_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_maleR2a.nr.fa.gz

value: male germline region M3


title: Japanese nasal polyp 2

value: Japanese chronic rhinosinusitis with nasal polyp


title: Japanese nasal polyp 1


title: RNAseq-PCB126-10nM-Rep6

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
DNA methylation analysis was carried out following Bisulfite Analysis Toolkit (BAT). The details are provided in this website: https://www.bioinf.uni-leipzig.de/Software/BAT/. This contains 4 different modules - Mapping,  Calling, Analysis and DMRs
RNAseq - pre-processing using FASTQC
RNAseq - mapping the reads to the genome using STAR
RNAseq - counting the reads using HT-seq count
RNAseq - statistical analysis using edgeR
Genome_build: GRCz10
Supplementary_files_format_and_content: Text format; RNAseq data files (Htseq-count) contains read counts. DMR data contains statistically significant DMRs and statistical data.
Supplementary_files_format_and_content: P0_3.metilene_qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO
Supplementary_files_format_and_content: P10.metilene_qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO
Supplementary_files_format_and_content: P0_3-overlap-P10.txt: Common DMRs between 3 and 10nM PCB126 groups

organism: Danio rerio

source_name: testis

extract_protocol:
Total RNA and DNA were isolated using the ZR-Duet™ DNA/RNA Mini Prep kit (Zymo Research, CA).
Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single-ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT-Dx, a Diagenode company (Ghent, Belgium). Briefly, libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI (New England Biolabs, MA), followed by end repair and A-tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor-ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end (PE) sequencing was performed on an Illumina HiSeq2500 platform.

treatment_protocol: Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant-free water for 7 days prior to sampling the testis tissue.

value: testis

tag: developmental stage

value: Adult


title: RNAseq-PCB126-10nM-Rep5


title: Male germline region M2 - WAGO1

description:
WAGO1_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M2


title: Control uncinate process 7

source_name: Uncinate process

value: Healthy control


title: Male germline region M3 - WAGO1_rep1

description:
WAGO1_M3_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_maleR2a.nr.fa.gz


title: Japanese nasal polyp 6


title: Control uncinate process 6


title: RNAseq-PCB126-10nM-Rep3


title: Male germline region M1 - WAGO1_rep1

description:
WAGO1_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_maleR1a.nr.fa.gz

value: male germline region M1


title: Male germline region M1 - WAGO1_rep2

description:
WAGO1_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit
WAGO1_maleR1a.nr.fa.gz


title: RNAseq-PCB126-10nM-Rep4


title: Caspase-8-/-Mlkl-/- BMDMs rep 2


title: Japanese nasal polyp 9


title: RNAseq-PCB126-10nM-Rep2


title: Control uncinate process 5


title: RNAseq-PCB126-10nM-Rep1


title: Male germline region M4 - WAGO1

description:
WAGO1_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M4


title: 4cell embryo - ALG4

description:
ALG4_4cell
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: 4 cells embryos

value: mono- and triphosphate


title: Control uncinate process 4


title: siHIF-1α Hypoxia rep1

city: Larissa

first: Antonis

last: Giakountis

address: Biopolis

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were trimmed for adaptor sequence using cutadapt software and mapped to hg19 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html).  Tags overlapping the Ensembl GRCh37 human exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each sample and Ensembl gene.

source_name: HeLa cell line

growth_protocol: HeLa cells treated with control (Nt) or NPM1 siRNA (siNPM1) for 24h and incubated at 21% or 1% O2 for 24h

extract_protocol:
Total RNA was extracted with nucleozol reagent
Total RNA samples were prepared and their concentration was measured in nanodrop (ND1000 Spectrophotometer – PEQLAB). The concentration required for library preparation varies from 5 to 500ng per 5μl. Samples with a concentration of more than 500ng/μl, were diluted accordingly to a mean concentration of approximately 100-150ng/μl. The RNA quality of each sample was measured in bioanalyzer (Agilent Technologies) using the Agilent RNA 6000 Nano Kit reagents and protocol. (RNA samples with RNA Integrity Number (RIN) >7 are preferred, although RNAs of lower quality can also be used, and further processed for library preparation and sequencing).  For library preparation, the 3’ mRNA-Seq Library Prep Kit Protocol and reagents, for Ion Torrent (QuantSeq-LEXOGEN™ Vienna, Austria) was used according to manufacturer’s instruction. Briefly, library generation is initiated by oligodT priming which contains the Ion Torrent compatible linker sequences. Approximately 300ng per 5μl of RNA from each sample was used to perform the first strand synthesis. Any remaining RNA is removed and 2nd strand synthesis is initiated by a random primer, containing Ion Torrent compatible linker sequences at its 5’ end, and a sequence polymerase. In line barcodes are introduced at this point. 2nd strand synthesis is followed by a magnetic bead-based purification step and the resulted purified library is amplified for 13 to 18 cycles and re-purified.  Each library’s quality and quantity was assessed in bioanalyzer using the DNA High Sensitivity Kit reagents and protocol (Agilent Technologies). The quantified libraries were pooled together in 12plex at a final concentration of 7pM.  The libraries pool was processed on the Ion Proton One Touch system where the libraries were templated and enriched with the Ion PI™ Hi-Q™ OT2 200 Kit (ThermoFisher Scientific) and sequenced, with the Ion PI™ Hi-Q™ Sequencing 200 Kit on Ion Proton PI™ V2 chips (ThermoFisher Scientific) according to commercially available protocols. 3’RNA-sequencing is performed on an Ion Proton™ System (Rothberg et al, 2011), according to the manufacturer's instructions.   Initial analysis took place in Ion Torrent server where the strand specific sequencing reads mapped to their corresponding strand on the genome.
3’RNA-sequencing

treatment_protocol: HeLa cells treated with control (Nt) or NPM1 siRNA (siNPM1) for 24h (Viromer reagent transfection)

tag: cell line

value: HeLa

tag: knockdown

value: HIF-1α siRNA

value: 1% Oxygen


title: ovary - ALG4

description:
ALG4_ovary
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total female germline

tag: tissue

value: total female germline


title: siNPM1 Hypoxia rep2

value: NPM1 siRNA


title: RNAseq-PCB126-3nM-Rep6


title: Control uncinate process 3

tag: disease state


title: siNPM1 Hypoxia rep1


title: RNAseq-PCB126-3nM-Rep4


title: RNAseq-PCB126-3nM-Rep5


title: Control uncinate process 2


title: Male germline region M7 - ALG4

description:
ALG4_M7
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M7

value: male germline region M7

tag: 5'-end modification

value: RNA 5' Pyrophosphohydrolase


title: Control uncinate process 1


title: testis - ALG4

description:
ALG4_testis
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline

tag: argonaute ip antibody


title: siNPM1 Normoxia rep2

tag: treatment

value: 21% Oxygen


title: Male germline region M6 - ALG4

description:
ALG4_M6
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M6

value: male germline region M6


title: siNPM1 Normoxia rep1


title: siHIF-1α Hypoxia rep2


title: RNAseq-PCB126-3nM-Rep3

value: testis

value: Adult


title: RNAseq-PCB126-3nM-Rep2


title: Nt Hypoxia rep2

value: Non-target siRNA


title: Male germline region M5 - ALG4

description:
ALG4_M5
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M5

value: male germline region M5


title: Male germline region M4 - ALG4

description:
ALG4_M4
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M4


title: RNAseq-PCB126-3nM-Rep1


title: Nt Hypoxia rep1


title: Male germline region M3 - ALG4

description:
ALG4_M3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M3

value: male germline region M3


title: Nt Normoxia rep1


title: Male germline region M2 - ALG4

description:
ALG4_M2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: male germline region M2

value: mono- and triphosphate


title: RNAseq-DMSO-Rep5

value: DMSO


title: DMD_IP_2 (CLIP-seq)

city: Wuhan

first: Shiyong

last: Liu

institute: Huazhong University of Science and Technology

description: CLIP-seq

data_processing:
remove adapter sequences with cutadapt and set the parameter as “cutadapt -a AGATCGGAAGAGC -u 3 -m 16”.
remove bases with quality below 20, and retain reads longer than 16 bases with FASTX-Toolkit package by setting parameter “fastq_quality_trimmer -t 20 -l 16 -Q 33”
remove reads if it has more than 30% base with quality below 20 (“fastq_quality_filter -q 20 -p 70 -Q 33”)
discard NN, polyG and polyA, retention reads longer than 16 bases(cutadapt -a N -m 16 -O 1 -N - | cutadapt -a GGGGGGGGGGGGGG -O 4 -e 0.1 -n 5 - | cutadapt -a AAAAAAAAAAAAAAA -m 16 --label clean -O 4 -e 0.1)
end2 in the double-ended sequencing data performs reverse complementation by fastx_reverse_complement of FASTX-Toolkit package and then cats to end1 to form single-ended data
Peaks called by Piranha or CIMS software.
Genome_build: GRCH38
Supplementary_files_format_and_content: bed files are all included in a tar archive available on the series record.

source_name: HeLa cell

extract_protocol:
For iRIP-seq, the libraries were prepared following the manufacturer's instructions and applied to Illumina Nextseq500 system for 150 nt paired-end sequencing by Ablife. For CLIP-seq, the libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).
For iRIP-seq, the cDNA libraries used the Illumina ScriptSeq™ v2 RNA-Seq Library Preparation Kit(Epicentre).The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing. For CLIP-seq, the recovered RNA was used to generate paired-end sequencing library with Balancer NGS Library Preparation Kit for small/microRNA (Gnomegen) following the manufacture instructions. Libraries corresponding to 150-250 bps were purified, quantified and stored at -80C until used for sequencing. The libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).

value: HeLa

tag: clip target

value: DMD


title: RNAseq-DMSO-Rep6


title: Male germline region M1 - ALG4_rep2

description:
ALG4_M1_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: male germline region M1

value: male germline region M1


title: RNAseq-DMSO-Rep3


title: Male germline region M1 - ALG4_rep1

description:
ALG4_M1_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: RNAseq-DMSO-Rep4


title: DMD_IP_1 (CLIP-seq)

description: CLIP-seq


title: 4cell embryo - ALG1

description:
ALG1_4cell
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: 4 cells embryos

value: 4 cells embryos


title: DMD_Input_1 (CLIP-seq)

description: CLIP-seq


title: DMD_Input_2 (CLIP-seq)

description: CLIP-seq


title: RNAseq-DMSO-Rep2


title: RNAseq-DMSO-Rep1


title: ovary - ALG1

description:
ALG1_ovary
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline

value: RNA 5' Pyrophosphohydrolase


title: Nt Normoxia rep2

value: 21% Oxygen


title: IHEC_63_scRNA-seq

status: Public on Dec 14 2021

city: Toulouse

first: Juliette

last: Coudert

address: 205 route de Narbonne

country: France

institute: CNRS

description: Re-analysis of GSM2839645

data_processing:
FASTQ file generated by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptors and low quality reads then mapped to the mm10 mouse genome using RSEM v1.2.18
FPKM measurements were compiled from RSEM output
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples

source_name: Lymph Node

extract_protocol:
Tumors were removed from mice, dissociated into single cell suspension and Tumor Associated High Endothelial Cells or Tumor Associated Blood Endothelial Cells were FACS sorted. Purified cells were sorted, RNA was extracted and cDNA constructed using the Fluidigm C1 System.
Libraries were constructed using the Nextera XT kit as per the manufacturer’s instructions

value: Lymph Node

value: High Endothelial Cell

tag: state

value: Inflamed

value: Treated with 4% Oxazolone on Skin, Harvest Day 3


title: IHEC_59_scRNA-seq

description: Re-analysis of GSM2839641


title: IHEC_64_scRNA-seq

description: Re-analysis of GSM2839646


title: IHEC_60_scRNA-seq

description: Re-analysis of GSM2839642


title: No Favorable response 5

first: ELISA

last: CONDE MORENO

address: Carretera de Colmenar KM9.100

department: Pathology

institute: Instituto Ramón y Cajal de Investigación Sanitaria, IRYCIS

data_processing: Array data was normalized using the average of the expression of all miRNAs exhibiting CT equal to or less than 34.Data was analyzed using GenEx v.6 software

label: SYBR Green

source_name: Serum

label_protocol: PCR assays were performed using quantitative PCR Array screening of 752 miRNAs using the miRCURY LNA miRNA miRNome PCR Panels I+II (YAHS-312 YG-8, Qiagen), following manufacturer´s indications. The Universal RT miRNA PCR System (Qiagen) was used for cDNA synthesis. 4ul of RNA was used as template for RT in a final volume of 20 μL. An external RNA (cell-miR-39) was added and further amplified as a control of cDNA synthesis efficiency. Quantitative real-time PCR were performed (Light Cycler 480, Roche. PCR initial heat activation 2 min 95°C; step cycling: Denaturation 10s 95°C, Combined annealing/extension 60 s 56°C .Number of cycles 45. Melting curve analysis 60–95°C

extract_protocol: Isolation of total RNA enriched in miRNAs was performed using the miniRNAeasy kit (Qiagen) and 200ul of serum

tag: sample type

value: No Favorable response

value: Metastatic Colorectal Cancer


title: No Favorable response 6


title: No Favorable response 3


title: IHEC_65_scRNA-seq

description: Re-analysis of GSM2839647


title: IHEC_62_scRNA-seq

description: Re-analysis of GSM2839644


title: IHEC_57_scRNA-seq

description: Re-analysis of GSM2839639


title: No Favorable response 4


title: No Favorable response 2


title: IHEC_61_scRNA-seq

description: Re-analysis of GSM2839643


title: IHEC_58_scRNA-seq

description: Re-analysis of GSM2839640


title: No Favorable response 1


title: Favorable response 6

value: Favorable response


title: Favorable response 5


title: IHEC_53_scRNA-seq

description: Re-analysis of GSM2839635


title: IHEC_54_scRNA-seq

description: Re-analysis of GSM2839636


title: IHEC_52_scRNA-seq

description: Re-analysis of GSM2839634


title: IHEC_55_scRNA-seq

description: Re-analysis of GSM2839637


title: Favorable response 3


title: Favorable response 4


title: Favorable response 1


title: IHEC_51_scRNA-seq

description: Re-analysis of GSM2839633


title: IHEC_50_scRNA-seq

description: Re-analysis of GSM2839632


title: IHEC_49_scRNA-seq

description: Re-analysis of GSM2839631


title: IHEC_56_scRNA-seq

description: Re-analysis of GSM2839638


title: IHEC_44_scRNA-seq

description: Re-analysis of GSM2839626


title: IHEC_47_scRNA-seq

description: Re-analysis of GSM2839629


title: IHEC_45_scRNA-seq

description: Re-analysis of GSM2839627


title: IHEC_46_scRNA-seq

description: Re-analysis of GSM2839628


title: IHEC_42_scRNA-seq

description: Re-analysis of GSM2839624


title: IHEC_41_scRNA-seq

description: Re-analysis of GSM2839623


title: IHEC_40_scRNA-seq

description: Re-analysis of GSM2839622


title: IHEC_43_scRNA-seq

description: Re-analysis of GSM2839625


title: Favorable response 2


title: IHEC_38_scRNA-seq

description: Re-analysis of GSM2839620


title: IHEC_39_scRNA-seq

description: Re-analysis of GSM2839621


title: IHEC_48_scRNA-seq

description: Re-analysis of GSM2839630


title: Caspase-8-/-Mlkl-/- BMDMs rep 3

value: overnight IFNgamma priming and 7hr LPS stimulation


title: IHEC_37_scRNA-seq

description: Re-analysis of GSM2839619


title: IHEC_36_scRNA-seq

description: Re-analysis of GSM2839618