title: AMLC, OMA, 4hours, rep3

city: Nagasaki

first: Naoki

last: Iwanaga

address: Sakamoto, 1-7-1

country: Japan

institute: Nagasaki University

description: Library name: OMA.4hr.3

data_processing:
RNA-seq libraries were sequenced using paired end reads (150nt of read1 and read2) on a DNBSEQ-G400RS instrument (MGI Tech).
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: AMLCs

extract_protocol:
RNA was harvested using Rneasy miini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit (Clontech, 634442) and MGIEasy Universal Library Conversion Kit (App-A) (MGI, 1000004155) according to the manufacturer’s instruction..

tag: cell type

value: AMLCs

value: OMA

tag: batch


title: 01-217_C1D1

status: Public on Feb 23 2026

type: protein

city: Portland

first: Lisa

last: Coussens

state: OR

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health and Science University

hyb_protocol: 25 uL of each sample combined with 50 uL of capture beads and 25 uL of universal assay buffer were incubated with shaking at room temperature for 2 hours. 25 uL Detection Antibody Mix was added to each sample and incubated with shaking at room temperature for 30 min. 50 uL of Streptavidin-PE was added to each sample and incubated with shaking at room temperature for 30 minutes. 120 uL of wash buffer was added and shaken at room temperature for 5 minutes. Values read on xMAP Multi-Analyte Profiling system.

scan_protocol: follow manufacture sample preparation protocol and scan on xMAP system

data_processing:
Proteins in the raw.txt file with expression less than the lower limit of detection were assigned to the lower limit of detection and saved as clean.txt (included in the sample data table)
Changes in concentration between time-points for each sampleID in clean.txt were calculated as log2(time2/time1) and saved in processed.txt, Where time2 is either C1D1, C2D1, or C4D1; time1 is Screen from characteristics: Timepoint

label: RPE

molecule: protein

organism: Homo sapiens

source_name: blood plasma

label_protocol: use antigen-specific detection antibodies bind to antigens, RPE fluorescence identifies the antibodies

extract_protocol: Human blood samples were collected with EDTA tubes. Plasma was separated from buffy coats by centrifugation for 15 min at 2000 rpm at 4 deg C with brake off. Supernatant transferred into separate 1.8 mL cryovials until all plasma was removed. Samples stored at -80 deg C.

tag: tissue

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

tag: best clinical response

value: PD

tag: survival


title: 1,3 Platin Input Rep 2

type: SRA

city: Washington

first: Sreejith

last: Nair

institute: Georgetown University

description: Library name: Sample 8

library_source: transcriptomic

data_processing:
Paired-end FASTQ files were quality checked using FastQC (v0.11.9).
Sequencing adapters were trimmed using CutAdapt (v4.0) in paired-end mode.
Trimmed reads were aligned to the human reference genome (GRCh38.p14, GENCODE Release 46) using STAR (v2.7.11).
Peaks were called using the peak calling software CLAM (CLIP-seq Analysis of Multi-mapped reads) (v1.2.3).
RPKM normalized bigWig files were generated using deeptools (v3.5.3) for visualization.

molecule: total RNA

growth_protocol: Human ovarian adenocarcinoma A2780 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin–streptomycin at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher, MAN0001271) according to the manufacturer’s protocol. RNA were fragmented by sonication and pre-cleared buy incubation with streptaidin Dynabeads T1. RNA was re-extracted using Trizol LS(Thermo Fisher, MAN0000806). Ten percent lysate was saved as input. Pre-cleared RNA was reacted with 100 µM DBCO-PEG4-Biotin in aqueous solution for 16 h at 37 °C. Following labeling, samples were treated with DNase  at 37 °C for 30 min. RNA was purified from unreacted DBCO-PEG4-Biotin with TRIzol LS. Labeled RNA was incubated with Dynabeads T1 for 30 min at room temperature with rotation. Bead–RNA complexes were washed 12 times: 6 times with 1 ml bead wash buffer II (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) pre-warmed to 65 °C, followed by 6 times at room temperature. After the final wash, RNA was eluted with TRIzol.
Pulldown and input RNA samples were depleted of rRNA using the RiboErase kit (Roche, KK8560) following the manufacturer’s protocol. The rRNA-depleted RNAs were processed for stranded cDNA library construction using the KAPA RNA HyperPrep Kit (Roche, KR1351 v4.21).

treatment_protocol: Two biological replicates of A2780 cells were treated with  30 µM concentrations of 1,3-Platin or DMF for 16 hours. For competition samples, the cells were treated with 10 µM cisplatin for 8 hours, followed by 1,3-Platin for an additional 16 hours.

tag: cell line


title: 01-217_Screen

value: Screen


title: Female, Old, 17-DMAG, rep 2

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

description:
Library name: UM60592
Female_Old_DMAG_2

data_processing:
Reads were mapped to mouse genome (GRCm39) with STAR (version 2.7.11b). Genes were counted via featureCounts (version 2.0.6).
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes gene counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted with PureLink RNA Mini Kit.
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: Mice were housed at the University of Michigan Medical School (UM), the University of Texas (UT), and The Jackson Laboratory (TJL). Animals were fed ad libitum with the Purina 5LG6 diet, produced in the same commercial diet facility (TestDiet, Richmond, IN, USA). Compounds were administered through food until the animals were sacrificed.

value: Liver

tag: strain

tag: Sex

value: Female

tag: cohort

tag: site

value: UM

tag: treatment

tag: treatment abbreviation

value: DMAG

tag: dose

value: 30 ppm

tag: age group

value: Old

tag: age

value: 22 months

tag: age at_start_of_treatment

value: 6 months

tag: replicate


title: AMLC, GAM, 4hours, rep3

description: Library name: GAM.4hr.3

tag: cell type

tag: batch


title: AMLC, OMA, 4hours, rep2

description: Library name: OMA.4hr.2


title: 1,3 Platin Input Rep 1

description: Library name: Sample 7


title: Female, Old, 17-DMAG, rep 1

description:
Library name: JL12712
Female_Old_DMAG_1

tag: tissue

value: JL


title: AMLC, OMA, 4hours, rep1

description: Library name: OMA.4hr.1


title: 1,3 Platin IP Rep 2

description: Library name: Sample 6


title: 02-216_C1D1

tag: timepoint

tag: sourceID

tag: outcome

tag: outcome type

tag: best clinical response


title: Female, Old, Control, rep 24

description:
Library name: UTC19X80
Female_Old_Control_24

tag: strain

tag: Sex

tag: cohort

value: UT

value: Control

value: 5 months


title: Female, Old, Control, rep 23

description:
Library name: UTC19X79
Female_Old_Control_23

tag: site

tag: treatment

tag: treatment abbreviation


title: AMLC, GAM, 4hours, rep2

description: Library name: GAM.4hr.2

value: AMLCs


title: 1,3 Platin  + Cisplatin Input Rep 2

description: Library name: Sample 4

tag: cell line


title: 1,3 Platin  + Cisplatin Input Rep 1

description: Library name: Sample 3


title: Female, Old, Control, rep 21

description:
Library name: UT10970
Female_Old_Control_21

tag: dose

tag: age group

tag: age

tag: age at_start_of_treatment


title: 02-216_C2D1

tag: tissue

value: primary breast cancer

value: radiographic

tag: survival


title: Female, Old, Control, rep 22

description:
Library name: UT10971
Female_Old_Control_22

tag: replicate


title: 1,3 Platin  IP Rep 1

description: Library name: Sample 5


title: 02-216_Screen

tag: timepoint

tag: sourceID

tag: outcome

value: progression

value: PD


title: Cerebral cortex, Klotho KO, 4

description:
Library name: Brain_KlothoKO
10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced raw data were then processed using Cell Ranger v7.0.0 and the R package Seurat (v5.0.1). For quality control, nuclei that were detected with a mitochondrial content > 10%, < 200 genes, or > 4,000 genes were considered dying cells, empty droplets, and doublets, respectively, and were excluded. Cells were annotated using established sets of marker genes for brain and kidney cell types.
Assembly: GRCm38
Supplementary files format and content: Tab-separated and matrix files from Cell Ranger output

molecule: nuclear RNA

source_name: Cerebral cortex (brain)

extract_protocol:
Brains and kidneys were harvested following cervical dislocation and flash frozen in liquid nitrogen. The cortical region of brain and radially section of kidney were dissected. Their nuclei were isolated with the Minute™ single nucleus isolation kit for neuronal tissue/cells and the Minute™ single nucleus isolation kit for tissue/cells (Cat# BN-020, SN-047, Invent Biotechnologies, INC), following manufacturer’s protocol with minor modifications. Specifically, the isolated nuclei were resuspended in 5% BSA solution with RNase inhibitor (Cat# 1000494; 10x genomics).
snRNA-seq was performed with Chromium Single Cell 5' Reagent Kits (Cat# PN1000265; 10x genomics) according to the manufacturer's instructions. Briefly, single-cell suspensions from the tissues were loaded into a Chromium Next GEM Chip K Single Cell Kit (Cat# PN-1000287; 10x Genomics), and a Chromium Controller was used for barcoding and cDNA synthesis. A Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v2 (Cat# PN1000265; 10x Genomics) was used to amplify the cDNA and construct the cDNA libraries. RNA sequencing was performed by DNAFORM (Yokohama, Kanagawa, Japan).

treatment_protocol: 8-week-old male WT mice (C57BL/6J) and α-klotho knockout mice were purchased from CLEA Japan. Mice were maintained under specific pathogen-free conditions, on a 12-h light–dark cycle and fed normal diet.

value: Cerebral cortex (brain)

tag: strain

value: Male

value: 8 weeks

tag: genotype

value: Klotho KO


title: AMLC, GAM, 4hours, rep1

description: Library name: GAM.4hr.1

tag: cell type

tag: batch


title: 01-215_Screen

value: Screen


title: 1,3 Platin  + Cisplatin IP Rep 2

description: Library name: Sample 2


title: 01-212_C2D1

tag: outcome type

tag: best clinical response


title: Female, Old, Control, rep 20

description:
Library name: UT09544
Female_Old_Control_20

value: Liver

tag: Sex

value: Female

tag: cohort

tag: site

tag: treatment

tag: treatment abbreviation

value: Old

value: 9 months


title: Cerebral cortex, WT, 3

description:
Library name: Brain_WT
10x Genomics

tag: tissue

tag: age

value: WT


title: 01-212_C1D1

tag: survival


title: Female, Old, Control, rep 19

description:
Library name: UT09506
Female_Old_Control_19

value: UT

value: Control

tag: dose

tag: age group

value: 22 months

tag: age at_start_of_treatment

tag: replicate


title: Female, Old, Control, rep 17

description:
Library name: UT08516
Female_Old_Control_17

tag: strain

value: 7 months


title: Female, Old, Control, rep 18

description:
Library name: UT08550
Female_Old_Control_18


title: 01-212_Screen

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic


title: Kidney, WT, 1

description:
Library name: Kidney_WT
10x Genomics

source_name: Kidney

value: Kidney

tag: genotype


title: Kidney, Klotho KO, 2

description:
Library name: Kidney_KlothoKO
10x Genomics

tag: Sex


title: 100nt_Urich_in_U20_Rep2

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: 100nt_Urich_in_U20_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

library_source: other

data_processing:
Illumina reads were processed by removing 3′ adapters with cutadapt {Martin, 2011 #646}, trimming 4 random nucleotides from each end and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4) . Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie {Langmead, 2009 #656}. Remaining unmapped reads were mapped to the OSC_r1.01 genome using bowtie allowing for 1 mismatch. Alignments were separated into uniquely and all‑mapping fractions. For visualization, HOMER was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC‑compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 1M miRNAs and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities), producing strand‑specific (sense and antisense) coverage profiles for genome browser display. For transposon histogram analysis, piRNA reads longer than 23 nucleotides were aligned to transposable element consensus sequences using bowtie (--best --strata -f -v 2 -a), permitting multiple mappings. Alignments were subsequently filtered to retain reads that mapped either uniquely or at most twice to a single transposon consensus, to account for long terminal repeat (LTR) redundancy. Reads mapping twice were assigned a fractional count of 0.5 to each location.
Assembly: OSC_r1.01
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense

molecule: other

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: Ovarian somatic cells (OSCs) were maintained at 27 °C in a humidified incubator with 2.5% CO₂, as previously described (Niki, Yamaguchi et al. 2006, Saito, Inagaki et al. 2009) Cells were cultured in M3 basal medium supplemented with 10% fetal bovine serum (FBS), insulin, glutathione, and fly extract.

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias and facilitate library multiplexing, adaptors were designed with random nucleotides placed adjacent to the ligating end. The 3′ adaptor carried six random bases at its 5′ terminus and contained sample barcodes (X) for multiplexing (5rApp/NNNNNNXXXX–Adaptor–/3ddC). The 5′ adaptor was an RNA oligo bearing four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adaptor ligation with T4 RNA ligase 2, truncated KQ, samples were pooled as necessary, spiked with fluorescently labeled and ligation-blocked oligos as size controls, and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adaptor ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, multiplexed and sequenced (SE50, Illumina NovaSeq6000).

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: 1,3 Platin  + Cisplatin IP Rep 1

description: Library name: Sample 1


title: 100nt_Urich_in_U20_Rep1

description:
Library name: 100nt_Urich_in_U20_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Female, Old, Control, rep 16

description:
Library name: UM78974
Female_Old_Control_16

tag: cohort

tag: site

value: UM

tag: treatment

value: 5 months


title: U-poorgypsy27_Rep1

description:
Library name: U-poorgypsy27_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: U-richgypsy27_Rep2

description:
Library name: U-richgypsy27_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 01-214_Screen

tag: tissue

value: Screen

tag: outcome type

value: toxicity

tag: best clinical response

value: PR


title: Female, Old, Control, rep 14

description:
Library name: UM70364
Female_Old_Control_14

value: Liver

value: Female

tag: treatment abbreviation

tag: dose

tag: age group

value: Old

tag: age

value: 9 months


title: S10 PLX+PTX+aPD-1.NR

type: RNA

hyb_protocol: Samples were then hybridized with NanoString immune profiling probes for 17 hours at 65°C

scan_protocol: Samples were loaded into an nCounter SPRINT cartridge

data_processing: Quality control of NanoString® data was performed with nSolver Analysis Software v4.0.70 (NanoString®), prior to further processing and normalization in R. Housekeeping gene stability and correlation were assessed using the geNorm and PairwiseV functions from the ctlGene package. Out of 20 genes included in the NanoString® ImmuneOncology 360 panel, 10 genes were deemed fit for data normalization of the raw data: Sdha, Tbc1d10b, G6pdx, Dnajc14, Sf3a1, Abcf1, Ercc3, Pum1, Polr2a, Nrde2. All selected genes had expression above NanoString® Limit of Detection (LOD). Data was normalized using the method established by Bhattacharya et al. First, distributional differences between sample lanes were scaled using upper-quartile normalization (69), before unwanted technical variance was estimated with RUVg from the RUVseq package (70), using only the subset of housekeeping genes selected with geNorm and PairwiseV. Two dimensions of unwanted variance was identified by RUVg. Raw counts were transformed using the varianceStabilizing transformation (VST) function from the DEseq2 package, and factors of unwanted variance estimated by RUVg were removed with removeBatchEffect from the Limma package.

label: not provided

source_name: mammary gland

label_protocol: cDNA was synthesized using SuperScript VILO according to the manufacturer’s instructions (Thermo Fisher) and 50 ng were used for multiplex target enrichment according to the manufacturer’s instructions (NanoString)

extract_protocol: 10-20 mg of snap frozen tumors were crushed on liquid nitrogen and RNA extracted using the RNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions.

value: mammary gland

value: MMTV-PyMT


title: 01-214_C2D1

value: primary breast cancer

tag: timepoint

tag: survival


title: Female, Old, Control, rep 13

description:
Library name: UM70231
Female_Old_Control_13

tag: strain

value: Control

value: 22 months

tag: age at_start_of_treatment

tag: replicate


title: Female, Old, Control, rep 15

description:
Library name: UM78967
Female_Old_Control_15

tag: Sex


title: S11 PLX+PTX+aPD-L1

tag: genotype


title: 01-214_C1D1

tag: sourceID

tag: outcome


title: S9 PLX+PTX+aPD-1.NR

tag: treatment


title: 02-213_C4D1

tag: tissue

value: radiographic

value: progression


title: U-poorgypsy27_Rep2

description:
Library name: U-poorgypsy27_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: 02-213_C2D1

tag: outcome type

tag: best clinical response


title: U45_siYB_Rep2

description:
Library name: U45_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: S12 PLX+PTX+aPD-L1


title: Female, Old, Control, rep 12

description:
Library name: UM70224
Female_Old_Control_12

tag: cohort

tag: site

value: UM

tag: treatment abbreviation

tag: dose

tag: age group

value: 7 months


title: S8 PLX+PTX+aPD-1.NR


title: U-richgypsy27_Rep1

description:
Library name: U-richgypsy27_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: S7 PLX+PTX+aPD-1.R


title: U40_siYB_Rep2

description:
Library name: U40_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 02-213_C1D1

tag: timepoint

value: PR

tag: survival


title: Female, Old, Control, rep 11

description:
Library name: UM70217
Female_Old_Control_11

value: Liver

tag: strain

tag: Sex

value: Female

tag: age

tag: age at_start_of_treatment

tag: replicate


title: S6 PLX+PTX+aPD-1.R

tag: tissue

tag: genotype

tag: treatment


title: Female, Old, Control, rep 10

description:
Library name: UM69468
Female_Old_Control_10

value: Old

value: 6 months


title: 01-214_C4D1

tag: sourceID

tag: outcome

tag: outcome type

value: toxicity


title: U40_siYB_Rep1

description:
Library name: U40_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

tag: cell type


title: 02-213_Screen

value: primary breast cancer

value: Screen

tag: best clinical response


title: S5 PLX+PTX+aPD-1.R

value: mammary gland

value: MMTV-PyMT


title: U40_siLuc_Rep2

description:
Library name: U40_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 01-218_C2D1

value: clinical

value: progression

value: PD


title: U45_siLuc_Rep2

description:
Library name: U45_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

value: ovarian somatic cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: S4 PLX+PTX

value: PLX+PTX


title: U40_siLuc_Rep1

description:
Library name: U40_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: 01-210_C4D1

value: radiographic

value: PR


title: Female, Old, Control, rep 7

description:
Library name: UM59262
Female_Old_Control_7

value: Liver

value: Female

tag: cohort

tag: site

value: UM

value: Control

tag: treatment abbreviation

tag: dose

tag: age group

value: Old

value: 22 months

value: 7 months


title: S3 PLX+PTX

value: mammary gland

value: MMTV-PyMT


title: Female, Old, Control, rep 6

description:
Library name: JL16317
Female_Old_Control_6

tag: strain

tag: Sex

value: JL

tag: age

value: 5 months


title: Female, Old, Control, rep 9

description:
Library name: UM68530
Female_Old_Control_9

tag: tissue

tag: age at_start_of_treatment

value: 6 months

tag: replicate


title: U35_siYB_Rep2

description:
Library name: U35_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

value: ovarian somatic cells

tag: genotype

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R

tag: treatment


title: 01-218_C1D1

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: clinical

tag: outcome type

value: progression

value: PD

tag: survival


title: Female, Old, Control, rep 8

description:
Library name: UM59283
Female_Old_Control_8

value: Liver

value: Female

tag: cohort

tag: site

value: UM


title: U35_siYB_Rep1

description:
Library name: U35_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

tag: cell type

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: 01-210_C1D1

value: radiographic

tag: best clinical response

value: PR


title: S1 PTX

value: mammary gland

value: MMTV-PyMT

value: PTX


title: 01-210_C2D1


title: S2 PTX


title: P16hiF480hi, replicate3

city: Shanghai

first: Jialei

last: Zheng

state: 上海

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

description: Library name: Sample12

data_processing:
Reads were mapped to the mouse genome assembly GRCm38 using HISAT.
Assembly: Mouse mm10
Supplementary files format and content: file includes norm read, tpm, fpkm, and raw counts for each Sample

source_name: heart

extract_protocol:
In p16-CreER;R26-mTmG mice subjected to MI surgery, cardiac P16-positive cells were lineage-traced by administering tamoxifen via oral gavage on day 5 post-MI. At day 7, the infarcted region of the heart was dissected, enzymatically digested and lysed, followed by the removal of cardiomyocytes. Cells were then sorted by flow cytometry using F4/80 and PDGFRα antibodies to isolate distinct populations: GFPhiF4/80hi, GFPloF4/80hi, GFPhiPDGFRαhi and GFPloPDGFRαhi cells.
Library preparation commenced with RNA quality control and reverse transcription into cDNA templates. Utilizing a transposase-mediated fragmentation and ligation strategy, cDNA molecules were prepared for sequencing. These molecules were then circularized to form single-stranded circular DNA. Subsequently, rolling circle amplification (RCA) was employed to generate DNA nanoballs (DNBs), each containing multiple copies of the template sequence. These DNBs were precisely loaded onto a proprietary patterned nanoarray chip using high-density nanoarray technology. Finally, sequencing-by-synthesis was performed employing combinatorial probe anchor ligation chemistry for high-throughput base detection and sequence determination.

value: heart

value: MI, tamoxifen i.g. on day5 post-MI


title: Female, Old, Control, rep 5

description:
Library name: JL16314
Female_Old_Control_5

tag: strain

tag: Sex

value: JL

value: Control

tag: treatment abbreviation

tag: dose

tag: age group

value: Old

value: 22 months

value: 5 months


title: Female, Old, Control, rep 4

description:
Library name: JL13949
Female_Old_Control_4

tag: tissue

tag: age

tag: age at_start_of_treatment

value: 9 months

tag: replicate


title: U35_siLuc_Rep2

description:
Library name: U35_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

value: ovarian somatic cells

tag: genotype

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R

tag: treatment


title: 01-210_Screen

value: primary breast cancer

tag: timepoint

value: Screen

tag: sourceID

tag: outcome

tag: outcome type

value: progression

tag: survival


title: P16hiF480hi, replicate1

description: Library name: Sample10


title: P16hiF480hi, replicate2

description: Library name: Sample11


title: 01-209_C4D1

value: radiographic

tag: best clinical response

value: SD


title: P16loF480hi, replicate3

description: Library name: Sample9


title: U27.5_siYB_Rep2

description:
Library name: U27.5_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

tag: cell type

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: U35_siLuc_Rep1

description:
Library name: U35_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Female, Old, Control, rep 3

description:
Library name: JL13948
Female_Old_Control_3

value: Liver

tag: strain

tag: Sex

value: Female

tag: cohort

tag: site

tag: treatment abbreviation


title: P16loF480hi, replicate2

description: Library name: Sample8

tag: tissue

value: heart

value: MI, tamoxifen i.g. on day5 post-MI


title: 01-209_C2D1


title: Female, Old, Control, rep 2

description:
Library name: JL12705
Female_Old_Control_2

value: JL

value: Control

tag: dose

tag: age group

value: Old

tag: age

tag: age at_start_of_treatment

value: 7 months

tag: replicate


title: U27.5_siYB_Rep1

description:
Library name: U27.5_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

tag: genotype

tag: treatment


title: 01-209_C1D1

tag: timepoint

tag: sourceID

tag: outcome

tag: outcome type

tag: survival


title: P16loF480hi, replicate1

description: Library name: Sample7


title: Female, Old, Control, rep 1

description:
Library name: JL12702
Female_Old_Control_1

tag: strain

tag: Sex

value: 22 months


title: Female, Old, Candesartan Cilexetil, rep 3

description:
Library name: UM69006
Female_Old_CC_3

tag: cohort

tag: site

value: UM

value: Candesartan Cilexetil

value: CC

value: 30 ppm

value: 8 months


title: U27.5_siLuc_Rep1

description:
Library name: U27.5_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

tag: cell type

value: ovarian somatic cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: 01-209_Screen

tag: tissue

value: primary breast cancer

value: Screen

value: radiographic

value: progression

tag: best clinical response

value: SD


title: P16hiPDGFRahi, replicate3

description: Library name: Sample6

value: heart

value: MI, tamoxifen i.g. on day5 post-MI


title: Female, Old, Candesartan Cilexetil, rep 2

description:
Library name: JL14039
Female_Old_CC_2

value: Liver

value: Female

value: JL

tag: treatment abbreviation

tag: dose

tag: age group

value: Old

tag: age

tag: age at_start_of_treatment


title: si-Yb-RepB

description:
Library name: si-Yb-RepB
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias, adapters were designed with four random nucleotides (4N) adjacent to the ligating ends. The 3′ adapter carried four random bases at its 5′ terminus (5rApp/NNNN–Adaptor–/3ddC), and the 5′ RNA adapter contained four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adapter ligation with T4 RNA ligase 2, truncated KQ, samples were spiked with fluorescently labeled and ligation-blocked oligos as size controls and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adapter ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers to enable multiplexing at the sequencing stage. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, and sequenced (SE50, Illumina NextSeq 2000).

value: OSC

tag: genotype

value: wildtype

tag: treatment

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: 02-208_C2D1

tag: timepoint

tag: sourceID

tag: outcome

value: rash

tag: outcome type

value: toxicity


title: U27.5_siLuc_Rep2

description:
Library name: U27.5_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: ovarian somatic cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: P16hiPDGFRahi, replicate2

description: Library name: Sample5


title: Female, Old, Captopril, rep 3

description:
Library name: UT10994
Female_Old_Capt_3

tag: strain

tag: Sex

tag: cohort

value: UT

value: Captopril

value: Capt

value: 180 ppm

value: 23 months

value: 5 months

tag: replicate


title: Female, Old, Captopril, rep 2

description:
Library name: UM79415
Female_Old_Capt_2

tag: tissue

value: Liver

tag: site

value: UM


title: Female, Old, Candesartan Cilexetil, rep 1

description:
Library name: UT09567
Female_Old_CC_1

value: Female

value: Candesartan Cilexetil

tag: treatment abbreviation

value: CC

value: 30 ppm

value: 22 months

value: 8 months


title: P16hiPDGFRahi, replicate1

description: Library name: Sample4

value: heart

value: MI, tamoxifen i.g. on day5 post-MI


title: si-Luc-RepC

description:
Library name: si-Luc-RepC
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: 02-208_C1D1

value: primary breast cancer

value: rash

value: toxicity

tag: best clinical response

value: SD

tag: survival


title: si-Luc-RepB

description:
Library name: si-Luc-RepB
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: genotype


title: P16loPDGFRahi, replicate3

description: Library name: Sample3

tag: treatment


title: si-Yb-RepA

description:
Library name: si-Yb-RepA
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Female, Old, Captopril, rep 1

description:
Library name: JL16257
Female_Old_Capt_1

value: Liver

value: JL

value: Captopril

value: Capt

tag: dose

value: 180 ppm

tag: age group

value: Old

tag: age

tag: age at_start_of_treatment

value: 5 months


title: P16loPDGFRahi, replicate2

description: Library name: Sample2

value: heart


title: 02-208_Screen

tag: timepoint

value: Screen

tag: sourceID

tag: outcome

tag: outcome type


title: Female, Old, Canagliflozin, rep 7

description:
Library name: UT09523
Female_Old_Cana_7

tag: tissue

tag: strain

tag: Sex

value: Female

tag: cohort

value: UT

value: Canagliflozin

value: Cana

value: 22 months

value: 7 months

tag: replicate


title: si-Luc-RepA

description:
Library name: si-Luc-RepA
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: 01-207_C2D1

value: primary breast cancer

value: radiographic

value: progression

tag: best clinical response

value: SD

tag: survival


title: TT-INPUT_10min_Rep1

description: Library name: TT-INPUT_10min_Rep1

data_processing:
Illumina reads were processed by removing 3′ adapters with(Martin 2011), trimming the first five nucleotides, and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4)(Bushnell 2014). Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie(Langmead, Trapnell et al. 2009). Remaining unmapped reads were mapped to the OSC_r1.01 genome using STAR in two pass mode with splice junction support (--alignEndsType Local, --outFilterType BySJout, --alignSJoverhangMin 15, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 1, --outFilterMultimapNmax 1000, --winAnchorMultimapNmax 2000)(Dobin, Davis et al. 2013). Alignments were separated into uniquely and all mapping fractions. For visualization, HOMER(Heinz, Benner et al. 2010) was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 10M uniquely aligned reads and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities)(Perez, Barber et al. 2025), producing strand specific (sense and antisense) coverage profiles for genome browser display. For RNA-seq quantification, reads were quantified against the reference transcriptome enriched for transposon consensus sequences using Salmon (v1.7.0). For gene expression visualization Salmon results were further processed to GeTMM values using edgeR and differential gene expression analysis was performed using DeSeq2.
Assembly: OSC_r1.01
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: DGE analysis for siRNA mediated knockdowns in OSC cells

extract_protocol:
Total RNA was extracted using Trizol with chloroform partitioning, precipitated with isopropanol in the presence of DTT and glycogen, and resuspended in nuclease-free water. RNA quality was assessed by Fragment Analyzer, and aliquots were reserved for input (1 µg).
Following TurboDNase treatment and column purification to remove residual DNA, Input RNA underwent rRNA depletion using Drosophila-specific oligos and RNase H, as previously described (ElMaghraby et al., 2019). For pulldown samples, the depletion was performed using 1/10th of the oligos and 1/5th of the enzyme concentration used for input samples. The depletion was followed by a final TurboDNase treatment and column-based cleanup. Strand-specific Illumina sequencing libraries were prepared from rRNA-depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit. Input samples were fragmented for 15 min during library preparation, whereas pulldown samples were fragmented for 8 min to account for prior fragmentation and maintain optimal insert sizes (200–600 nt). Libraries were amplified and sequenced on an Illumina platform.

tag: genotype

tag: treatment

value: labelling with 4mM 4-thiouridine for 10 minutes right before harvesting


title: TT-INPUT_10min_Rep2

description: Library name: TT-INPUT_10min_Rep2


title: Female, Old, Canagliflozin, rep 5

description:
Library name: UM69594
Female_Old_Cana_5

value: Liver

tag: site

value: UM

tag: treatment abbreviation

tag: dose

value: 180 ppm

tag: age group

value: Old

tag: age


title: 01-207_C1D1

tag: timepoint

tag: sourceID

tag: outcome

tag: outcome type


title: Phf2 KO soleus muscle 2

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

institute: Aichi Medical University

description:
Library name: So_KO2
TPMs(Sol).xlsx

data_processing:
MGI DNB seq (strand-specific).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers.
Second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
Assembly: mm10
Supplementary files format and content: TPM values for each Sample

source_name: skeletal muscle

growth_protocol: Mice were housed under a 12-hour light/dark cycle at 23 °C with free access to food (MF feed, Oriental Yeast) and water.

extract_protocol:
RNA was isolated using RNAiso and the NucleoSpin RNA Kit (740955.50, TaKaRa).
NEBNext® Ultra™II Directional RNA Library Prep Kit

treatment_protocol: Gastrocnemius and soleus muscles were collected from 4-week-old male mice and flash frozen in liquid nitrogen in triplicate.

tag: tissue

value: skeletal muscle

tag: strain background

tag: tissue type

value: soleus muscle

value: KO

value: Phf2 flox/flox;Acta1 Cre+

value: 4 week old


title: P16loPDGFRahi, replicate1

description: Library name: Sample1

value: heart

value: MI, tamoxifen i.g. on day5 post-MI


title: 01-207_Screen

value: Screen


title: Phf2 KO soleus muscle 3

description:
Library name: So_KO3
TPMs(Sol).xlsx


title: Female, Old, Canagliflozin, rep 6

description:
Library name: UM70525
Female_Old_Cana_6

tag: strain

tag: Sex

value: Female

tag: cohort

value: Canagliflozin

value: Cana

value: 22 months

tag: age at_start_of_treatment

value: 7 months

tag: replicate


title: 01-207_C4D1

value: primary breast cancer

value: radiographic

value: progression

tag: best clinical response

value: SD

tag: survival


title: Phf2 Ctrl soleus muscle 3

description:
Library name: So_Ct3
TPMs(Sol).xlsx

value: skeletal muscle

tag: genotype

value: Ctrl

value: Phf2 flox/flox;Acta1 Cre-


title: TT-SLAMseq_10min_Rep1

description: Library name: TT-SLAMseq_10min_Rep1

extract_protocol:
Total RNA was extracted using Trizol with chloroform partitioning, precipitated with isopropanol in the presence of DTT and glycogen, and resuspended in nuclease-free water. RNA quality was assessed by Fragment Analyzer, and aliquots were reserved for input (1 µg) and pulldown (50 µg) fractions. For pulldown samples, total RNA was fragmented to 200–600 nt by heating at 94 °C for 60 s in fragmentation buffer, followed by precipitation with sodium acetate and ethanol. 4sU-labeled transcripts were selectively biotinylated using MTSEA-biotin-XX (MTS-biotin) in a freshly prepared 10× biotinylation buffer (20 mM HEPES pH 7.8, 1 mM EDTA) for 2 h at 25 °C with rotation, protected from light. Unreacted biotin was removed by acid phenol–chloroform extraction, and biotinylated RNA was recovered by ethanol precipitation. Biotinylated transcripts were enriched using µMACS streptavidin magnetic beads (Duffy et al., 2015). Denatured RNA (65°C, 10 min, snap cool on ice) was incubated with streptavidin beads for 15 min at room temperature, loaded onto pre-equilibrated µMACS columns, washed three times with high-salt buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20), and eluted twice with 100 mM DTT. Eluted RNA was purified using RNeasy MinElute columns and concentrated to 15 µL.
To introduce 4sU-dependent mismatch signatures for SLAM-seq identification, both input and pulldown fractions were subjected to iodoacetamide (IAA) alkylation. RNA was incubated with 10 mM IAA in 50 mM sodium phosphate buffer (pH 8.0) and 50% DMSO at 50 °C for 15 min; the reaction was then immediately quenched with DTT and the RNA was ethanol precipitated. Following TurboDNase treatment and column purification to remove residual DNA, both fractions underwent rRNA depletion using Drosophila-specific oligos and RNase H, as previously described (ElMaghraby et al., 2019). For pulldown samples, the depletion was performed using 1/10th of the oligos and 1/5th of the enzyme concentration used for input samples. The depletion was followed by a final TurboDNase treatment and column-based cleanup. Strand-specific Illumina sequencing libraries were prepared from rRNA-depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit. Input samples were fragmented for 15 min during library preparation, whereas pulldown samples were fragmented for 8 min to account for prior fragmentation and maintain optimal insert sizes (200–600 nt). Libraries were amplified and sequenced on an Illumina platform.

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: wildtype

tag: treatment

value: labelling with 4mM 4-thiouridine for 10 minutes right before harvesting


title: 01-206_C2D1

tag: timepoint

tag: sourceID

value: PD


title: 01-206_C1D1

tag: outcome

tag: outcome type


title: Phf2 Ctrl soleus muscle 2

description:
Library name: So_Ct2
TPMs(Sol).xlsx

tag: tissue

tag: strain background

value: soleus muscle

tag: age

value: 4 week old


title: TT-SLAMseq_10min_Rep2

description: Library name: TT-SLAMseq_10min_Rep2


title: 01-205_C1D1

value: toxicity


title: Phf2 Ctrl soleus muscle 1

description:
Library name: So_Ct1
TPMs(Sol).xlsx

tag: tissue type


title: Phf2 KO soleus muscle 1

description:
Library name: So_KO1
TPMs(Sol).xlsx

value: KO

value: Phf2 flox/flox;Acta1 Cre+


title: 01-206_Screen

value: primary breast cancer

value: Screen


title: Female, Old, Canagliflozin, rep 3

description:
Library name: UM68726
Female_Old_Cana_3

value: Liver

tag: strain

tag: Sex

value: Female

tag: cohort

tag: site

value: UM

value: Canagliflozin

tag: treatment abbreviation

value: Cana

tag: dose

value: 180 ppm

tag: age group

value: Old

value: 22 months

value: 7 months


title: siARMI_RZ_Rep2

description: Library name: siARMI_RZ_Rep2

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was treated with DNase I (ThermoFisher Scientific) and purified using RCC25 kit (Zymo Research) with on-column Zymo DNaseI according to the manufacturer’s instructions.
Eluted RNA was poly(A)-selected twice using magnetic Dynabeads Oligo (dT)25 (ThermoFisher Scientific). Libraries were  generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions, with the exception of the final amplification. Libraries were PCR amplified with KAPA HiFi polymerase and barcoded Illumina primers, with amplification monitored in real time using EvaGreen fluorescence. Reactions were stopped once predetermined RFU thresholds were reached to avoid over amplification. Libraries were then purified, quantified by Qubit, assessed for fragment size, and multiplexed for Illumina sequencing.

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

tag: genotype

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: Female, Old, Canagliflozin, rep 2

description:
Library name: UM68719
Female_Old_Cana_2

tag: treatment

tag: age at_start_of_treatment

tag: replicate


title: Female, Old, Canagliflozin, rep 4

description:
Library name: UM68831
Female_Old_Cana_4

tag: tissue


title: siARMI_RZ_Rep3

description: Library name: siARMI_RZ_Rep3


title: Female, Old, Canagliflozin, rep 1

description:
Library name: JL13987
Female_Old_Cana_1

value: JL


title: 03-204_Screen

tag: timepoint

tag: sourceID


title: siARMI_RZ_Rep1

description: Library name: siARMI_RZ_Rep1


title: Phf2 KO gastroceiumus muscle 3

description:
Library name: Ga_KO3
TPMs(GA).xlsx

value: skeletal muscle

tag: strain background

tag: tissue type

value: gastroceiumus muscle

value: KO

value: Phf2 flox/flox;Acta1 Cre+

tag: age

value: 4 week old


title: Female, Old, bGPA, rep 2

description:
Library name: UM58800
Female_Old_bGPA_2

value: Liver

tag: strain

tag: Sex

value: Female

tag: cohort

value: UM

value: bGPA

value: 6 months


title: Female, Old, bGPA, rep 1

description:
Library name: JL12786
Female_Old_bGPA_1

tag: site

tag: treatment abbreviation

tag: dose

value: Old

value: 22 months


title: Phf2 KO gastroceiumus muscle 1

description:
Library name: Ga_KO1
TPMs(GA).xlsx


title: 01-205_Screen

value: primary breast cancer

value: Screen

tag: outcome

tag: outcome type

value: toxicity

tag: best clinical response

value: PD

tag: survival


title: Phf2 KO gastroceiumus muscle 2

description:
Library name: Ga_KO2
TPMs(GA).xlsx

tag: genotype


title: Female, Old, bGPA, rep 3

description:
Library name: UT08499
Female_Old_bGPA_3

tag: tissue

value: UT

tag: treatment

tag: age group

tag: age at_start_of_treatment

tag: replicate


title: 03-204_C1D1

tag: timepoint

tag: sourceID


title: Phf2 Ctrl gastroceiumus muscle 3

description:
Library name: Ga_Ct3
TPMs(GA).xlsx

value: skeletal muscle

tag: strain background

tag: tissue type

value: Ctrl

value: Phf2 flox/flox;Acta1 Cre-

tag: age


title: siYB_RZ_Rep3

description: Library name: siYB_RZ_Rep3

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: siYB_RZ_Rep2

description: Library name: siYB_RZ_Rep2


title: 02-202_C1D1

tag: outcome

value: radiographic

value: progression


title: Female, Old, 1,3-butanediol, rep 3

description:
Library name: UT10906
Female_Old_BD_3

value: Liver

tag: strain

tag: Sex

value: Female

tag: cohort

tag: site

tag: treatment abbreviation

value: BD

tag: dose

value: 6 months


title: Phf2 Ctrl gastroceiumus muscle 2

description:
Library name: Ga_Ct2
TPMs(GA).xlsx

tag: tissue

value: gastroceiumus muscle

tag: genotype

value: 4 week old


title: 02-203_Screen

value: primary breast cancer

value: Screen

tag: outcome type

tag: best clinical response

value: SD

tag: survival


title: Female, Old, 1,3-butanediol, rep 1

description:
Library name: JL16221
Female_Old_BD_1

value: JL

tag: treatment

tag: age group

value: Old

value: 22 months

tag: age at_start_of_treatment

tag: replicate


title: Female, Old, 1,3-butanediol, rep 2

description:
Library name: UM78757
Female_Old_BD_2

value: UM

tag: age


title: siLUC_RZ_Rep3

description: Library name: siLUC_RZ_Rep3

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cells

value: wildtype


title: Phf2 Ctrl gastroceiumus muscle 1

description:
Library name: Ga_Ct1
TPMs(GA).xlsx

value: skeletal muscle

tag: strain background

tag: tissue type

value: Ctrl

value: Phf2 flox/flox;Acta1 Cre-


title: siLUC_RZ_Rep2

description: Library name: siLUC_RZ_Rep2

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: siYB_RZ_Rep1

description: Library name: siYB_RZ_Rep1


title: 02-203_C1D1

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic

value: progression


title: Skeletal muscle, Klotho KO, rep 6

description:
Library name: RNA_122M
SkMuscle_KlothoKO_6

source_name: Skeletal muscle

extract_protocol:
RNA was extracted with PureLink RNA Mini Kit.
mRNA library preparation with polyA enrichment was performed by Novogene.

tag: tissue

value: Skeletal muscle

tag: strain

tag: Sex

value: Male

value: 8 weeks

value: Klotho KO


title: 02-202_Screen

value: primary breast cancer

value: Screen

tag: outcome type

tag: best clinical response

value: PD


title: Skeletal muscle, Klotho KO, rep 5

description:
Library name: RNA_120M
SkMuscle_KlothoKO_5

tag: genotype


title: siLUC_RZ_Rep1

description: Library name: siLUC_RZ_Rep1

tag: treatment


title: S. aureus in SSF2 rep4

city: Gent

first: Amber

last: De Bleeckere

address: Ottergemsesteenweg 460

department: Laboratory of Pharmaceutical Microbiology

country: Belgium

institute: Ghent University

description: Library name: SAU060112_SSF2_4

data_processing:
Using CLC Biosystems Genomic Workbench v.25.0.2 (CLC Bio, Qiagen), quality trimming was performed, and the quality filtered reads of each sample were mapped (length fraction 0.80 and similarity fraction 0.95) against the genome sequence of S. aureus SAU060112.
Assembly: SAU060112
Supplementary files format and content: The file Additional file 1.xlsx contains identified genes that were differentially expressed and include locus tag, gene symbol, chromosome, region, protein, max group mean, log2 fold change, fold change and statistics

organism: Staphylococcus aureus

source_name: Synovial fluid

extract_protocol:
RNA was extracted using the RNeasy Protect Mini Kit (Qiagen), additional enzymatic lysis of cell walls was done using lysostaphin (Sigma-Aldrich). Genomic DNA was removed using Rnase-free DNase I (Qiagen). Total RNA was depleted for rRNA using the PAN-Bacteria riboPOOL depletion kit (siTOOLs)
cDNA

tag: clinical isolate


title: wor-GAL4>UAS-mCD8-GFP+ cells isolated by FACS, at 24 hours after larval hatching, 2nd replicate

city: New York

first: Jocelyn L.Y.

last: Tang

address: 540 1st Avenue

country: United Kingdom

institute: NYU School of Medicine

description: Library name: Larval_24ALH_biolrep2

data_processing:
Reads were processed using Cell Ranger v3
Assembly: dm6
Supplementary files format and content: Each single cell sample contains a barcodes.tsv, features.tsv and matrix.mtx file generated from Cell Ranger

molecule: cytoplasmic RNA

source_name: Brain

extract_protocol:
Brains from stage 17 embryos were dissociated and 24ALH larval brains were dissected and dissociated. These samples were kept separate and NSCs were enriched for by sorting for GFP+ cells via flow cytometry (using wor-GAL4>UAS-mCD8-GFP).
Cells isolated by FACS were processed using the 10X Genomics Chromium Platform, using v3 chemistry (3' end gene expression), with the exception of Embryo_St17_biolrep1, which used v2 chemistry.

value: Brain

value: NSCs, neurons, glia


title: 01-201_C1D1

value: rash

value: toxicity

value: SD

tag: survival


title: 01-201_Screen


title: Skeletal muscle, Klotho KO, rep 4

description:
Library name: RNA_119M
SkMuscle_KlothoKO_4

tag: age

tag: replicate


title: S. aureus in SSF2 rep2

description: Library name: SAU060112_SSF2_2


title: Syn, Mfd_KO, rep 2

city: Cambridge

first: Jennifer

last: Cascino

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

description:
Library name: 1829
biological replicate (cells harvested from unique flask)

data_processing:
To convert FASTQ files to WIGs, 3′ linker sequences were stripped, and Bowtie version 1.0.0 (-m 1) was used for sequence alignment of uniquely mapping reads to CP000100.1. The 5′ and 3′ (end-specific) mapped reads were added separately and strand-specifically at genomic positions. WIG files for the WT technical replicates were combined and processed together in the remaining data processing steps.
Peak calling: Next, peaks were called on all WIG files in the 5′ and 3′ channels. For each genomic position, two modified z-scores were computed by comparing the read count at that position to a surrounding 50-nt upstream and downstream window, excluding a 5-nt gap on either side to avoid artifactual effects from contiguous peaks (i.e., peak widths > 1 nt). We refer to these as the upstream z-score and downstream z-score. Prior to z-score calculation, read values within the window were winsorized to mitigate the effect of extreme values by replacing outlier values (> 1.5 standard deviations away from the mean) with the mean of non-outliers. The mean (avg) and standard deviation (stdev) for the winsorized window were calculated, and the modified z-score (z) was computed as z=(reads-avg)/stdev, where reads refers to the read counts at the genomic position being assessed. Z-scores were only reported for positions with sufficient position-specific read counts and read density in the surrounding window (read threshold ≥ 10 reads, density threshold ≥ 0.25 reads/nt) to avoid false-positives due to counting noise. For these positions, the final z-score was defined as the minimum of the upstream and downstream z-scores. If one of the two could not be computed (e.g., insufficient read density in one of the windows), the available z-score was retained. Peaks were then called by thresholding on the z-scores. The inverse cumulative distribution of z-scores was computed, and a threshold was set where the distribution shows a transition between two populations (peaks vs. non-peaks). A z-score threshold of ≥ 12 was used to call peaks on both the original and shadow-removed WIGs for all datasets.
Collapsing peaks: In Rend-seq data, multiple closely spaced peaks may initially be called in the same channel, such that the peak width for a given genomic region is > 1 nt. Peaks within ±5 nt were collapsed to the one with the highest z-score to facilitate definition of transcription unit (TU) end positions. The next step (shadow removal) also requires collapsed peaks as input.
Shadow removal: Performed as previously reported (Lalanne et al., Cell 2018). Briefly, this process involves removing regions of elevated read density adjacent to peaks (peak “shadows”) that arise as an artifact of Rend-seq end-enrichment.
Peaks were re-called on the shadow-removed WIGs and collapsed again. These final shadow-removed WIG and peak sets were used for TU end calling. The following approximate number of reads (in millions, M) were obtained for the datasets after processing: 13.5 M (WT), 10.2 M (Mfd_KO rep 1), and 10.7 M (Mfd_KO rep 1).
Assembly: CP000100.1
Supplementary files format and content: WIG files include reads mapped per genomic position in the 5' and 3' channels for each sample after shadow removal.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: bacterial

growth_protocol: WT and Mfd_KO cells were cultured in BG-11 media, and Mfd_KO cultures were supplemented with 5 µg/mL kanamycin. Cells were grown at 30C with shaking (120 rpm) under a 12 hour:12 hour (12:12) light:dark diel cycle (140-160 µE light intensity). For Rend-seq, 25 mL cultures were inoculated from axenic WT and Mfd_KO glycerol stocks in 125 mL Erlenmeyer flasks. When cultures reached ~mid-exponential phase (OD730 = 0.26-0.35), they were back-diluted in a total volume of 250 mL in 2.8 L Erlenmeyer flasks such that 4 doublings were required to reach an OD730 = 0.05, the beginning of exponential phase in our growth conditions (target OD730 in back-dilution = 0.003125). One flask of WT and two biological replicate flasks of Mfd_KO were prepared. When cultures had grown up again to exponential phase, cells were collected for RNA extraction.

extract_protocol:
Cells were harvested in mid-exponential phase at hour 7 in the 12:12 light:dark diel cycle by pelleting 3 x 35-40 mL of cells at OD730 = 0.14-0.22 for 10 minutes (min) at 4,000 rpm at 4C. After pelleting, supernatants were dumped, and the three pellets per sample were flash frozen in liquid nitrogen and stored at -80C until RNA extraction. To extract RNA, cell pellets were thawed on ice in 1 mL phenol stop media (6.5:1 BG-11:phenol stop solution; phenol stop solution is composed of 30:18:1:1 100% ethanol:H2O:phenol:0.5 M EDTA). One pellet from each Mfd_KO biological replicate and two WT pellets (technical replicates) were processed, for a total of 4 samples. Thawed pellets were vortexed briefly and centrifuged at 4,000 rpm for 5 min at 4C, then resuspended in TE buffer. Cells were enzymatically lysed using NEBExpress® T4 lysozyme. Following enzymatic lysis, 2 mL of Buffer RLT (Qiagen) with beta-mercaptoethanol (β-ME) were added and samples were vortexed, followed by addition of 2 mL of 70% ethanol. Samples were vortexed, and the resulting ~4.5 mL lysates were loaded onto RNeasy Midi columns (Qiagen), and RNA was column purified per the manufacturer’s instructions. Eluate was further purified by 2x SPRI bead cleanup. To protect RNA, 1 µL of SuperaseIn RNase Inhibitor (Thermo) was added. Samples were then treated with Turbo DNase (Invitrogen) per the manufacturer’s protocol to remove contaminating genomic DNA. DNase was heat-inactivated per manufacturer guidelines, and the reactions were purified by 2x SPRI bead cleanup. 19-20 µg total RNA per sample were used to prepare Rend-seq libraries.
Library strategy: Rend-seq. rRNA was depleted from 19-20 µg total RNA with MICROBexpress (Invitrogen) following the manufacturer’s instructions. Reactions were precipitated in isopropanol. RNA was then fragmented using RNA Fragmentation reagents (Thermo) by first incubating RNA in 10 mM Tris pH 7 at 95C for 2 min, then adding 10x Fragmentation Buffer and incubating at 95C for 25 seconds. The reaction was quenched with Stop Buffer. Samples were precipitated in isopropanol and resuspended in 10 mM Tris pH 7. To size-select RNA, samples were run on a 15% TBE-Urea gel (Thermo) for 65 min at 200 V. 15-45 nt RNA fragments were excised and purified, then precipitated in isopropanol. RNA was dephosphorylated with T4 polynucleotide kinase (NEB) by incubating at 37C for 1 hour, then the reaction was inactivated at 75C for 10 min. RNA was precipitated in isopropanol. Linker-1 (5′ App/CTGTAGGCACCATCAAT/3ddC) was then ligated to the 3′ end of 3 picomoles (pmol) of RNA using T4 RNA Ligase 2, truncated K227Q (NEB) in a reaction containing 25% PEG 8000, T4 RNA Ligase 2 Buffer at 1x, and 100 pmol of Linker-1 by incubating for 2.5 hours at 25C. Ligated RNA was precipitated in isopropanol and resuspended in 10 mM Tris pH 7. The ligated product was then purified by size excision on a 10% TBE-Urea gel (Thermo) run for 50 min at 200 V and precipitated in isopropanol. cDNA was generated by reverse transcription (RT) with SuperScript III (Invitrogen) by first incubating ligated RNA with 25 pmol of RT primer oCJ485 at 65C for 5 min. The remaining reagents (First Strand Buffer at 1x, 20 U SuperaseIn, 5 mM DTT, 0.5 mM dNTPs, and SuperScript III) were then added on ice. The reactions were incubated at 50C for 45 min and then quenched by adding NaOH to a final concentration of 0.1 M and incubating at 95C for 15 min to hydrolyze template RNA. cDNA was purified by size excision on a 10% TBE-Urea gel run for 80 min at 200 V and precipitated in isopropanol. Purified cDNA was resuspended in 10 mM Tris pH 8. Single-stranded cDNA was then circularized with CircLigase (VWR) and additional reagents (2.5 mM MgCl2, 50 µM ATP, CircLigase Buffer at 1x) by incubating at 60C for 1 hour. After an hour, 1 µL of CircLigase was spiked in, and the reaction was incubated at 60C for another hour and then inactivated at 80C for 10 min. The final libraries were amplified by PCR of circularized cDNA and purified by size excision on an 8% TBE gel (Thermo) run for 45 min at 180 V. Amplified libraries were precipitated in isopropanol, resuspended in 10 mM Tris pH 8, and stored at -30C until sequencing.

tag: cell type

value: bacterial

value: mfd_KO (Synpcc7942_1326::KanR)

tag: batch


title: wor-GAL4>UAS-mCD8-GFP+ cells isolated by FACS, at 24 hours after larval hatching

description: Library name: Larval_24ALH_biolrep1


title: Syn, Mfd_KO, rep 1

description:
Library name: 1828
biological replicate (cells harvested from unique flask)


title: Skeletal muscle, Klotho KO, rep 3

description:
Library name: RNA_115M
SkMuscle_KlothoKO_3


title: wor-GAL4>UAS-mCD8-GFP+ cells isolated by FACS, at embryonic stage 17, 2nd replicate

description: Library name: Embryo_St17_biolrep2


title: S. aureus in SSF2 rep1

description: Library name: SAU060112_SSF2_1


title: Syn, WT, rep 2

description:
Library name: 1826
technical replicate (cells harvested from same flask)

value: WT


title: Skeletal muscle, Klotho KO, rep 2

description:
Library name: RNA_114M
SkMuscle_KlothoKO_2


title: Syn, WT, rep 1

description:
Library name: 1825
technical replicate (cells harvested from same flask)


title: Bronchial epithelium, all conditions, 3 donors

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Library name: Sublibrary_1_5_7

data_processing:
Raw reads were processed using the Parse Biosciences split-pipe pipeline (v1.0.5) with the following parameters: --mode all, --chemistry v2, and --kit WT
Assembly: hg38
Supplementary files format and content: Filtered raw counts matrix file, cells and genes annotation tables

source_name: Lung

growth_protocol: Human bronchial epithelial ALI cultures from three healthy donnors were purchased from Epithelix (Switzerland)

extract_protocol:
Cell fixation and permeabilization were carried out according to the Evercode fixation kit protocol (PARSE bioscience).
Barcoding and library generation were carried out as described in the Evercode WT v2 kit.

treatment_protocol: ALI cultures from three healthy donnors were incubated for 6 hours (basal and apical sides) in medium, DMSO  0,1% or CdCl2 (10µM) in 0,1% DMSO.Unicellular cell suspension were then obtained.

value: Lung

tag: subject status

value: healthy donors

value: Basal, Multiciliated, Secretory


title: S. aureus in LB rep4

description: Library name: SAU060112_LB4


title: 29_B6_aCD4

city: Cairns

first: Andreas

last: Kupz

state: Queensland

address: McGregor Road, Smithfield

department: Australian Institute of Tropical Health and Medicine

country: Australia

institute: James Cook University

description:
Library name: 29_B6_aCD4.fastq
29_B6_aCD4

data_processing:
quality controlled on a Fragment Analyzer System using the DNF-474 using the HS-DNA kit (1-6000 bp) (Agilent)
cDNA libraries were sequenced with an Illumina NextSeq 2000 platform using 100 nt single end read length, with 5 million reads on average per sample
Sequencing quality control of the raw reads was assessed using FastqQC software
adapter sequences were removed with cutadapt
Alignment to the Mus musculus reference genome (GRCm38, Ensembl release 102) and read counting were performed using STAR and featureCounts.  The DESeq2 R package was used to perform differential gene expression analysis.
Assembly: GRCm38, Ensambl release 102
Supplementary files format and content: Processed_data file is in format xlsx contains counts, baseMean, log2FoldChange, lfcSE, pvalue, padj, baseMean, log2FoldChange, lfcSE, pvalue, padj for each sample

source_name: cervical lymph nodes

growth_protocol: C57BL/6, B6.muMT-/-, B6.Rag1-/-, and B6.Rag2-/-Il2rg-/- (e) mice were naïve or  infected i.d. with Mtb and anti-CD4 mAb.

extract_protocol:
RNA from cLNs was isolated using PureLink FFPE RNA Isolation Kit (ThermoFisher)
The libraries were constructed using Lexogen’s QuantSeq 3' mRNA-Seq Library Prep Kit FWD

value: cervical lymph nodes

tag: cell line

value: Paraformaldehyde-fixed and paraffin-embedded tissue

value: Treated with aCD4 antibody weekly (17 weeks )


title: tjUTR_sensor_wtCIS_Rep2

description:
Library name: tjUTR_sensor_wtCIS_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

value: ovarian somatic cells

value: OSC cells with tj-UTR sensor stably integrated on chromosome 3R


title: Skeletal muscle, WT, rep 6

description:
Library name: RNA_100M
SkMuscle_WT_6

value: Skeletal muscle

value: Male

value: 8 weeks


title: S. aureus in LB rep3

description: Library name: SAU060112_LB3


title: Skeletal muscle, Klotho KO, rep 1

description:
Library name: RNA_113M
SkMuscle_KlothoKO_1

value: Klotho KO


title: S. aureus in LB rep2

description: Library name: SAU060112_LB2


title: Skeletal muscle, WT, rep 5

description:
Library name: RNA_99M
SkMuscle_WT_5


title: 30_B6_aCD4

description:
Library name: 30_B6_aCD4.fastq
30_B6_aCD4


title: S. aureus in LB rep1

description: Library name: SAU060112_LB1


title: 27_R2_Mtb

description:
Library name: 27_R2_Mtb.fastq
27_R2_Mtb

value: Infected with Mycobacteria tuberculosis


title: mIg+5

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol,  raw counts and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).
Supplementary files format and content: Raw_and DESeq_normalized_counts_per_gene.xslx

organism: Mus

source_name: parotid gland

growth_protocol: mice were breeded in SPF conditions, and their parotid gland was extracted at the age of 4 weeks old

extract_protocol:
RNA was extracted using QIAGEN RNeasy Micro Kit according to the manufacturer's instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: both groups are WT mice but the experiment group lacked maternal antibodies during their development

value: parotid gland

value: recived maternal antibbodies


title: tjUTR_sensor_shuffledCIS_Rep2

description:
Library name: tjUTR_sensor_shuffledCIS_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: S. aureus in SSF2 rep3

description: Library name: SAU060112_SSF2_3


title: 26_R2_Mtb

description:
Library name: 26_R2_Mtb.fastq
26_R2_Mtb


title: Skeletal muscle, WT, rep 4

description:
Library name: RNA_96M
SkMuscle_WT_4

value: WT


title: Skeletal muscle, WT, rep 3

description:
Library name: RNA_95M
SkMuscle_WT_3


title: mIg+ 4


title: Skeletal muscle, WT, rep 2

description:
Library name: RNA_94M
SkMuscle_WT_2


title: tjUTR_sensor_wtCIS_Rep1

description:
Library name: tjUTR_sensor_wtCIS_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 28_B6_aCD4

description:
Library name: 28_B6_aCD4_Mtb.fastq
28_B6_aCD4_Mtb


title: Skeletal muscle, WT, rep 1

description:
Library name: RNA_93M
SkMuscle_WT_1


title: 24_R2_Naive

description:
Library name: 24_R2_Naive.fastq
24_R2_Naive

value: No treatment


title: 25_R2_Mtb

description:
Library name: 25_R2_Mtb.fastq
25_R2_Mtb


title: Translation_sensor_GFP-STOP-BFP_Rep2

description:
Library name: Translation_sensor_GFP-STOP-BFP_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: tjUTR_sensor_shuffledCIS_Rep1

description:
Library name: tjUTR_sensor_shuffledCIS_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: mIg+ 1


title: 23_R2_Naive

description:
Library name: 23_R2_Naive.fastq
23_R2_Naive


title: Translation_sensor_GFP-STOP-BFP_Rep1

description:
Library name: Translation_sensor_GFP-STOP-BFP_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Translation_sensor_GFP-BFP-STOP_Rep1

description:
Library name: Translation_sensor_GFP-BFP-STOP_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Kidney, Klotho KO, rep 5

description:
Library name: Klo120K
Kidney_KlothoKO_5

value: Kidney


title: mIg- 5

value: lack maternal antibodies


title: Translation_sensor_GFP-BFP-STOP_Rep2

description:
Library name: Translation_sensor_GFP-BFP-STOP_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: mIg+ 2


title: mIg+ 3


title: Kidney, Klotho KO, rep 6

description:
Library name: Klo122K
Kidney_KlothoKO_6


title: Kidney, Klotho KO, rep 4

description:
Library name: Klo119K
Kidney_KlothoKO_4


title: 22_R2_Naive

description:
Library name: 22_R2_Naive.fastq
22_R2_Naive

value: cervical lymph nodes

value: Paraformaldehyde-fixed and paraffin-embedded tissue


title: singleU_Rep2

description:
Library name: singleU_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC


title: 21_R1_Mtb

description:
Library name: 21_R1_Mtb.fastq
21_R1_Mtb


title: singleU_Rep1

description:
Library name: singleU_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: ovarian somatic cells


title: mIg- 4


title: Kidney, Klotho KO, rep 2

description:
Library name: Klo114K
Kidney_KlothoKO_2


title: mIg- 3


title: mIg- 1


title: 20_R1_Mtb

description:
Library name: 20_R1_Mtb.fastq
20_R1_Mtb


title: Kidney, Klotho KO, rep 3

description:
Library name: Klo115K
Kidney_KlothoKO_3


title: 19_R1_Mtb

description:
Library name: 19_R1_Mtb.fastq
19_R1_Mtb


title: Kidney, Klotho KO, rep 1

description:
Library name: Klo113K
Kidney_KlothoKO_1


title: trippleU_Rep1

description:
Library name: trippleU_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Kidney, WT, rep 6

description:
Library name: Klo100K
Kidney_WT_6


title: 17_R1_Naive

description:
Library name: 17_R1_Naive.fastq
17_R1_Naive


title: 18_R1_Naive

description:
Library name: 18_R1_Naive.fastq
18_R1_Naive


title: mIg- 2


title: PBMC, Group 4, SIV-infected+long-term ART, rep 6

city: New Orleans

first: Xuebin

last: Qin

state: LA

address: 1430 Tulane Avenue

department: Pathology

institute: Tulane University

description:
Library name: Sample 18
10x Genomics

data_processing:
Raw reads were evaluated with FastQC and aligned to Mmul10 using Hisat2. Transcript assembly and abundance estimation were performed with the featurecounts R package. Gene-level differential expression was analyzed with DESeq2. Volcano plots were created with the Enhanced Volcano package (v1.16.0) to visualize gene-level changes. Gene ontology (GO) analysis used DAVID Functional Annotation Bioinformatics Microarray Analysis; gene sets with p-value < 0.05 were deemed significantly enriched, and results were visualized with enrichplot, ggplot2, and base R graphics.
Assembly: Mmul10
Supplementary files format and content: matrix files of featurecounts

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Blood collected in EDTA tubes (Sarstedt) was processed immediately. PBMCs were isolated by density gradient centrifugation (Lymphocyte Separation Medium, MP Biomedicals) at 1500 rpm for 45 min for phenotyping and functional assays. Tissues were collected in 1 mL Trizol reagent (15596026; Invitrogen) and extracted with RNeasy Mini Kit (Cat. No.74104; QIAGEN, Hilden, Germany) following the manufacturer’s protocol. The concentration of RNA was determined by NanoDrop 2000.
Final cDNA libraries carrying TruSeq RNA CD indexes (Illumina, 20019792) were quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Library quality was assessed on an Agilent TapeStation 4150 using Agilent D1000 ScreenTape (Agilent, 5067-5582). Smear analysis (Agilent TapeStation Software, Version 4.1.1) with a 600 bp window was used to determine the average library size. Library molarity was then calculated from the measured size and concentration. Libraries were pooled to a final concentration of 750pM with a 2% spike-in of PhiX control library v3 (Illumina, FC-110-3001). The pooled mixture was loaded onto an Illumina NextSeq P1 (300) reagent cartridge (Illumina, 20050264). Paired-end, dual-index sequencing (150×8×8×150) was run on the NextSeq2000, generating ~20 M paired-end reads per sample. Fastq files produced by Illumina BaseSpace DRAGEN Analysis Software (Version 1.2.1) were used for downstream analyses.

value: PBMC

value: Wild-type

value: SIV-infected+Long-term ART (20 months)


title: doubleU_Rep1

description:
Library name: doubleU_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: doubleU_Rep2

description:
Library name: doubleU_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: trippleU_Rep2

description:
Library name: trippleU_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Kidney, WT, rep 5

description:
Library name: Klo99K
Kidney_WT_5

value: Male

value: 8 weeks


title: 15_Mu_Mtb

description:
Library name: 15_Mu_Mtb_.fastq
15_Mu_Mtb

value: Infected with Mycobacteria tuberculosis


title: U45_siLuc_Rep1

description:
Library name: U45_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: U45_siYB_Rep1

description:
Library name: U45_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Kidney, WT, rep 4

description:
Library name: Klo96K
Kidney_WT_4


title: PBMC, Group 4, SIV-infected+long-term ART, rep 4

description:
Library name: Sample 16
10x Genomics

value: SIV-infected+Long-term ART (12 months)


title: 13_Mu_Mtb

description:
Library name: 13_Mu_Mtb.fastq
13_Mu_Mtb


title: 14_Mu_Mtb

description:
Library name: 14_Mu_Mtb.fastq
14_Mu_Mtb


title: Kidney, WT, rep 3

description:
Library name: Klo95K
Kidney_WT_3

value: WT


title: Kidney, WT, rep 1

description:
Library name: Klo93K
Kidney_WT_1


title: 16_R1_Naive

description:
Library name: 16_R1_Naive.fastq
16_R1_Naive

value: No treatment


title: PBMC, Group 4, SIV-infected+long-term ART, rep 2

description:
Library name: Sample 14
10x Genomics


title: U32.5_siYB_Rep2

description:
Library name: U32.5_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R


title: U32.5_siYB_Rep1

description:
Library name: U32.5_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 11_Mu_Naive

description:
Library name: 11_Mu_Naive.fastq
11_Mu_Naive


title: PBMC, Group 3, SIV-infected+short-term ART, rep 4

description:
Library name: Sample 12
10x Genomics

value: SIV-infected+short-term ART (2 months)


title: PBMC, Group 4, SIV-infected+long-term ART, rep 5

description:
Library name: Sample 17
10x Genomics


title: PBMC, Group 4, SIV-infected+long-term ART, rep 3

description:
Library name: Sample 15
10x Genomics


title: U32.5_siLuc_Rep1

description:
Library name: U32.5_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: PBMC, Group 3, SIV-infected+short-term ART, rep 3

description:
Library name: Sample 11
10x Genomics


title: U30_siYB_Rep2

description:
Library name: U30_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 12_Mu_Naive

description:
Library name: 12_Mu_Naive.fastq
12_Mu_Naive


title: 9_aCD4_Mtb

description:
Library name: 9_aCD4_Mtb.fastq
9_B6_aCD4_Mtb

value: Infected with Mycobacteria tuberculosis Treated with aCD4 antibody weekly (17 weeks ) and Infected with Mycobacteria tuberculosis


title: U32.5_siLuc_Rep2

description:
Library name: U32.5_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 4get_C57BL/6N_and_dblGATA-1_4get_C57BL/6_mice_50_days_after_Leishmania_mexicana_infection

city: Erlangen

first: David

last: Barinberg

address: Wasserturmstraße 3/5

department: Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Universitätsklinikum Erlangen and Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg

description: BD Rhapsody

data_processing:
Paired-end scRNA-seq FASTQ files were processed on the Seven Bridges Genomics (https://igor.sbgenomics.com/home) platform with default parameters
Assembly: mm9
Supplementary files format and content: Comma-seperated value files and matrix files

source_name: Skin

extract_protocol:
Foot skin: Whole foot skin was cut into small pieces which were digested for 45-60 minutes at 37°C under gentle vibration in RPMI 1640 containing 0.2 mg/ml collagenase P and 0.1mg/ml DNAse I (both Roche Diagnostics GmbH). Cell suspensions were passed through a 70 µm and 40 µm cell strainer (Corning), resuspended in 2.5 ml of 40% Percoll preparation (20 ml Percoll [GE Healthcare], 2.2 ml 10×PBS, 27.8 ml HBSS without Ca2+ and Mg2+ [Sigma-Aldrich]) and layered onto 1.5 ml 60% Percoll (30 ml Percoll, 3.3 ml 10×PBS, 16.7 ml HBSS). After centrifugation for 20 min at 931 x g (room temperature), the cell layer at the interface was collected, washed and resuspended in PBS. Viability was increased by removing dead cells using the MACS Dead cell removal kit (Miltenyi Biotec) according to the manufacturer’s instructions. Discrimination between viable and dead cells was enabled by 5 μM Calcein AM and 0.3 μM DRAQ 7, as described Single-Cell Capture and cDNA Synthesis Protocol for BD Rhapsody (BD Bioscience). Samples which were subsequently pooled were labelled with sample tags (BD Bioscience, BD Mouse Single-Cell Multiplexing Set, 626545, Rat anti-mouse MHC-H2 Class I(M1/42)) according to manufacturer’s protocol. Cell loading in the BD Rhapsody 8-Lane Cartridge (BD Bioscience) and single-cell capture with the BD Rhapsody HT Single-Cell Analysis System was performed as mentioned in the manufacturer’s instructions.
Single-cell whole transcriptome mRNA and Sample Tag libraries were generated according to the manufacturer’s instructions (BD Rhapsody, BD Bioscience). The final libraries were quantified using a Qubit Fluorometer (Thermo Fisher Scientific) with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: 7x 4get C57BL/6N and 7x 4get dblGATA-1 C57BL/6N mice were infected subcutaneously in the skin of both hind feet with 3 x 106 Leishmania mexicana (MNYC/BZ/62/M379) in 50 µl of PBS for 50 days

value: Skin

value: 4get C57BL/6N and 4get dblGATA-1 C57BL/6N

value: 50 days infected with Leishmania mexicana


title: PBMC, Group 3, SIV-infected+short-term ART, rep 2

description:
Library name: Sample 10
10x Genomics


title: 10_Mu_Naive

description:
Library name: 10_Mu_Naive.fastq
10_Mu_Naive

value: cervical lymph nodes

value: Paraformaldehyde-fixed and paraffin-embedded tissue


title: C57BL/6N_mouse_skin_blood_bone_marrow_14_days_after_Leishmania_mexicana_infection

description: BD Rhapsody

source_name: Skin, blood, bone marrow

extract_protocol:
Foot skin: Whole foot skin was cut into small pieces which were digested for 45-60 minutes at 37°C under gentle vibration in RPMI 1640 containing 0.2 mg/ml collagenase P and 0.1mg/ml DNAse I (both Roche Diagnostics GmbH). Cell suspensions were passed through a 70 µm and 40 µm cell strainer (Corning), resuspended in 2.5 ml of 40% Percoll preparation (20 ml Percoll [GE Healthcare], 2.2 ml 10×PBS, 27.8 ml HBSS without Ca2+ and Mg2+ [Sigma-Aldrich]) and layered onto 1.5 ml 60% Percoll (30 ml Percoll, 3.3 ml 10×PBS, 16.7 ml HBSS). After centrifugation for 20 min at 931 x g (room temperature), the cell layer at the interface was collected, washed and resuspended in PBS. Viability was increased by removing dead cells using the MACS Dead cell removal kit (Miltenyi Biotec) according to the manufacturer’s instructions. Bone marrow (BM): Femur and tibia were flushed using complete RPMI medium and a 23-gauge needle (BD Biosciences). The content was collected, filtered through a 70 µm cell strainer and red blood cells were lysed using Red Blood Cell Lysis Buffer (Miltenyi Biotec) according to the manufacturer’s protocol. A density gradient centrifugation was then conducted using Histopaque 1077/1119 (Sigma-Aldrich), following the manufacturers protocol. Afterwards, the granulocyte layer was carefully transferred and washed with PBS. The viability was increased by removing dead cells using the MACS Dead cell removal kit according to the manufacturer’s instructions. Blood: Following euthanasia of the mice, a midline laparotomy was performed to expose the abdominal cavity, and the vena cava was carefully isolated and accessed using a 26G needle attached to an Omnfix-F Luer Solo syringe (Braun). Blood was drawn from the vena cava and transferred into a  EDTA-coated tubes (Micro tube 1.3 mL, Sarstedt).A density gradient centrifugation was then conducted using Histopaque 1077/1119 (Sigma-Aldrich), following the manufacturers protocol. Afterwards, the granulocyte layer was carefully transferred and washed with PBS. Red blood cells were lysed twice in ice-cold water for 10 seconds. The viability was increased by removing dead cells using the MACS Dead cell removal kit according to the manufacturer’s instructions. Discrimination between viable and dead cells was enabled by 5 μM Calcein AM and 0.3 μM DRAQ 7, as described Single-Cell Capture and cDNA Synthesis Protocol for BD Rhapsody (BD Bioscience). Samples which were subsequently pooled were labelled with sample tags (BD Bioscience, BD Mouse Single-Cell Multiplexing Set, 626545, Rat anti-mouse MHC-H2 Class I(M1/42)) according to manufacturer’s protocol. Cell loading in the BD Rhapsody 8-Lane Cartridge (BD Bioscience) and single-cell capture with the BD Rhapsody HT Single-Cell Analysis System was performed as mentioned in the manufacturer’s instructions.
Single-cell whole transcriptome mRNA and Sample Tag libraries were generated according to the manufacturer’s instructions (BD Rhapsody, BD Bioscience). The final libraries were quantified using a Qubit Fluorometer (Thermo Fisher Scientific) with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: 10x C57BL/6N mice were infected subcutaneously in the skin of both hind feet with 3 x 106 Leishmania mexicana (MNYC/BZ/62/M379) in 50 µl of PBS for 14 days

value: Skin, blood, bone marrow

value: 14 days infected with Leishmania mexicana


title: 8_aCD4_Mtb

description:
Library name: 8_aCD4_Mtb.fastq
8_B6_aCD4_Mtb


title: U30_siYB_Rep1

description:
Library name: U30_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias and facilitate library multiplexing, adaptors were designed with random nucleotides placed adjacent to the ligating end. The 3′ adaptor carried six random bases at its 5′ terminus and contained sample barcodes (X) for multiplexing (5rApp/NNNNNNXXXX–Adaptor–/3ddC). The 5′ adaptor was an RNA oligo bearing four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adaptor ligation with T4 RNA ligase 2, truncated KQ, samples were pooled as necessary, spiked with fluorescently labeled and ligation-blocked oligos as size controls, and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adaptor ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, multiplexed and sequenced (SE50, Illumina NovaSeq6000).

value: OSC

value: ovarian somatic cells


title: mESCs, DKO2-pMCM2

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

library_source: genomic

data_processing:
Nextflow/chip
Fastq files were mapped and quality controlled using the nfcore/chip pipeline. Merged bigwig files were generated from bam files using multiBamSummary function of deepTools2.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: mESCs

growth_protocol: Mouse ESCs were grown in the presence of Lif+2i.

extract_protocol:
SimpleChIP Plus Sonication Chromatin IP Kit
NEBNext Ultra II

value: mESCs

tag: culture conditions

value: Naive

tag: chip antibody

value: pMCM2 (MCM2-S40P ab133243 Abcam)


title: PBMC, Group 3, SIV-infected+short-term ART, rep 1

description:
Library name: Sample 9
10x Genomics

value: PBMC

value: Wild-type


title: 7_aCD4_Mtb

description:
Library name: 7_aCD4_Mtb.fastq
7_B6_aCD4_Mtb

tag: tissue


title: PBMC, Group 2, SIV-infected, rep 4

description:
Library name: Sample 8
10x Genomics

value: SIV-infected


title: 6_B6_Mtb

description:
Library name: 6_B6_Mtb.fastq
6_B6_Mtb

value: Infected with Mycobacteria tuberculosis


title: PBMC, Group 4, SIV-infected+long-term ART, rep 1

description:
Library name: Sample 13
10x Genomics

value: SIV-infected+Long-term ART (12 months)


title: U30_siLuc_Rep1

description:
Library name: U30_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: PBMC, Group 2, SIV-infected, rep 3

description:
Library name: Sample 7
10x Genomics


title: U30_siLuc_Rep2

description:
Library name: U30_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: Kidney, WT, rep 2

description:
Library name: Klo94K
Kidney_WT_2

value: Kidney

tag: strain

value: Male

value: 8 weeks

value: WT


title: U25_siYB_Rep2

description:
Library name: U25_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: mESCs, DKO1-MCM2

value: MCM2 (MCM2 3619 Cell Signaling)


title: 4_B6_Mtb

description:
Library name: 4_B6_Mtb.fastq
4_B6_Mtb

value: cervical lymph nodes

value: Paraformaldehyde-fixed and paraffin-embedded tissue


title: mESCs, DKO1-IgG

description: DKO-merged-IgG.mLb.clN.sorted.bw

value: mESCs

value: IgG (Rabbit IgG ab171870 Abcam)


title: 5_B6_Mtb

description:
Library name: 5_B6_Mtb.fastq
5_B6_Mtb


title: PBMC, Group 2, SIV-infected, rep 2

description:
Library name: Sample 6
10x Genomics


title: mESCs, DKO2-MCM2

value: Naive


title: mESCs, DKO1-pMCM2

value: pMCM2 (MCM2-S40P ab133243 Abcam)


title: mESCs, CKO2-pMCM2


title: U25_siYB_Rep1

description:
Library name: U25_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

value: ovarian somatic cells


title: U25_siLuc_Rep1

description:
Library name: U25_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: PBMC, Group 2, SIV-infected, rep 1

description:
Library name: Sample 5
10x Genomics

value: PBMC

value: Wild-type

value: SIV-infected


title: mESCs, DKO2-IgG

description: DKO-merged-IgG.mLb.clN.sorted.bw


title: 1_B6_Naive

description:
Library name: 1_B6_naive.fastq
1_B6_Naive

value: No treatment


title: 3_B6_Naive

description:
Library name: 3_B6_Naive.fastq
3_B6_Naive


title: U25_siLuc_Rep2

description:
Library name: U25_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: MGO.53 biol rep 3

description:
Library name: MGO53_3_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

data_processing:
Raw reads were aligned to the mouse transcriptome and genome version GRCh39 with annotations from Ensembl release 106 using STAR aligner v.2.7.10a. Counts per gene quantification was done using htseq-count v2.01 (ref. 2). Genes with a sum of counts below 10 over all samples were filtered out. Base mean counts (mormc) were calculated using DESeq2 package
Assembly: GRCh39
Supplementary files format and content: raw and norm counts per gene per sample.xlsx

source_name: skin

growth_protocol: B16 were all grown in complete DMEM (supplemented with 10% fetal bovine serum (FBS), 1 % penicillin/streptomycin, and 1 % L-glutamine, Gibco). Cells were grown at 37C with 5 % CO2

extract_protocol:
MicroPure™ RNA Isolation Kit
Poly(A)+ RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Strand-specific RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit according to the manufacturer’s protocol, with an expected fragment length of approximately 350 bp including adapters.

treatment_protocol: 4 antibodies were incubated (Mel321-31, Mel322-34, Mel321-35 and isotype control-MGO.53) with B16 cancer line and RNA was produced following 24 hours

value: skin

value: melanoma

value: wild type

value: batch 1


title: PBMC, Group 1, Baseline, rep 4

description:
Library name: Sample 4
10x Genomics

value: Baseline


title: U20_siLuc_Rep2

description:
Library name: U20_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: 2_B6_Naive

description:
Library name: 2_B6_Naive.fastq
2_B6_Naive

value: cervical lymph nodes

value: Paraformaldehyde-fixed and paraffin-embedded tissue


title: mESCs, CKO1-IgG

description: CKO-merged-IgG.mLb.clN.sorted.bw

value: mESCs

value: Naive

value: IgG (Rabbit IgG ab171870 Abcam)


title: MGO.53 biol rep 2

description:
Library name: MGO53_2_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.


title: mESCs, CKO1-MCM2

value: MCM2 (MCM2 3619 Cell Signaling)