title: lingua, female, 9-5489-S3-NextRUN13

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: Library name: 9__lingua__5489__female__S3__NextRUN13

data_processing:
The reads were aligned to the hg38 genome using HISAT2 (v.2.2.1) with GENCODE comprehensive annotation (v.44) and a very-sensitive preset.
Multimapped reads were filtered with samtools (v.1.13) view -q 60 followed by counting the reads-per-gene with featureCounts (v.2.0.6) -s 1.
bedGraph tracks were generated with bedtools (v.2.30.0) genomecov using -bg -5 options to calculate 5'-end coverage.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files. File contents: the files contain the read counts per gene estimated by featureCounts.
Supplementary files format and content: File format: bedGraph. File contents: aggregated 5' profiles of the mapped CAGE tags, separately for the direct and reverse complementary strands (+ and -).

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from muscle samples using the RNeasy Fibrous Tissue Kit (Qiagen, Germany) according to the manufacturer’s protocol with minor modifications. 19-30 mg of tissue was homogenized with a mortar and pestle using liquid nitrogen. After that lysis buffer was added, and the lysate was collected into clean tubes. The samples were then incubated with proteinase K solution for 10 minutes at 55°C and centrifuged in an Eppendorf mini spin centrifuge at maximum speed. To precipitate long and short RNAs, one volume of 96% ethanol was added to the supernatant, and all was applied to a column. The column was washed twice with RPE wash buffer, dried, and eluted with nuclease-free water.
Libraries were prepared utilizing the standard nAnT-iCAGE (non-Amplified non-Tagging Illumina Cap Analysis of Gene Expression) protocol described in Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M et al. (2014). Detecting expressed genes using CAGE. In: Miyamoto-Sato E, Ohashi H, Sasaki H, Nishikawa J-I, Yanagawa H (eds) Transcription factor regulatory networks: methods and protocols. Springer, New York, NY, pp 67–85. doi:10.1007/978-1-4939-0805-9_7. 5 μg of total RNA was used as a template for synthesis of the first cDNA strand (nAnT-iCAGE Library Preparation kit DNA form, Yokohama, Japan, and SuperScript III Reverse Transcriptase, Invitrogen, Waltham, MA, USA). Next, RNA/DNA heteroduplexes were biotinylated at 5´-ends (nAnT-iCAGE Library Preparation kit, DNA form, Yokohama, Japan), which allowed selection of the 5´-cap containing molecules with streptavidin beads (Dynabeads M-270 Streptavidin, ThermoFisher Scientific, USA). Then, cDNA was treated with RNase I and H (nAnT-iCAGE Library Preparation kit, DNA form, Japan) and purified using RNACleanUP (Beckman Coulter, Brea, CA, USA). Next, linkers were ligated to the 5′and 3′ ends (nAnT-iCAGE Library Preparation kit, DNAform, Japan) of the cap-trapped cDNA. The 5′- linker employed contained recognition sites for the XmaJI restriction endonuclease (nAnT-iCAGE Library Preparation kit, DNA form, Japan) and the MmeI class II restriction enzyme (nAnT-iCAGE Library Preparation kit, DNA form, Japan), as well as a barcode for multiplexing. The 3′- linker contained a recognition site of the XbaI restriction enzyme (nAnT-iCAGE Library Preparation kit, DNAform, Japan). Treatment with these restriction enzymes yielded short CAGE tags to which a sequencing primer was ligated. In the final stage, a second cDNA strand was synthesized from these short CAGE tags (nAnT-iCAGE Library Preparation kit, DNAform, Japan). The concentration of the resulting libraries was determined by the PicoGreen Assay in a GloMax® Multi Detection System (Promega, Madison, WI, USA), and the libraries were validated using real-time PCR (KAPA Library Quantification Kits Illumina, KAPA Biosystems, Wilmington, MA, South Africa). The sequencing on a either Hiseq2500, Nextseq 550, or Novaseq6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: Tissue samples were fixed in RNA-later solution (Invitrogen), stored at +4C overnight, and then stored at -80C until RNA isolation.

value: skeletal muscle

tag: muscle short_id

value: lingua

tag: muscle short_latin_name

tag: muscle full_latin_name

value: Lingua

tag: body part

value: Tongue

tag: replicate id

tag: person id

tag: Sex

value: female

tag: batch


status: Public on Apr 11 2026

type: SRA

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description: Library name: ENU57226B6G37_D11_neuro2008rep_S36_R1_2367729897

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38 using GSNAP 74. Only uniquely mapping reads were carried forward to downstream analysis. Sample quality was further assessed on a per-plate basis based on total read counts, percentage of reads mapping to the reference genome, and percentage of reads mapping to exons. Reads predominantly mapped to transcript 3’ ends, as expected from the library preparation method.
Assembly: GRCm38

molecule: total RNA

organism: Mus musculus

source_name: Whole brain

growth_protocol: Founder C57BL/6NCrl males were treated with 3 x 100 mg/kg ENU (Sigma) and mutations bred to homozygosity in three generations. Generation 3 mice were collected usually between 8-12 weeks old, and an ear notch for DNA and brain samples were collected. Typically, 12 siblings from each pedigree were screened.

extract_protocol:
To homogenize the tissue, RNAlater was removed, and a 5 mm stainless steel bead (Qiagen) and 1.6 mL of Qiazol (Qiagen) was added. The tissue was homogenized using a Tissue Lyser II (Qiagen) for at least 30 minutes until a homogenous solution was confirmed. 400 µL of the homogenate solution was transferred into a new tube and allowed to sit for 5 minutes before adding 100 µL of chloroform (Sigma). The homogenate-chloroform mixture was shaken vigorously, allowed to stand for 2 minutes before centrifugation for 5 minutes at 4°C and 1000 x g. The top clear layer was removed and stored at -80 °C. For RNA extraction, 120 µL was transferred into a QIAgen S-block and processed on the QIAcube using the RNeasy 96 QIAcube HT Kit.
cDNA fragment libraries were constructed using the SMART-Seq® v4 3’ DE Kit (Takara Bio) following manufacturer’s recommendations, with minor modifications. Total RNA samples were processed in batches of 1152, distributed across twelve 96-well plates. For each sample, 4 ng total RNA was used as input for cDNA synthesis, then amplified for 8 cycles, with each sample in a row receiving a unique in-line index. Amplified cDNAs within a row were then combined into a 12-plex pool, cleaned up with Ampure XP beads (Beckman Coulter) and quantified using the Qubit HS DNA assay kit (Thermo Fisher Scientific). For each of the 96 cDNA pools generated from 12 plates, 400 pg were carried into Nextera XT library preparations (Illumina Inc.), each assigned with one of the 96 unique combinations of Forward and Reverse HT Index Primers included in the SMART-Seq® v4 3’ DE kit. After Ampure XP clean up and Qubit quantification, the 96 pools were combined in an equimolar manner to generate a 1152-plex Illumina library.  This library was concentrated with Ampure XP beads, quantified with Qubit and assessed on the TapeStation with the High Sensitivity D1000 assay (Agilent Technologies).

treatment_protocol: Mice were euthanized by cervical dislocation, then whole brains were collected. Each cerebellum was removed and the remaining brain matter was transferred to RNAlater and stored at 4C for up to 5 days.

tag: tissue

value: Whole brain

tag: partofsubset

value: FALSE


title: pterygoideus lat, male, 7-5879-S2-NextRUN5

description: Library name: 7__pterygoideus_lat__5879__male__S2__NextRUN5

organism: Homo sapiens

value: m. pterygoideus lateralis

value: Musculus pterygoideus lateralis caput inferius, Musculus pterygoideus lateralis caput superius

value: Head

value: male


title: temporalis, male, 8-5879-S3-NextRUN2

description: Library name: 8__temporalis__5879__male__S3__NextRUN2

value: temporalis

value: m. temporalis

value: Musculus temporalis


description: Library name: ENU57231B6G311_D6_neuro2218_S12_R1_2367729388


title: temporalis, male, 8-5708-S7-NextRUN19

description: Library name: 8__temporalis__5708__male__S7__NextRUN19


title: temporalis, female, 8-5489-S5-NextRUN14

description: Library name: 8__temporalis__5489__female__S5__NextRUN14


title: lingua, male, 9-5879-S7-NextRUN3

description: Library name: 9__lingua__5879__male__S7__NextRUN3


description: Library name: ENU57226B6G35_D10_neuro2008rep_S36_R1_2367729094


title: gluteus min, male, 74-5709-S8-NextRUN20

description: Library name: 74__gluteus_min__5709__male__S8__NextRUN20

value: m. gluteus minimus

value: Musculus gluteus minimus

value: Lower limbs


title: gluteus min, male, 74-5708-S4-NextRUN6

description: Library name: 74__gluteus_min__5708__male__S4__NextRUN6

value: skeletal muscle


title: pterygoideus lat, female, 7-5489-S1-NextRUN9

description: Library name: 7__pterygoideus_lat__5489__female__S1__NextRUN9


description: Library name: ENU57224B6G314_E5_neuro2008rep_S37_R1_2367729464


description: Library name: ENU57231B6G310_D5_neuro2218_S12_R1_2367729387


title: gluteus med, male, 73-5879-S5-NextRUN11

description: Library name: 73__gluteus_med__5879__male__S5__NextRUN11

value: m. gluteus medius

value: Musculus gluteus medius


title: gluteus min, female, 74-5489-S7-NextRUN21

description: Library name: 74__gluteus_min__5489__female__S7__NextRUN21


description: Library name: ENU57193B6G37_D1_neuro2008rep_S36_R1_2367729045


description: Library name: ENU57307B6G36_C4_neuro2222_S51_R1_2367729701


title: gluteus max, male, 72_2-5879-S1-NextRUN19

description: Library name: 72_2__gluteus_max__5879__male__S1__NextRUN19

value: m. gluteus maximus

value: Musculus gluteus maximus


description: Library name: ENU57190B6G310_D8_neuro2008rep_S36_R1_2367729117

value: Whole brain


title: gluteus max, male, 72_2-5708-S2-NextRUN15

description: Library name: 72_2__gluteus_max__5708__male__S2__NextRUN15


description: Library name: ENU57183B6G35_F3_neuro2008rep_S38_R1_2367729822

value: FALSE


description: Library name: ENU57193B6G32_C12_neuro2008rep_S35_R1_2367729087


description: Library name: ENU57226B6G314_D9_neuro2008rep_S36_R1_2367728760


description: Library name: ENU57183B6G34_F2_neuro2008rep_S38_R1_2367728898


description: Library name: ENU57190B6G35_D7_neuro2008rep_S36_R1_2367728840


title: vastus medial, male, 71-5879-S5-NextRUN12

description: Library name: 71__vastus_medial__5879__male__S5__NextRUN12

value: m. vastus medialis

value: Musculus vastus medialis


title: gluteus max, female, 72_2-5489-S2-NextRUN3

description: Library name: 72_2__gluteus_max__5489__female__S2__NextRUN3

value: female


title: gluteus max, male, 72_1-5709-S8-NextRUN18

description: Library name: 72_1__gluteus_max__5709__male__S8__NextRUN18

value: male


description: Library name: ENU57167B6G38_D4_neuro2008rep_S36_R1_2367729769


description: Library name: ENU57165B6G32_E12_neuro2008rep_S37_R1_2367728817


description: Library name: ENU57165B6G311_F1_neuro2008rep_S38_R1_2367729611


title: vastus lat, male, 70-5879-S8-NextRUN8

description: Library name: 70__vastus_lat__5879__male__S8__NextRUN8

value: m. vastus lateralis

value: Musculus vastus lateralis


title: vastus lat, female, 70-5489-S3-NextRUN16

description: Library name: 70__vastus_lat__5489__female__S3__NextRUN16


title: vastus medial, male, 71-5708-S4-NextRUN10

description: Library name: 71__vastus_medial__5708__male__S4__NextRUN10


title: vastus lat, male, 70-5708-S6-NextRUN16

description: Library name: 70__vastus_lat__5708__male__S6__NextRUN16


description: Library name: ENU57163B6G317_A5_neuro2008rep_S33_R1_2367729803


title: infer oblique, male, 6-5879-S6-NextRUN3

description: Library name: 6__infer_oblique__5879__male__S6__NextRUN3

value: m. obliquus inferior

value: Musculus obliquus inferior

value: Eyes


description: Library name: ENU57156B6G36_E4_neuro2008rep_S37_R1_2367728829


description: Library name: ENU57140B6G32_E10_neuro2008rep_S37_R1_2367729839


description: Library name: ENU57140B6G31_E9_neuro2008rep_S37_R1_2367729069


description: Library name: ENU57140B6G36_E11_neuro2008rep_S37_R1_2367729150


title: infer oblique, female, 6-5489-S6-NextRUN19

description: Library name: 6__infer_oblique__5489__female__S6__NextRUN19


description: Library name: ENU57163B6G37_A6_neuro2008rep_S33_R1_2367729704


title: vastus intermed, male, 69-5879-S7-NextRUN8

description: Library name: 69__vastus_intermed__5879__male__S7__NextRUN8

value: m. vastus intermedius

value: Musculus vastus intermedius

value: Lower limbs


title: vastus intermed, male, 69-5708-S7-NextRUN5

description: Library name: 69__vastus_intermed__5708__male__S7__NextRUN5

value: skeletal muscle


description: Library name: ENU57156B6G34_E3_neuro2008rep_S37_R1_2367729540


title: vastus intermed, female, 69-5489-S1-NextRUN15

description: Library name: 69__vastus_intermed__5489__female__S1__NextRUN15


title: tibialis post, male, 68-5879-S6-NextRUN8

description: Library name: 68__tibialis_post__5879__male__S6__NextRUN8

value: m. tibialis posterior

value: Musculus tibialis posterior


description: Library name: ENU57090B6G318_E1_neuro2008rep_S37_R1_2367729225

value: Whole brain


title: tibialis post, male, 68-5708-S6-NextRUN11

description: Library name: 68__tibialis_post__5708__male__S6__NextRUN11


title: tibialis post, female, 68-5489-S1-NextRUN3

description: Library name: 68__tibialis_post__5489__female__S1__NextRUN3


description: Library name: ENU57116B6G315_D5_neuro2008rep_S36_R1_2367729569

value: FALSE


title: infer oblique, male, 6-5709-S3-NextRUN21

description: Library name: 6__infer_oblique__5709__male__S3__NextRUN21


description: Library name: ENU57090B6G321_E2_neuro2008rep_S37_R1_2367729310


description: Library name: ENU57071B6G31_C11_neuro2008rep_S35_R1_2367728952


description: Library name: ENU57067B6G39_D3_neuro2008rep_S36_R1_2367728896


title: tibialis ant, female, 67-5489-S2-NextRUN16

description: Library name: 67__tibialis_ant__5489__female__S2__NextRUN16

value: m. tibialis anterior

value: Musculus tibialis anterior


title: tibialis ant, male, 67-5708-S3-NextRUN15

description: Library name: 67__tibialis_ant__5708__male__S3__NextRUN15


title: soleus, male, 66-5879-S8-NextRUN7

description: Library name: 66__soleus__5879__male__S8__NextRUN7

value: soleus

value: m. soleus

value: Musculus soleus


description: Library name: ENU57050B6G35_A12_neuro2008rep_S33_R1_2367729634


description: Library name: ENU57067B6G38_D2_neuro2008rep_S36_R1_2367729325


description: Library name: ENU57041B6G31_D6_neuro2008rep_S36_R1_2367729729


title: semitendinosus, male, 65-5708-S3-NextRUN6

description: Library name: 65__semitendinosus__5708__male__S3__NextRUN6

value: semitendinosus

value: m. semitendinosus

value: Musculus semitendinosus

value: male


description: Library name: ENU57040B6G318_A4_neuro2008rep_S33_R1_2367729193


title: tibialis ant, male, 67-5879-S5-NextRUN17

description: Library name: 67__tibialis_ant__5879__male__S5__NextRUN17


description: Library name: ENU57034B6G35_A11_neuro2008rep_S33_R1_2367729023


title: semitendinosus, female, 65-5489-S8-NextRUN13

description: Library name: 65__semitendinosus__5489__female__S8__NextRUN13

value: female


description: Library name: ENU57029B6G312_A10_neuro2008rep_S33_R1_2367729412


description: Library name: ENU57027B6G315_A9_neuro2008rep_S33_R1_2367729765


title: semimembranosus, female, 64-5489-S1-NextRUN16

description: Library name: 64__semimembranosus__5489__female__S1__NextRUN16

value: semimembranosus

value: m. semimembranosus

value: Musculus semimembranosus


title: semitendinosus, male, 65-5879-S5-NextRUN8

description: Library name: 65__semitendinosus__5879__male__S5__NextRUN8

value: skeletal muscle

value: Lower limbs


description: Library name: ENU57040B6G317_A3_neuro2008rep_S33_R1_2367728802

value: Whole brain


description: Library name: ENU57069B6G31_C10_neuro2008rep_S35_R1_2367728754

value: FALSE


description: Library name: ENU57027B6G310_A7_neuro2008rep_S33_R1_2367729063


title: semimembranosus, male, 64-5709-S7-NextRUN20

description: Library name: 64__semimembranosus__5709__male__S7__NextRUN20


title: sartorius, male, 63-5708-S8-NextRUN14

description: Library name: 63__sartorius__5708__male__S8__NextRUN14

value: sartorius

value: m. sartorius

value: Musculus sartorius


title: sartorius, female, 63-5489-S8-NextRUN9

description: Library name: 63__sartorius__5489__female__S8__NextRUN9


description: Library name: ENU57027B6G312_A8_neuro2008rep_S33_R1_2367729052


description: Library name: ENU57024B6G36_C6_neuro2008rep_S35_R1_2367728894


title: rectus femoris, male, 62-5708-S3-NextRUN10

description: Library name: 62__rectus_femoris__5708__male__S3__NextRUN10

value: m. rectus femoris

value: Musculus rectus femoris caput rectum, Musculus rectus femoris caput reflexum


title: rectus femoris, male, 62-5879-S3-NextRUN8

description: Library name: 62__rectus_femoris__5879__male__S3__NextRUN8


description: Library name: ENU57012B6G311_C9_neuro2008rep_S35_R1_2367728870


title: sartorius, male, 63-5879-S7-NextRUN7

description: Library name: 63__sartorius__5879__male__S7__NextRUN7


title: semimembranosus, male, 64-5879-S4-NextRUN8

description: Library name: 64__semimembranosus__5879__male__S4__NextRUN8


title: rectus femoris, female, 62-5489-S7-NextRUN13

description: Library name: 62__rectus_femoris__5489__female__S7__NextRUN13


description: Library name: ENU57001B6G36_C7_neuro2008rep_S35_R1_2367729723


description: Library name: ENU57012B6G312_C8_neuro2008rep_S35_R1_2367728857


title: peroneus long, male, 61-5879-S4-NextRUN17

description: Library name: 61__peroneus_long__5879__male__S4__NextRUN17

value: m. peroneus longus

value: Musculus peroneus longus


title: peroneus long, male, 61-5708-S4-NextRUN3

description: Library name: 61__peroneus_long__5708__male__S4__NextRUN3


description: Library name: ENU56479B6G310_F4_neuro2008rep_S38_R1_2367729673


title: peroneus brev, male, 60-5879-S10-NextRUN10

description: Library name: 60__peroneus_brev__5879__male__S10__NextRUN10

value: m. peroneus brevis

value: Musculus peroneus brevis


title: peroneus brev, male, 60-5708-S7-NextRUN1

description: Library name: 60__peroneus_brev__5708__male__S7__NextRUN1

value: male


description: Library name: ENU56454B6G38_C5_neuro2008rep_S35_R1_2367729054


description: Library name: ENU56458B6G35_B4_neuro2008rep_S34_R1_2367729120


description: Library name: ENU56456B6G37_E8_neuro2008rep_S37_R1_2367729840


description: Library name: ENU56428B6G314_C2_neuro2008rep_S35_R1_2367729338


title: super oblique, male, 5-5708-S3-NextRUN3

description: Library name: 5__super_oblique__5708__male__S3__NextRUN3

value: m. obliquus superior

value: Musculus obliquus superior

value: Eyes


description: Library name: ENU56446B6G327_C4_neuro2008rep_S35_R1_2367729092


title: gastrocnemius caput mediale, male, 59-5708-S2-NextRUN2

description: Library name: 59__gastrocnemius_caput_mediale__5708__male__S2__NextRUN2

value: skeletal muscle

value: m. gastrocnemius caput mediale

value: Musculus gastrocnemius caput mediale


description: Library name: ENU56428B6G312_C3_neuro2008rep_S35_R1_2367728842

value: Whole brain

value: FALSE


description: Library name: ENU56418B6G317_A1_neuro2008rep_S33_R1_2367729557


title: gastrocnemius caput mediale, male, 59-5879-S3-NextRUN11

description: Library name: 59__gastrocnemius_caput_mediale__5879__male__S3__NextRUN11

value: Lower limbs


description: Library name: ENU56418B6G315_A2_neuro2008rep_S33_R1_2367729479


description: Library name: ENU56403B6G33_B12_neuro2008rep_S34_R1_2367729295


title: hiPSC-derived-neuron_CHX_replicate_3

city: Chicago

first: Xiaochang

last: Zhang

state: IL

department: Department of Human Genetics

institute: University of Chicago

description:
Library name: iPSC-neuron_CHX rep3
iNeurons (day 4) weretreated with CHX (200 μg/mL for 5 hours), biological replicate 3

data_processing:
Differential expressed gene (DEG) analysis was performed using the STAR-FeatureCounts-DESeq2 workflow. Briefly, short reads were aligned to the reference genome using the STAR aligner with the sameparameters as AS-events detection, and the gene expression quantification was performed using FeatureCounts. DESeq2 was then used to identify DEGs based on the criteria of adjusted p < 0.001 and |log₂FC|>1 as default.
Assembly: hg38
Supplementary files format and content: iPSC.raw_count.txt

molecule: polyA RNA

source_name: iNGN (P69)-derived neuron

extract_protocol:
RNA was extractedfrom cultured cells using Direct-zol RNA Microprep Kit(ZYMO)
Illumina Stranded mRNA Prep Ligation Kit, 20040534

treatment_protocol: iNeurons (day 4) weretreated with CHX (200 μg/mL for 5 hours, three replicates in parallel with three DMSO controls) in 12-well plateswith 1 mL culture media in each well

tag: cell line

value: iNGN (P69)-derived neuron

tag: treatment

value: CHX


title: gastrocnemius caput lat, male, 58-5708-S1-NextRUN2

description: Library name: 58__gastrocnemius_caput_lat__5708__male__S1__NextRUN2

value: m. gastrocnemius caput laterale

value: Musculus gastrocnemius caput laterale


title: gastrocnemius caput mediale, female, 59-5489-S6-NextRUN13

description: Library name: 59__gastrocnemius_caput_mediale__5489__female__S6__NextRUN13

value: female


title: gastrocnemius caput lat, male, 58-5709-S2-NextRUN20

description: Library name: 58__gastrocnemius_caput_lat__5709__male__S2__NextRUN20


title: gastrocnemius caput lat, female, 58-5489-S8-NextRUN15

description: Library name: 58__gastrocnemius_caput_lat__5489__female__S8__NextRUN15


title: gracilis, male, 57-5879-S8-NextRUN10

description: Library name: 57__gracilis__5879__male__S8__NextRUN10

value: gracilis

value: m. gracilis

value: Musculus gracilis


title: hiPSC-derived-neuron_CHX_replicate_2

description:
Library name: iPSC-neuron_CHX rep2
iNeurons (day 4) weretreated with CHX (200 μg/mL for 5 hours), biological replicate 2


description: Library name: ENU56403B6G315_B11_neuro2008rep_S34_R1_2367729487


title: gracilis, female, 57-5489-S7-NextRUN9

description: Library name: 57__gracilis__5489__female__S7__NextRUN9


title: gracilis, male, 57-5708-S2-NextRUN14

description: Library name: 57__gracilis__5708__male__S2__NextRUN14

value: male


description: Library name: ENU56403B6G316_B10_neuro2008rep_S34_R1_2367728834


title: FHL, male, 56-5879-S2-NextRUN11

description: Library name: 56__FHL__5879__male__S2__NextRUN11

value: FHL

value: m. flexor hallucis longus

value: Musculus flexor hallucis longus


description: Library name: ENU56403B6G310_C1_neuro2008rep_S35_R1_2367729624


title: hiPSC-derived-neuron_CHX_replicate_1

description:
Library name: iPSC-neuron_CHX rep1
iNeurons (day 4) weretreated with CHX (200 μg/mL for 5 hours), biological replicate 1


title: super oblique, male, 5-5879-S1-NextRUN14

description: Library name: 5__super_oblique__5879__male__S1__NextRUN14

value: skeletal muscle

value: m. obliquus superior

value: Musculus obliquus superior

value: Eyes


title: FHL, male, 56-5709-S6-NextRUN20

description: Library name: 56__FHL__5709__male__S6__NextRUN20

value: Lower limbs


title: hiPSC-derived-neuron_DMSO_replicate_3

description:
Library name: iPSC-neuron_DMSO rep3
iNeurons (day 4) weretreated with DMSO for 5 hours, biological replicate 3

value: iNGN (P69)-derived neuron

value: DMSO


description: Library name: ENU56382B6G329_B1_neuro2008rep_S34_R1_2367728854

value: Whole brain

value: FALSE


title: FDL, male, 55-5879-S4-NextRUN12

description: Library name: 55__FDL__5879__male__S4__NextRUN12

value: FDL

value: m. flexor digitorum longus

value: Musculus flexor digitorum longus


title: FDL, male, 55-5708-S2-NextRUN13

description: Library name: 55__FDL__5708__male__S2__NextRUN13


title: hiPSC-derived-neuron_DMSO_replicate_1

description:
Library name: iPSC-neuron_DMSO rep1
iNeurons (day 4) weretreated with DMSO for 5 hours, biological replicate 1


description: Library name: ENU56363B6G315_B9_neuro2008rep_S34_R1_2367729281


title: hiPSC-derived-neuron_DMSO_replicate_2

description:
Library name: iPSC-neuron_DMSO rep2
iNeurons (day 4) weretreated with DMSO for 5 hours, biological replicate 2


title: EHL, male, 54-5879-S7-NextRUN10

description: Library name: 54__EHL__5879__male__S7__NextRUN10

value: EHL

value: m. extensor hallucis longus

value: Musculus extensor hallucis longus


title: FDL, male, 55-5709-S4-NextRUN21

description: Library name: 55__FDL__5709__male__S4__NextRUN21

value: male


title: EHL, female, 54-5489-S6-NextRUN1

description: Library name: 54__EHL__5489__female__S6__NextRUN1

value: female


title: EDL, male, 53-5879-S9-NextRUN10

description: Library name: 53__EDL__5879__male__S9__NextRUN10

value: skeletal muscle

value: EDL

value: m. extensor digitorum longus

value: Musculus extensor digitorum longus


description: Library name: ENU56351B6G38_E7_neuro2008rep_S37_R1_2367729488


description: Library name: ENU56363B6G316_B8_neuro2008rep_S34_R1_2367729752


title: 7dpa

city: Seattle

first: Avery

last: Angell Swearer

state: Washington

address: UW Box 357350, 1705 NE Pacific St.

department: Biochemistry

institute: University of Washington

description: Library name: 7dpa

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed thorugh CellRanger v9.01 Count and Aggregate to generate the filtered_feature_bc_matrix file. This file was processed using the Seurat v3.1 pipeline  in R Studio v4.4.3. Cells expressing < 200 genes were removed from downstream analysis, with a mitochondrial RNA read cutoff of 25%. The data was normalized then scaled by Sample and nFeature_RNA before clustering. Data was integrated by Sample using RPCA Integration. Three poor quality clusters indicated by a high percentage of cells with abnormally low UMI count (nFeature < 500) were manually removed. Cell cycle was predicted as previously described. Cell types were annotated using common cell markers as well as via analysis of differentially expressed cluster markers to generate the tail_final.rds. The neural dataset was subset based on the expression of sox2, pax6, and tubb2b in neural progenitors and/or neurons. The neural subset was re-normalized, scaled by Sample and nFeature_RNA, then integrated by Sample with RPCA. Five clusters were manually removed based on their presence in only one sample (1 cluster), their expression of sclerotome and/or muscle markers (3 clusters), or abnormally low UMI count (nFeature < 500) (1 cluster) to generate the neural_final.rds file.
Assembly: To generate the reference genome, the Xenopus tropicalis v10.0 reference genome and gene models were downloaded from Xenbase
Supplementary files format and content: The filtered_feature_bc_matrix folder is directly from the CellRanger output
Supplementary files format and content: The tail_final.rds file to be opened in Seurat. It contains clearly labeled columns detailing the Sample along with complete cell annotations.
Supplementary files format and content: The neural_final.rds file to be opened in Seurat, with the neural specific subset from the tail. It contains clearly labeled columns detailing the Sample along with complete cell annotations.

organism: Xenopus tropicalis

source_name: tail

extract_protocol:
Tail tissues were collected within 30 minutes of amputation and added to a vial with 72 µl trypLE (ThermoFisher Scientific:12604013) and 3 µl 100 mg/mL collagenase P (ROCHE:11213857001) for every 100 tail tissues. Samples were moved to a 28C water bath for dissociation and triturated with a p200 every 5 minutes until dissociated fully and no chunks was visible (30-60 minutes). To quench the reaction, 150 µl of ice cold 10% FBS was added for every 100 tail tissues. Samples were then spun down for 5 minutes at 1000xg. Supernatant was disposed and cells were resuspended in 300 µl 10% FBS for FACS. For each sample, 22-294 tadpoles were used (tail tip: 294 tadpoles; un1dpa: 222 tadpoles; un3dpa: 133 tadpoles; un7dpa: 22 tadpoles; mid-trunk: 294 tadpoles; 1dpa: 208 tadpoles; 3dpa: 144 tadpoles; 7dpa: 25 tadpoles). Tail tip and mid-trunk tissues were collected from the same specimens.  Cell sorting and collecting were performed with an Aria III Cell Sorter (BD Biosciences) and a 70 µm nozzle as previously described.32 Live singlets were sorted for based size and granularity with FSC and SSC. For GFP gate setting, initial setting was done with positive control transgenic Xtr.Et(eef1a1:GFP)16FMead tadpoles to test for GFP signal and autofluorescence. Selection areas were drawn to exclude most autofluorescent GFP- cells.
Cells were collected into 500 µl solutions of 1x PBS with 1 mg/ml BSA (NEB:B9200S) and counted with a Countess 3 FL Automated Cell Counter (ThermoFisher Scientific). Single-cell mRNA libraries were prepared using the GEM-X single cell 3’ v4 kit (10x Genomics), with a target capture of 10,000 cells. Quality control and quantification assays were performed using a Qubit fluorometer (Thermofisher) and a Screentape Assay (Agilent). Libraries were sequenced on an Illumina NextSeq2000 using a 100 cycle, P4 XLEAP-SBS™ kit. Each sample was sequenced to an average read depth of 226 million total reads, which resulted in an average read depth of ~28,000 reads/cell after normalization.

treatment_protocol: Tadpoles were anesthetized with 0.05% MS-222 in 1/9x MR and tested for response to touch prior to amputation surgery. Once fully anesthetized, a sterilized scalpel was used to amputate and collect intended tissue.

value: tail

tag: genotype


title: EDL, female, 53-5489-S5-NextRUN1

description: Library name: 53__EDL__5489__female__S5__NextRUN1

value: Lower limbs


title: EDL, male, 53-5709-S4-NextRUN19

description: Library name: 53__EDL__5709__male__S4__NextRUN19


description: Library name: ENU56270B6G39_B3_neuro2008rep_S34_R1_2367729148


title: EDB, male, 52-5709-S7-NextRUN18

description: Library name: 52__EDB__5709__male__S7__NextRUN18

value: EDB

value: m. extensor digitorum brevis

value: Musculus extensor digitorum brevis


title: 3dpa

description: Library name: 3dpa


title: EDB, female, 52-5489-S6-NextRUN9

description: Library name: 52__EDB__5489__female__S6__NextRUN9


title: mid-trunk

description: Library name: 0dpa

value: mid-trunk


title: 1dpa

description: Library name: 1dpa


title: adductor magnus, male, 50-5879-S5-NextRUN7

description: Library name: 50__adductor_magnus__5879__male__S5__NextRUN7

value: m. adductor magnus

value: Musculus adductor magnus


title: biceps femoris, male, 51_2-5879-S6-NextRUN7

description: Library name: 51_2__biceps_femoris__5879__male__S6__NextRUN7

value: m. biceps femoris

value: Musculus biceps femoris caput longum, Musculus biceps femoris caput breve


description: Library name: ENU56266B6G312_B7_neuro2008rep_S34_R1_2367729147

value: Whole brain

value: FALSE


title: infer rectus, female, 4-5489-S5-NextRUN19

description: Library name: 4__infer_rectus__5489__female__S5__NextRUN19

value: m. rectus inferior

value: Musculus rectus inferior

value: Eyes

value: female


title: infer rectus, male, 4-5708-S7-NextRUN14

description: Library name: 4__infer_rectus__5708__male__S7__NextRUN14

value: skeletal muscle

value: male


title: adductor magnus, male, 50-5708-S2-NextRUN6

description: Library name: 50__adductor_magnus__5708__male__S2__NextRUN6

value: Lower limbs


title: un3dpa

description: Library name: un3dpa

value: tail


description: Library name: ENU56104B6G36_D12_neuro2008rep_S36_R1_2367729352


title: un7dpa

description: Library name: un7dpa


title: un1dpa

description: Library name: un1dpa


description: Library name: ENU43055B6G2RN45_H4_neuro2008rep_S40_R1_2367728981

value: TRUE

value: Inpp5d W8X


description: Library name: ENU43055B6G2RN414_G12_neuro2008rep_S39_R1_2367729899


title: trapezius, male, 45-5879-S3-NextRUN7

description: Library name: 45__trapezius__5879__male__S3__NextRUN7

value: trapezius

value: m. trapezius

value: Musculus trapezius pars transversa, Musculus trapezius pars descendens, Musculus trapezius pars ascendens

value: Back


title: trapezius, male, 45-5708-S4-NextRUN16

description: Library name: 45__trapezius__5708__male__S4__NextRUN16


title: iliocostalis lumborum, male, 46-5709-S2-NextRUN19

description: Library name: 46__iliocostalis_lumborum__5709__male__S2__NextRUN19

value: m. spinalis lumbar

value: Musculus spinalis lumbar


title: serratus ant, male, 44-5879-S2-NextRUN7

description: Library name: 44__serratus_ant__5879__male__S2__NextRUN7

value: m. serratus anterior

value: Musculus serratus anterior

value: Chest


title: 4T1 Breast Cancer Cells treated with Blueberry Nanoparticle 1

city: Wilmington

first: Oladapo

middle: Fisoye

last: Fagbohun

state: OH

address: 1870 Quaker Way

department: Biology

institute: Wilmington College

description: Library name: BLUA1

data_processing:
Raw data were converted into FASTQ format, demultiplexed, and filtered for reads passing QC filters. Adapter and low-quality sequences were trimmed and only sequences with Q30 or higher quality were used.
RNA data
RNA high quality sequencing reads were subjected wo quality control to access base quality scores, GC content, and adapter contamination.
They were further trimmed to remove low-quality bases and sequencing adapters, followed alignment to the reference genome (GCA_000001635.9/27_GRCm39).
Raw RNA sequencing expression data were subjected to rigorous pre-processing to ensure analytical robustness. Transcripts with low expression levels (CPM)<1 were filtered out to eliminate noise and improve statistical power. The remaining data were normalized using the DESeq function within the DESeq2 R package (v. 1.36.0), with normalization parameters adjusted to account for biological treatment conditions associated with pathogen infection. A generalized linear model (GLM) design matrix was constructed to incorporate experimental conditions and relevant biological covariates.
Assembly: (GCA_000001635.9/27_GRCm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Mammary Gland

growth_protocol: 4T1 breast cancer cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested after treatment at the indicated point time in Trizol reagent. Total RNA was extracted via Norgen BiotekTM total RNA purification kit (Alkali Scientific, Fort Lauderdale, FL, USA). DNase treatment and RNA cleanup were performed on the extracted RNA samples to generate high RNA quality with RNA integrity number between 9.70 – 10. RNA samples were evaluated with Fluorometry by DeNovix QFX Fluorometer using the Qubit RNA BR Assay and the 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit.
mRNA libraries were prepared using the flowing reagents from QIASeq FastSelect RNA Lib HMR and QIA UX96 Index UDI-B (96) 331825 Kits (Qiagen Inc., Santa Clarita, CA, USA; Cat#: 334235) with primers N6-T RT and ODT-RT. The quality of the libraries was evaluated with fluorometry by DeNovix QFX fluorometer (DeNovix Inc., Wilmington, DE, USA; S/N: S-04083) and with 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA; S/N: DE72903137).

treatment_protocol: The cells were treated with BLA, BLU, BLAA, and BLUA after 24 hours of seeding.

value: Mammary Gland

tag: cell type

value: Breast Cancer

value: WT

value: Blueberry Nanoparticle Treated


title: serratus ant, male, 44-5708-S6-NextRUN5

description: Library name: 44__serratus_ant__5708__male__S6__NextRUN5

value: skeletal muscle

value: male


title: 4T1 Breast Cancer Cells treated with Blueberry Nanoparticle 2

description: Library name: BLUA2


title: 4T1 Breast Cancer Cells treated with Blueberry Nanoparticle 3

description: Library name: BLUA3


description: Library name: ENU56051B6G37_B2_neuro2008rep_S34_R1_2367729766

value: Whole brain

value: FALSE


title: adductor brev, male, 48-5879-S2-NextRUN8

description: Library name: 48__adductor_brev__5879__male__S2__NextRUN8

value: m. adductor brevis

value: Musculus adductor brevis

value: Lower limbs


description: Library name: ENU43055B6G2RN42_H3_neuro2008rep_S40_R1_2367729143

value: TRUE

value: Inpp5d W8X

value: m/m


title: longissimus thoracis, male, 47-5709-S1-NextRUN20

description: Library name: 47__longissimus_thoracis__5709__male__S1__NextRUN20

value: m. spinalis torcis

value: Musculus spinalis torcis

value: Back


title: rhomboideus, male, 43-5879-S1-NextRUN11

description: Library name: 43__rhomboideus__5879__male__S1__NextRUN11

value: rhomboideus

value: m. rhomboideus

value: Musculus rhomboideus major, Musculus rhomboideus minor


title: adductor long, male, 49-5879-S4-NextRUN7

description: Library name: 49__adductor_long__5879__male__S4__NextRUN7

value: m. adductor longus

value: Musculus adductor longus


title: serratus ant, female, 44-5489-S5-NextRUN18

description: Library name: 44__serratus_ant__5489__female__S5__NextRUN18

value: skeletal muscle

value: m. serratus anterior

value: Musculus serratus anterior

value: Chest

value: female


description: Library name: ENU43055B6G2RN413_G11_neuro2008rep_S39_R1_2367728919

value: Whole brain


title: rhomboideus, male, 43-5708-S4-NextRUN14

description: Library name: 43__rhomboideus__5708__male__S4__NextRUN14

value: male


title: 4T1 Breast Cancer Cells treated with Blackberry Nanoparticle 3

description: Library name: BLAA3

value: Mammary Gland

value: Breast Cancer

value: WT

value: Blackberry Nanoparticle Treated


title: psoas, male, 42-5879-S1-NextRUN7

description: Library name: 42__psoas__5879__male__S1__NextRUN7

value: psoas

value: m. psoas major

value: Musculus psoas major

value: Lower limbs


description: Library name: ENU43055B6G2RN367_H12_neuro2008rep_S40_R1_2367729508

value: TRUE

value: Inpp5d W8X


description: Library name: ENU43055B6G2RN363_H5_neuro2008rep_S40_R1_2367729814

value: m/m


title: Blueberry treated 4T1 Breast Cancer Cells 3

description: Library name: BLU3

value: Blueberry Treated


description: Library name: ENU43055B6G2RN362_H10_neuro2008rep_S40_R1_2367729436


title: psoas, male, 42-5709-S2-NextRUN21

description: Library name: 42__psoas__5709__male__S2__NextRUN21

value: skeletal muscle


title: Blueberry treated 4T1 Breast Cancer Cells 1

description: Library name: BLU1


title: psoas, female, 42-5489-S5-NextRUN9

description: Library name: 42__psoas__5489__female__S5__NextRUN9


description: Library name: ENU43055B6G2RN360_H8_neuro2008rep_S40_R1_2367729400


title: latissimus dorsi, male, 40-5879-S1-NextRUN8

description: Library name: 40__latissimus_dorsi__5879__male__S1__NextRUN8

value: m. latissimus dorsi

value: Musculus latissimus dorsi

value: Back


title: super rectus, female, 3-5489-S6-NextRUN21

description: Library name: 3__super_rectus__5489__female__S6__NextRUN21

value: m. rectus superior

value: Musculus rectus superior

value: Eyes

value: female


description: Library name: ENU43055B6G2RN364_H6_neuro2008rep_S40_R1_2367729675

value: Whole brain


title: Blackberry treated 4T1 Breast Cancer Cells 3

description: Library name: BLA3

value: Mammary Gland

value: Breast Cancer

value: WT

value: Blackberry Treated


title: intercostales, male, 39-5708-S5-NextRUN3

description: Library name: 39__intercostales__5708__male__S5__NextRUN3

value: intercostales

value: mm. intercostales

value: Musculi intercostales externi, Musculi intercostales interni, Musculi intercostales intimi

value: Chest

value: male


title: pectoralis major, male, 41-5708-S1-NextRUN6

description: Library name: 41__pectoralis_major__5708__male__S1__NextRUN6

value: skeletal muscle

value: m. pectoralis major

value: Musculus pectoralis major pars sternocostalis, Musculus pectoralis major pars clavicularis, Musculus pectoralis major pars abdominalis


title: 4T1 Breast Cancer Cells treated with Blackberry Nanoparticle 1

description: Library name: BLAA1

value: Blackberry Nanoparticle Treated


title: 4T1 Breast Cancer Cells treated with Blackberry Nanoparticle 2

description: Library name: BLAA2


title: super rectus, male, 3-5709-S1-NextRUN21

description: Library name: 3__super_rectus__5709__male__S1__NextRUN21

value: m. rectus superior

value: Musculus rectus superior


title: super rectus, male, 3-5879-S4-NextRUN11

description: Library name: 3__super_rectus__5879__male__S4__NextRUN11

value: Eyes


description: Library name: ENU43055B6G2RN366_H11_neuro2008rep_S40_R1_2367729566

value: Whole brain

value: TRUE

value: Inpp5d W8X


title: intercostales, male, 39-5879-S6-NextRUN6

description: Library name: 39__intercostales__5879__male__S6__NextRUN6


title: pectoralis major, male, 41-5709-S5-NextRUN20

description: Library name: 41__pectoralis_major__5709__male__S5__NextRUN20


title: intercostales, female, 39-5489-S4-NextRUN1

description: Library name: 39__intercostales__5489__female__S4__NextRUN1

value: female


title: Blueberry treated 4T1 Breast Cancer Cells 2

description: Library name: BLU2

value: Mammary Gland

value: Breast Cancer

value: WT

value: Blueberry Treated


title: latissimus dorsi, male, 40-5708-S6-NextRUN17

description: Library name: 40__latissimus_dorsi__5708__male__S6__NextRUN17

value: m. latissimus dorsi

value: Musculus latissimus dorsi

value: Back


description: Library name: ENU43055B6G2RN361_H9_neuro2008rep_S40_R1_2367729369


title: subscapularis, male, 38-5879-S3-NextRUN17

description: Library name: 38__subscapularis__5879__male__S3__NextRUN17

value: skeletal muscle

value: subscapularis

value: m. subscapularis

value: Musculus subscapularis

value: Upper limbs

value: male


description: Library name: ENU43055B6G2RN358_H7_neuro2008rep_S40_R1_2367729018

value: Whole brain


title: Blackberry treated 4T1 Breast Cancer Cells 2

description: Library name: BLA2

value: Blackberry Treated


description: Library name: ENU43055B6G2RN357_G10_neuro2008rep_S39_R1_2367729818

value: TRUE

value: Inpp5d W8X


title: diaphragm, male, 36-5879-S2-NextRUN17

description: Library name: 36__diaphragm__5879__male__S2__NextRUN17

value: diaphragm

value: diaphragma

value: Diaphragma

value: Diaphragm


title: rectus abdominis, male, 37-5708-S1-NextRUN13

description: Library name: 37__rectus_abdominis__5708__male__S1__NextRUN13

value: m. rectus abdominis

value: Musculus rectus abdominis

value: Abdominal


title: Blackberry treated 4T1 Breast Cancer Cells 1

description: Library name: BLA1

value: Mammary Gland

value: Breast Cancer

value: WT


title: diaphragm, male, 36-5708-S5-NextRUN16

description: Library name: 36__diaphragm__5708__male__S5__NextRUN16

value: skeletal muscle


title: Untreated 4T1 Breast Cancer Cells 2

description: Library name: 4T1C2

value: Untreated


description: Library name: ENU43055B6G2RN356_G9_neuro2008rep_S39_R1_2367729050


title: diaphragm, female, 36-5489-S3-NextRUN1

description: Library name: 36__diaphragm__5489__female__S3__NextRUN1

value: female


description: Library name: ENU43055B6G2RN355_G8_neuro2008rep_S39_R1_2367729152

value: Whole brain

value: m/m


title: Untreated 4T1 Breast Cancer Cells 3

description: Library name: 4T1C3


title: FCU, male, 34-5879-S8-NextRUN6

description: Library name: 34__FCU__5879__male__S8__NextRUN6

value: FCU

value: m. flexor carpi ulnaris

value: Musculus flexor carpi ulnaris caput humerale, Musculus flexor carpi ulnaris caput ulnare

value: Upper limbs

value: male


description: Library name: ENU43055B6G2RN354_G7_neuro2008rep_S39_R1_2367729271

value: TRUE

value: Inpp5d W8X


title: subscapularis, male, 38-5708-S3-NextRUN14

description: Library name: 38__subscapularis__5708__male__S3__NextRUN14

value: subscapularis

value: m. subscapularis

value: Musculus subscapularis


title: rectus abdominis, male, 37-5879-S8-NextENC3

description: Library name: 37__rectus_abdominis__5879__male__S8__NextENC3

value: m. rectus abdominis

value: Musculus rectus abdominis

value: Abdominal


title: FDMB, male, 35-5879-S7-NextENC3

description: Library name: 35__FDMB__5879__male__S7__NextENC3

value: skeletal muscle

value: FDMB

value: m. flexor digiti minimi brevis

value: Musculus flexor digiti minimi brevis


title: ECRB, male, 33-5879-S8-NextRUN1

description: Library name: 33__ECRB__5879__male__S8__NextRUN1

value: ECRB

value: m. extensor carpi radialis brevis

value: Musculus extensor carpi radialis brevis


title: Untreated 4T1 Breast Cancer Cells 1

description: Library name: 4T1C1

value: Mammary Gland

value: Breast Cancer

value: WT

value: Untreated


title: FDS, male, 32-5879-S7-NextRUN6

description: Library name: 32__FDS__5879__male__S7__NextRUN6

value: FDS

value: m. flexor digitorum superficialis

value: Musculus flexor digitorum superficialis caput humeroulnare, Musculus flexor digitorum superficialis caput radiale

value: Upper limbs

value: male


description: Library name: ENU43055B6G2RN353_G6_neuro2008rep_S39_R1_2367729857

value: Whole brain

value: TRUE

value: Inpp5d W8X


title: FDS, male, 32-5709-S4-NextRUN20

description: Library name: 32__FDS__5709__male__S4__NextRUN20

value: skeletal muscle


title: FCR, male, 31-5879-S5-NextRUN6

description: Library name: 31__FCR__5879__male__S5__NextRUN6

value: FCR

value: m. flexor carpi radialis

value: Musculus flexor carpi radialis


title: FCR, male, 31-5709-S3-NextRUN20

description: Library name: 31__FCR__5709__male__S3__NextRUN20


title: brachialis, male, 30-5879-S3-NextRUN12

description: Library name: 30__brachialis__5879__male__S3__NextRUN12

value: brachialis

value: m. brachialis

value: Musculus brachialis


description: Library name: ENU43055B6G2RN349_H2_neuro2008rep_S40_R1_2367729192

value: m/m


title: brachialis, male, 30-5708-S8-NextRUN5

description: Library name: 30__brachialis__5708__male__S8__NextRUN5


title: nlp67_-K_2

type: RNA

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

country: Japan

institute: The University of Tokyo

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: root tissues from 9 day-old wild-type and dof1.7-KO seedlings grown under potassium-sufficient and potassium-defficient conditions

tag: agent

value: deficient potassium


title: anconeus, male, 29_2-5879-S6-NextRUN15

description: Library name: 29_2__anconeus__5879__male__S6__NextRUN15

value: anconeus

value: m. anconeus

value: Musculus anconeus


description: Library name: ENU43055B6G2RN349_G5_neuro2008rep_S39_R1_2367728908


description: Library name: ENU43055B6G2RN348_G4_neuro2008rep_S39_R1_2367729090


title: anconeus, male, 29_2-5708-S8-NextRUN12

description: Library name: 29_2__anconeus__5708__male__S8__NextRUN12

value: Upper limbs


title: nlp67_-K_3


description: Library name: ENU43055B6G2RN347_G3_neuro2008rep_S39_R1_2367729083


title: SIBL, male, 29_1-5708-S8-NextRUN19

description: Library name: 29_1__SIBL__5708__male__S8__NextRUN19

value: SIBL

value: septum intermusculare brachii laterale

value: Septum intermusculare brachii laterale

value: male


title: SIBL, male, 29_1-5879-S7-NextRUN15

description: Library name: 29_1__SIBL__5879__male__S7__NextRUN15

value: skeletal muscle


title: anconeus, female, 29_2-5489-S3-NextRUN18

description: Library name: 29_2__anconeus__5489__female__S3__NextRUN18

value: female


description: Library name: ENU43055B6G2RN341_H1_neuro2008rep_S40_R1_2367728942

value: Whole brain

value: TRUE

value: Inpp5d W8X


title: nlp67_-K_1


title: triceps brachii, male, 28-5879-S7-NextRUN4

description: Library name: 28__triceps_brachii__5879__male__S7__NextRUN4

value: m. triceps brachii

value: Musculus triceps brachii caput mediale, Musculus triceps brachii caput longum, Musculus triceps brachii caput laterale


title: SIBL, female, 29_1-5489-S4-NextRUN18

description: Library name: 29_1__SIBL__5489__female__S4__NextRUN18


description: Library name: ENU43040B6G2RN59_G12_neuro2222_S55_R1_2367729586


title: Col-0_-K_2


title: nlp67_+K_3

value: sufficient potassium


title: interossei palmares, male, 27-5879-S6-NextRUN4

description: Library name: 27__interossei_palmares__5879__male__S6__NextRUN4

value: mm. interossei palmares

value: Musculi interossei palmares


title: triceps brachii, female, 28-5489-S5-NextRUN13

description: Library name: 28__triceps_brachii__5489__female__S5__NextRUN13


title: Col-0_-K_3

value: deficient potassium


description: Library name: ENU43040B6G2RN56_G10_neuro2222_S55_R1_2367728976


title: interossei palmares, male, 27-5708-S2-NextRUN10

description: Library name: 27__interossei_palmares__5708__male__S2__NextRUN10


title: ODM, male, 25-5879-S5-NextRUN15

description: Library name: 25__ODM__5879__male__S5__NextRUN15

value: ODM

value: m. opponens digiti minimi

value: Musculus opponens digiti minimi


title: nlp67_+K_2


description: Library name: ENU43040B6G2RN55_G9_neuro2222_S55_R1_2367729240


title: opponens pollicis, male, 26-5708-S7-NextRUN12

description: Library name: 26__opponens_pollicis__5708__male__S7__NextRUN12

value: m. opponens pollicis

value: Musculus opponens pollicis

value: Upper limbs


title: opponens pollicis, male, 26-5879-S8-NextRUN3

description: Library name: 26__opponens_pollicis__5879__male__S8__NextRUN3

value: skeletal muscle

value: male


description: Library name: ENU43040B6G2RN54_G8_neuro2222_S55_R1_2367729121

value: Whole brain


title: Col-0_-K_1


title: pronator teres, male, 23_3-5879-S4-NextRUN15

description: Library name: 23_3__pronator_teres__5879__male__S4__NextRUN15

value: m. pronator teres

value: Musculus pronator teres caput humerale, Musculus pronator teres caput ulnare


description: Library name: ENU43040B6G2RN544_H12_neuro2222_S56_R1_2367729257

value: TRUE


description: Library name: ENU56266B6G322_B6_neuro2008rep_S34_R1_2367728897

value: FALSE


description: Library name: ENU56266B6G321_B5_neuro2008rep_S34_R1_2367729878


title: ODM, female, 25-5489-S4-NextRUN9

description: Library name: 25__ODM__5489__female__S4__NextRUN9

value: female


title: lumbricales, male, 24-5879-S5-NextRUN4

description: Library name: 24__lumbricales__5879__male__S5__NextRUN4

value: lumbricales

value: mm. lumbricales

value: Musculi lumbricales


title: pronator quadratus, male, 23_2_e1-5879-S2-NextRUN12

description: Library name: 23_2_e1__pronator_quadratus__5879__male__S2__NextRUN12

value: m. pronator quadratus

value: Musculus pronator quadratus


title: nlp67_+K_1

value: sufficient potassium


title: adductor brev, female, 48-5489-S2-NextRUN18

description: Library name: 48__adductor_brev__5489__female__S2__NextRUN18

value: m. adductor brevis

value: Musculus adductor brevis

value: Lower limbs


title: lingua, male, 9-5708-S10-NovaRUN1

description: Library name: 9__lingua__5708__male__S10__NovaRUN1

value: skeletal muscle

value: lingua

value: Lingua

value: Tongue


description: Library name: ENU43040B6G2RN58_G11_neuro2222_S55_R1_2367729554

value: Whole brain


title: Col-0_+K_1


title: biceps femoris, male, 51_1-5879-S6-NextRUN10

description: Library name: 51_1__biceps_femoris__5879__male__S6__NextRUN10

value: m. biceps femoris

value: Musculus biceps femoris caput longum, Musculus biceps femoris caput breve

value: male


title: pronator quadratus, female, 23_2_e1-5489-S1-NextRUN18

description: Library name: 23_2_e1__pronator_quadratus__5489__female__S1__NextRUN18

value: Upper limbs

value: female


description: Library name: ENU43040B6G2RN543_H11_neuro2222_S56_R1_2367728812

value: TRUE


title: palmaris long, male, 23_1-5708-S1-NextRUN10

description: Library name: 23_1__palmaris_long__5708__male__S1__NextRUN10

value: m. palmaris longus

value: Musculus palmaris longus


description: Library name: ENU43040B6G2RN541_H9_neuro2222_S56_R1_2367729263


description: Library name: ENU43040B6G2RN542_H10_neuro2222_S56_R1_2367729614


title: palmaris long, male, 23_1-5879-S3-NextRUN4

description: Library name: 23_1__palmaris_long__5879__male__S3__NextRUN4


title: FPB, male, 22-5708-S10-NextRUN9

description: Library name: 22__FPB__5708__male__S10__NextRUN9

value: FPB

value: m. flexor pollicis brevis

value: Musculus flexor pollicis brevis caput superficiale, Musculus flexor pollicis brevis caput profundum


title: FPB, male, 22-5879-S2-NextRUN4

description: Library name: 22__FPB__5879__male__S2__NextRUN4


title: pterygoideus lat, male, 7-5708-S9-NovaRUN1

description: Library name: 7__pterygoideus_lat__5708__male__S9__NovaRUN1

value: m. pterygoideus lateralis

value: Musculus pterygoideus lateralis caput inferius, Musculus pterygoideus lateralis caput superius

value: Head


title: gluteus med, female, 73-5489-S34-NovaRUN1

description: Library name: 73__gluteus_med__5489__female__S34__NovaRUN1

value: skeletal muscle

value: m. gluteus medius

value: Musculus gluteus medius

value: Lower limbs


title: Col-0_+K_3

value: sufficient potassium


title: FPB, female, 22-5489-S2-NextRUN1

description: Library name: 22__FPB__5489__female__S2__NextRUN1


description: Library name: ENU43040B6G2RN540_H8_neuro2222_S56_R1_2367729320

value: Whole brain


title: gluteus med, male, 73-5708-S14-NovaRUN1

description: Library name: 73__gluteus_med__5708__male__S14__NovaRUN1

value: male


title: FDP, male, 21-5708-S4-NextRUN5

description: Library name: 21__FDP__5708__male__S4__NextRUN5

value: FDP

value: m. flexor digitorum profundus

value: Musculus flexor digitorum profundus

value: Upper limbs


title: FDP, male, 21-5879-S1-NextRUN4

description: Library name: 21__FDP__5879__male__S1__NextRUN4


title: FDP, female, 21-5489-S7-NextRUN11

description: Library name: 21__FDP__5489__female__S7__NextRUN11

value: female


title: vastus medial, female, 71-5489-S33-NovaRUN1

description: Library name: 71__vastus_medial__5489__female__S33__NovaRUN1

value: m. vastus medialis

value: Musculus vastus medialis


description: Library name: ENU43040B6G2RN539_H7_neuro2222_S56_R1_2367729821

value: TRUE


title: interossei dors, male, 20-5879-S1-NextRUN12

description: Library name: 20__interossei_dors__5879__male__S1__NextRUN12

value: m. interossei dorsales

value: Musculus interossei dorsales


title: soleus, male, 66-5708-S20-NovaRUN1

description: Library name: 66__soleus__5708__male__S20__NovaRUN1

value: skeletal muscle

value: soleus

value: m. soleus

value: Musculus soleus


title: super oblique, female, 5-5489-S28-NovaRUN1

description: Library name: 5__super_oblique__5489__female__S28__NovaRUN1

value: m. obliquus superior

value: Musculus obliquus superior

value: Eyes


title: medial rectus, male, 1-5879-S1-NextRUN5

description: Library name: 1__medial_rectus__5879__male__S1__NextRUN5

value: m. rectus medialis

value: Musculus rectus medialis

value: male


title: interossei dors, female, 20-5489-S3-NextRUN9

description: Library name: 20__interossei_dors__5489__female__S3__NextRUN9

value: Upper limbs


description: Library name: ENU43040B6G2RN53_G7_neuro2222_S55_R1_2367729676

value: Whole brain


description: Library name: ENU43040B6G2RN52_G4_neuro2222_S55_R1_2367729714


title: deltoideus, male, 19-5879-S8-NextRUN16

description: Library name: 19__deltoideus__5879__male__S8__NextRUN16

value: deltoideus

value: m. deltoideus

value: Musculus deltoideus pars acromialis, Musculus deltoideus pars clavicularis, Musculus deltoideus pars spinalis


title: biceps femoris, male, 51_1-5708-S27-NovaRUN1

description: Library name: 51_1__biceps_femoris__5708__male__S27__NovaRUN1

value: m. biceps femoris

value: Musculus biceps femoris caput longum, Musculus biceps femoris caput breve

value: Lower limbs


title: medial rectus, female, 1-5489-S5-NextRUN21

description: Library name: 1__medial_rectus__5489__female__S5__NextRUN21

value: skeletal muscle

value: female


title: deltoideus, female, 19-5489-S6-NextRUN14

description: Library name: 19__deltoideus__5489__female__S6__NextRUN14


title: Col-0_+K_2

value: sufficient potassium


title: EHL, male, 54-5708-S19-NovaRUN1

description: Library name: 54__EHL__5708__male__S19__NovaRUN1

value: EHL

value: m. extensor hallucis longus

value: Musculus extensor hallucis longus


description: Library name: ENU43040B6G2RN525_H5_neuro2222_S56_R1_2367728794

value: TRUE


title: deltoideus, male, 19-5708-S6-NextRUN12

description: Library name: 19__deltoideus__5708__male__S6__NextRUN12


title: brachioradialis, male, 18-5879-S7-NextRUN16

description: Library name: 18__brachioradialis__5879__male__S7__NextRUN16

value: brachioradialis

value: m. brachioradialis

value: Musculus brachioradialis


description: Library name: ENU43040B6G2RN526_H6_neuro2222_S56_R1_2367729222

value: Whole brain


title: adductor brev, male, 48-5708-S13-NovaRUN1

description: Library name: 48__adductor_brev__5708__male__S13__NovaRUN1

value: m. adductor brevis

value: Musculus adductor brevis

value: male


description: Library name: ENU43040B6G2RN524_H4_neuro2222_S56_R1_2367729423


title: biceps brachii, female, 17_2-5489-S2-NextRUN9

description: Library name: 17_2__biceps_brachii__5489__female__S2__NextRUN9

value: m. biceps brachii

value: Musculus biceps brachii caput longum, Musculus biceps brachii caput brevis

value: Upper limbs


title: adductor long, male, 49-5708-S26-NovaRUN1

description: Library name: 49__adductor_long__5708__male__S26__NovaRUN1

value: skeletal muscle

value: m. adductor longus

value: Musculus adductor longus

value: Lower limbs


title: biceps brachii, male, 17_2-5879-S1-NextRUN17

description: Library name: 17_2__biceps_brachii__5879__male__S1__NextRUN17


description: Library name: ENU43040B6G2RN522_G5_neuro2222_S55_R1_2367729024


title: longissimus thoracis, male, 47-5708-S25-NovaRUN1

description: Library name: 47__longissimus_thoracis__5708__male__S25__NovaRUN1

value: m. spinalis torcis

value: Musculus spinalis torcis

value: Back


title: adductor pollicis, male, 16-5879-S3-NextRUN5

description: Library name: 16__adductor_pollicis__5879__male__S3__NextRUN5

value: m. adductor pollicis

value: Musculus adductor pollicis caput transversum, Musculus adductor pollicis caput obliquum


title: biceps brachii, male, 17_1-5879-S8-NextRUN2

description: Library name: 17_1__biceps_brachii__5879__male__S8__NextRUN2


title: adductor pollicis, female, 16-5489-S1-NextRUN1

description: Library name: 16__adductor_pollicis__5489__female__S1__NextRUN1

value: female


description: Library name: ENU43040B6G2RN523_G6_neuro2222_S55_R1_2367729736

value: Whole brain

value: TRUE


title: abductor pollicis, male, 15-5879-S7-NextRUN2

description: Library name: 15__abductor_pollicis__5879__male__S7__NextRUN2

value: m. abductor pollicis

value: Musculus abductor pollicis brevis


title: longissimus thoracis, female, 47-5489-S8-NovaRUN1

description: Library name: 47__longissimus_thoracis__5489__female__S8__NovaRUN1


title: ADM, male, 14-5879-S6-NextRUN2

description: Library name: 14__ADM__5879__male__S6__NextRUN2

value: ADM

value: m. abductor digiti minimi

value: Musculus abductor digiti minimi

value: male


description: Library name: ENU43040B6G2RN521_H3_neuro2222_S56_R1_2367729277


description: Library name: ENU43040B6G2RN520_H2_neuro2222_S56_R1_2367729118


title: iliocostalis lumborum, male, 46-5708-S24-NovaRUN1

description: Library name: 46__iliocostalis_lumborum__5708__male__S24__NovaRUN1

value: skeletal muscle

value: m. spinalis lumbar

value: Musculus spinalis lumbar


title: ADM, male, 14-5708-S9-NextRUN9

description: Library name: 14__ADM__5708__male__S9__NextRUN9

value: Upper limbs


description: Library name: ENU43040B6G2RN51_G3_neuro2222_S55_R1_2367729334


title: ADM, male, 14-5709-S3-NextRUN19

description: Library name: 14__ADM__5709__male__S3__NextRUN19


description: Library name: ENU43040B6G2RN518_G2_neuro2222_S55_R1_2367728938


title: RCP major, male, 12-5708-S5-NextRUN10

description: Library name: 12__RCP_major__5708__male__S5__NextRUN10

value: m. rectus capitis posterior major

value: Musculus rectus capitis posterior major

value: Neck


title: RCP major, female, 12-5489-S4-NextRUN13

description: Library name: 12__RCP_major__5489__female__S4__NextRUN13


title: RCP major, male, 12-5879-S5-NextRUN2

description: Library name: 12__RCP_major__5879__male__S5__NextRUN2


title: RCP minor, male, 13-5879-S8-NextRUN4

description: Library name: 13__RCP_minor__5879__male__S8__NextRUN4

value: m. rectus capitis posterior minor

value: Musculus rectus capitis posterior minor


title: latissimus dorsi, female, 40-5489-S5-NovaRUN1

description: Library name: 40__latissimus_dorsi__5489__female__S5__NovaRUN1

value: m. latissimus dorsi

value: Musculus latissimus dorsi

value: Back

value: female


description: Library name: ENU43040B6G2RN517_G1_neuro2222_S55_R1_2367729099

value: Whole brain

value: TRUE


title: pectoralis major, female, 41-5489-S6-NovaRUN1

description: Library name: 41__pectoralis_major__5489__female__S6__NovaRUN1

value: m. pectoralis major

value: Musculus pectoralis major pars sternocostalis, Musculus pectoralis major pars clavicularis, Musculus pectoralis major pars abdominalis

value: Chest


description: Library name: ENU43040B6G2RN516_F12_neuro2222_S54_R1_2367729748


title: longissimus cervicis, male, 10-5879-S4-NextRUN2

description: Library name: 10__longissimus_cervicis__5879__male__S4__NextRUN2

value: skeletal muscle

value: m. paraspinalis сervical

value: Musculus paraspinalis сervical

value: male


title: Intestine_4

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: Sample 22

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: intestine

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and max. 10ng used of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit following manufacture’s protocol (Takara Bio).

treatment_protocol: Activation of CreER or DreER was achieved by intraperitoneal injection of 0.75 mg tamoxifen per 10g body weight  for three days. Tamoxifen was dissolved in corn oil at a concentration of 20mg/mL.

value: intestine

value: arterial smooth muscle cells

value: Tamoxifen


title: SCM, male, 11-5708-S7-NextRUN17

description: Library name: 11__SCM__5708__male__S7__NextRUN17

value: SCM

value: m. sternocleidomastoideus

value: Musculus sternocleidomastoideus

value: Neck


title: subscapularis, female, 38-5489-S4-NovaRUN1

description: Library name: 38__subscapularis__5489__female__S4__NovaRUN1

value: subscapularis

value: m. subscapularis

value: Musculus subscapularis

value: Upper limbs

value: female


title: rhomboideus, female, 43-5489-S7-NovaRUN1

description: Library name: 43__rhomboideus__5489__female__S7__NovaRUN1

value: rhomboideus

value: m. rhomboideus

value: Musculus rhomboideus major, Musculus rhomboideus minor

value: Back


title: rectus abdominis, female, 37-5489-S3-NovaRUN1

description: Library name: 37__rectus_abdominis__5489__female__S3__NovaRUN1

value: skeletal muscle

value: m. rectus abdominis

value: Musculus rectus abdominis

value: Abdominal


title: Intestine_3

description: Library name: Sample 21

value: intestine

value: arterial smooth muscle cells

value: Tamoxifen


title: Intestine_2

description: Library name: Sample 20


title: SCM, male, 11-5879-S6-NextRUN18

description: Library name: 11__SCM__5879__male__S6__NextRUN18

value: SCM

value: m. sternocleidomastoideus

value: Musculus sternocleidomastoideus

value: Neck

value: male


title: Intestine_1

description: Library name: Sample 19


description: Library name: ENU43040B6G2RN515_F11_neuro2222_S54_R1_2367729507

value: Whole brain

value: TRUE


description: Library name: ENU43040B6G2RN514_F10_neuro2222_S54_R1_2367729788


title: Heart_3

description: Library name: Sample 18

source_name: heart

value: heart


title: Heart_2

description: Library name: Sample 17


description: Library name: ENU43040B6G2RN513_F9_neuro2222_S54_R1_2367729622


title: Heart_1

description: Library name: Sample 16


title: Stomach_3

description: Library name: Sample 15

source_name: stomach

value: stomach


title: FDMB, male, 35-5708-S23-NovaRUN1

description: Library name: 35__FDMB__5708__male__S23__NovaRUN1

value: FDMB

value: m. flexor digiti minimi brevis

value: Musculus flexor digiti minimi brevis

value: Upper limbs


title: FCU, male, 34-5708-S22-NovaRUN1

description: Library name: 34__FCU__5708__male__S22__NovaRUN1

value: skeletal muscle

value: FCU

value: m. flexor carpi ulnaris

value: Musculus flexor carpi ulnaris caput humerale, Musculus flexor carpi ulnaris caput ulnare


title: Stomach_2

description: Library name: Sample 14

value: arterial smooth muscle cells

value: Tamoxifen


description: Library name: ENU43040B6G2RN512_F8_neuro2222_S54_R1_2367729666


title: Lung_3

description: Library name: Sample 12

source_name: lung

value: lung


title: Stomach_1

description: Library name: Sample 13


description: Library name: ENU43040B6G2RN511_F7_neuro2222_S54_R1_2367729527


title: Kidney_3

description: Library name: Sample 9

source_name: kidney

value: kidney


title: FCU, female, 34-5489-S1-NovaRUN1

description: Library name: 34__FCU__5489__female__S1__NovaRUN1

value: female


title: Lung_1

description: Library name: Sample 10


description: Library name: ENU43040B6G2RN510_H1_neuro2222_S56_R1_2367729422

value: Whole brain


title: FDS, male, 32-5708-S21-NovaRUN1

description: Library name: 32__FDS__5708__male__S21__NovaRUN1

value: FDS

value: m. flexor digitorum superficialis

value: Musculus flexor digitorum superficialis caput humeroulnare, Musculus flexor digitorum superficialis caput radiale

value: male


title: FDMB, female, 35-5489-S2-NovaRUN1

description: Library name: 35__FDMB__5489__female__S2__NovaRUN1

value: FDMB

value: m. flexor digiti minimi brevis


title: brachialis, female, 30-5489-S32-NovaRUN1

description: Library name: 30__brachialis__5489__female__S32__NovaRUN1

value: brachialis

value: m. brachialis

value: Musculus brachialis

value: Upper limbs


title: ECRB, male, 33-5708-S12-NovaRUN1

description: Library name: 33__ECRB__5708__male__S12__NovaRUN1

value: skeletal muscle

value: ECRB

value: m. extensor carpi radialis brevis

value: Musculus extensor carpi radialis brevis


title: Kidney_2

description: Library name: Sample 8

value: kidney

value: arterial smooth muscle cells

value: Tamoxifen


title: Bladder_3

description: Library name: Sample 6

source_name: bladder

value: bladder


title: Kidney_1

description: Library name: Sample 7


title: Lung_2

description: Library name: Sample 11

value: lung


description: Library name: ENU43040B6G2RN449_F5_neuro2222_S54_R1_2367729184

value: Whole brain

value: TRUE


description: Library name: ENU43040B6G2RN450_F6_neuro2222_S54_R1_2367729077


title: triceps brachii, male, 28-5708-S18-NovaRUN1

description: Library name: 28__triceps_brachii__5708__male__S18__NovaRUN1

value: m. triceps brachii

value: Musculus triceps brachii caput mediale, Musculus triceps brachii caput longum, Musculus triceps brachii caput laterale

value: male


title: soleus, female, 66-5489-S63-HiRUN42

description: Library name: 66__soleus__5489__female__S63__HiRUN42

value: soleus

value: m. soleus

value: Musculus soleus

value: Lower limbs

value: female


description: Library name: ENU43040B6G2RN444_F4_neuro2222_S54_R1_2367728859


title: Aorta_3

description: Library name: Sample 3

source_name: aorta

value: aorta


description: Library name: ENU43040B6G2RN443_F3_neuro2222_S54_R1_2367729153


title: Bladder_2

description: Library name: Sample 5


title: Aorta_2

description: Library name: Sample 2


title: ODM, male, 25-5708-S17-NovaRUN1

description: Library name: 25__ODM__5708__male__S17__NovaRUN1

value: skeletal muscle

value: ODM

value: m. opponens digiti minimi

value: Musculus opponens digiti minimi

value: Upper limbs


title: interossei palmares, female, 27-5489-S31-NovaRUN1

description: Library name: 27__interossei_palmares__5489__female__S31__NovaRUN1

value: mm. interossei palmares

value: Musculi interossei palmares


title: peroneus long, female, 61-5489-S62-HiRUN42

description: Library name: 61__peroneus_long__5489__female__S62__HiRUN42

value: m. peroneus longus

value: Musculus peroneus longus


title: lumbricales, male, 24-5708-S11-NovaRUN1

description: Library name: 24__lumbricales__5708__male__S11__NovaRUN1

value: lumbricales

value: mm. lumbricales

value: Musculi lumbricales


description: Library name: ENU43040B6G2RN441_F1_neuro2222_S54_R1_2367729493

value: Whole brain

value: TRUE


title: peroneus brev, female, 60-5489-S61-HiRUN42

description: Library name: 60__peroneus_brev__5489__female__S61__HiRUN42

value: m. peroneus brevis

value: Musculus peroneus brevis

value: Lower limbs


title: Aorta_1

description: Library name: Sample 1

value: aorta

value: arterial smooth muscle cells

value: Tamoxifen


title: interossei dors, male, 20-5708-S15-NovaRUN1

description: Library name: 20__interossei_dors__5708__male__S15__NovaRUN1

value: skeletal muscle

value: m. interossei dorsales

value: Musculus interossei dorsales

value: male


description: Library name: ENU43040B6G2RN439_E11_neuro2222_S53_R1_2367729538


title: FHL, female, 56-5489-S60-HiRUN42

description: Library name: 56__FHL__5489__female__S60__HiRUN42

value: FHL

value: m. flexor hallucis longus

value: Musculus flexor hallucis longus

value: female


title: adductor magnus, female, 50-5489-S58-HiRUN42

description: Library name: 50__adductor_magnus__5489__female__S58__HiRUN42

value: m. adductor magnus

value: Musculus adductor magnus


description: Library name: ENU43040B6G2RN440_E12_neuro2222_S53_R1_2367729680

value: Whole brain

value: TRUE


title: dENL/AF9-IR_young_rep2

city: Chiang Mai, Thailand

first: Ranchana

last: Yeewa

state: State/Province

address: Faculty of Medicine, Chiang Mai University 110 Intawaroros Road, Si Phum, Muang, Chiang Mai

country: Thailand

institute: Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University

description:
Library name: dENLAF9-IR_2
Column name in raw_counts_ALL_samples.txt: dENLAF9-IR_2
Column name in DESeq2_norm_count_ALL_sample.csv: dENLAF9-IR_2

data_processing:
the nf-core/rnaseq pipeline v3.14.0
Per-sample quality control was performed with FastQC v0.12.0.
Adapter trimming was conducted with Trim Galore! v0.6.5.
Putative genome contaminants were removed using BBSplit.
rRNA was depleted in silico with SortMeRNA.
Clean reads were aligned to the Drosophila melanogaster reference genome BDGP6 (dm6) using HiSat2.
The resulting BAM files were coordinate-sorted and indexed using SAMtools.
Duplicate molecules in UMI-tagged libraries were collapsed with UMI-tools, while duplicates in non-UMI libraries were marked with Picard MarkDuplicates.
Reference-guided quantification was performed with StringTie2 in quantification-only mode against the Ensembl release 81.
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file include DESeq2 normalized count for each sample

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
3-day-old male flies from each genotype were collected, snap-frozen in liquid nitrogen, and stored at −80 °C until a sufficient number of flies had been obtained. The frozen flies were then decapitated, and total RNA was isolated from 50 heads per replicate using an RNeasy Mini Kit (Qiagen, Valencia, CA), according to the manufacturer’s protocol. The RNA samples, stabilized under ethanol precipitation conditions, were submitted to Macrogen, Inc. (Korea) for RNA sequencing (RNA-Seq). Prior to sequencing, the samples were analyzed with an Agilent 2100 Bioanalyzer to assess overall quality. Only samples with an RNA Integrity Number (RIN) > 7 and an rRNA ratio > 1 were processed further.
RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Head

value: nSyb>dENL/AF9 IR

tag: age

value: 3 day old


description: Library name: ENU43040B6G2RN442_F2_neuro2222_S54_R1_2367729163


title: dENL/AF9-IR_young_rep3

description:
Library name: dENLAF9-IR_3
Column name in raw_counts_ALL_samples.txt: dENLAF9-IR_3
Column name in DESeq2_norm_count_ALL_sample.csv: dENLAF9-IR_3


title: dENL/AF9-IR_young_rep1

description:
Library name: dENLAF9-IR_1
Column name in raw_counts_ALL_samples.txt: dENLAF9-IR_1
Column name in DESeq2_norm_count_ALL_sample.csv: dENLAF9-IR_1


title: pronator quadratus, male, 23_2_e1-5708-S16-NovaRUN1

description: Library name: 23_2_e1__pronator_quadratus__5708__male__S16__NovaRUN1

value: m. pronator quadratus

value: Musculus pronator quadratus

value: Upper limbs


description: Library name: ENU43040B6G2RN438_E10_neuro2222_S53_R1_2367729842


title: brachioradialis, male, 18-5708-S40-NovaRUN1

description: Library name: 18__brachioradialis__5708__male__S40__NovaRUN1

value: skeletal muscle

value: brachioradialis

value: m. brachioradialis

value: Musculus brachioradialis


title: adductor long, female, 49-5489-S56-HiRUN42

description: Library name: 49__adductor_long__5489__female__S56__HiRUN42

value: m. adductor longus

value: Musculus adductor longus

value: Lower limbs


title: brachioradialis, female, 18-5489-S30-NovaRUN1

description: Library name: 18__brachioradialis__5489__female__S30__NovaRUN1

value: female


title: NTC IR-2_young_rep3

description:
Library name: NTC-IR-2_3
Column name in raw_counts_ALL_samples.txt: NTC-IR-2_3
Column name in DESeq2_norm_count_ALL_sample.csv: NTC-IR-2_3

value: nSyb>Luciferase IR

value: male


title: biceps femoris, female, 51_2-5489-S59-HiRUN42

description: Library name: 51_2__biceps_femoris__5489__female__S59__HiRUN42

value: m. biceps femoris

value: Musculus biceps femoris caput longum, Musculus biceps femoris caput breve


title: trapezius, female, 45-5489-S57-HiRUN42

description: Library name: 45__trapezius__5489__female__S57__HiRUN42

value: trapezius

value: m. trapezius

value: Musculus trapezius pars transversa, Musculus trapezius pars descendens, Musculus trapezius pars ascendens

value: Back


title: NTC IR-2_young_rep2

description:
Library name: NTC-IR-2_2
Column name in raw_counts_ALL_samples.txt: NTC-IR-2_1
Column name in DESeq2_norm_count_ALL_sample.csv: NTC-IR-2_1

value: Head

value: 3 day old


description: Library name: ENU43040B6G2RN426_E8_neuro2222_S53_R1_2367729645

value: Whole brain

value: TRUE


title: ECRB, female, 33-5489-S8-HiRUN42

description: Library name: 33__ECRB__5489__female__S8__HiRUN42

value: skeletal muscle

value: ECRB

value: m. extensor carpi radialis brevis

value: Musculus extensor carpi radialis brevis

value: Upper limbs


title: adductor pollicis, male, 16-5708-S35-NovaRUN1

description: Library name: 16__adductor_pollicis__5708__male__S35__NovaRUN1

value: m. adductor pollicis

value: Musculus adductor pollicis caput transversum, Musculus adductor pollicis caput obliquum


title: NTC IR-2_young_rep1

description:
Library name: NTC-IR-2_1
Column name in raw_counts_ALL_samples.txt: NTC-IR-1_1
Column name in DESeq2_norm_count_ALL_sample.csv: NTC-IR-1_1

value: nSyb>Luciferase IR

value: male


description: Library name: ENU43040B6G2RN425_E7_neuro2222_S53_R1_2367728877


title: dYEATS2-IR_rep3

description:
Library name: dYEATS2-IR_3
Column name in raw_counts_ALL_samples.txt: dYEATS2-IR_3
Column name in DESeq2_norm_count_ALL_sample.csv: dYEATS2-IR_3

value: nSyb>dYEATS2 IR


title: abductor pollicis, male, 15-5708-S38-NovaRUN1

description: Library name: 15__abductor_pollicis__5708__male__S38__NovaRUN1

value: m. abductor pollicis

value: Musculus abductor pollicis brevis


description: Library name: ENU43040B6G2RN424_E6_neuro2222_S53_R1_2367729446


title: opponens pollicis, female, 26-5489-S6-HiRUN42

description: Library name: 26__opponens_pollicis__5489__female__S6__HiRUN42

value: m. opponens pollicis

value: Musculus opponens pollicis

value: female


title: dYEATS2-IR_rep2

description:
Library name: dYEATS2-IR_2
Column name in raw_counts_ALL_samples.txt: dYEATS2-IR_2
Column name in DESeq2_norm_count_ALL_sample.csv: dYEATS2-IR_2

value: Head

value: 3 day old


title: RCP minor, male, 13-5708-S37-NovaRUN1

description: Library name: 13__RCP_minor__5708__male__S37__NovaRUN1

value: skeletal muscle

value: m. rectus capitis posterior minor

value: Musculus rectus capitis posterior minor

value: Neck


title: biceps brachii, male, 17_2-5708-S39-NovaRUN1

description: Library name: 17_2__biceps_brachii__5708__male__S39__NovaRUN1

value: m. biceps brachii

value: Musculus biceps brachii caput longum, Musculus biceps brachii caput brevis

value: Upper limbs


description: Library name: ENU43040B6G2RN437_E9_neuro2222_S53_R1_2367728912

value: Whole brain

value: TRUE


description: Library name: ENU43040B6G2RN423_E5_neuro2222_S53_R1_2367729074


title: dYEATS2-IR_rep1

description:
Library name: dYEATS2-IR_1
Column name in raw_counts_ALL_samples.txt: dYEATS2-IR_1
Column name in DESeq2_norm_count_ALL_sample.csv: dYEATS2-IR_1

value: nSyb>dYEATS2 IR

value: male


title: lumbricales, female, 24-5489-S5-HiRUN42

description: Library name: 24__lumbricales__5489__female__S5__HiRUN42

value: lumbricales

value: mm. lumbricales

value: Musculi lumbricales


title: RCP minor, female, 13-5489-S29-NovaRUN1

description: Library name: 13__RCP_minor__5489__female__S29__NovaRUN1

value: female


title: pronator teres, female, 23_3-5489-S4-HiRUN42

description: Library name: 23_3__pronator_teres__5489__female__S4__HiRUN42

value: m. pronator teres

value: Musculus pronator teres caput humerale, Musculus pronator teres caput ulnare


title: NTC IR-1_rep3

description:
Library name: NTC-IR-1_3
Column name in raw_counts_ALL_samples.txt: NTC-IR-1_3
Column name in DESeq2_norm_count_ALL_sample.csv: NTC-IR-1_3

value: Head

value: nSyb>mCherry IR

value: 3 day old


description: Library name: ENU43040B6G2RN421_E3_neuro2222_S53_R1_2367728915


title: abductor pollicis, female, 15-5489-S3-HiRUN42

description: Library name: 15__abductor_pollicis__5489__female__S3__HiRUN42

value: skeletal muscle

value: m. abductor pollicis

value: Musculus abductor pollicis brevis


title: D425_PP2A_WT_RT_rep3

city: San Francisco

first: Rongze

middle: Olivia

last: Lu

address: 1450 3rd St, 4th floor

department: Department of Neurological Surgery

institute: University of California, San Francisco

description:
Library name: WT_RT_rep3
Column name in FPKM_All_samples.txt: WT_RT_3

data_processing:
Trimmed sequence reads were mapped to hg38/mm39 using RSEM v.1.2.28. Gene expression was quantified as fragments per kilobase of transcript per million (FPKM).
Assembly: hg38 and mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: csv files include FPKM values for each sample

extract_protocol:
Total RNA was isolated using the PureLink™RNA Mini Kit (Invitrogen, 12183025)
Poly(A) enrichment was performed. mRNA was isolated from total RNA using thePoly(A) Purist-MAG kit, libraries were prepared according to manufacturer’s instructions for the NEBNext Ultra IIDirectional RNA kit

value: Medulloblastoma group 3

value: WT

value: RT


title: NTC IR-1_rep2

description:
Library name: NTC-IR-1_2
Column name in raw_counts_ALL_samples.txt: NTC_IR-1-2
Column name in DESeq2_norm_count_ALL_sample.csv: NTC-IR-1_2


title: SCM, female, 11-5489-S2-HiRUN42

description: Library name: 11__SCM__5489__female__S2__HiRUN42

value: SCM

value: m. sternocleidomastoideus

value: Musculus sternocleidomastoideus

value: Neck


title: longissimus cervicis, male, 10-5708-S36-NovaRUN1

description: Library name: 10__longissimus_cervicis__5708__male__S36__NovaRUN1

value: m. paraspinalis сervical

value: Musculus paraspinalis сervical

value: Back

value: male


description: Library name: ENU43040B6G2RN422_E4_neuro2222_S53_R1_2367729419

value: Whole brain

value: TRUE


description: Library name: ENU43040B6G2RN420_E2_neuro2222_S53_R1_2367729433


title: NTC IR-1_rep1

description:
Library name: NTC-IR-1_1
Column name in raw_counts_ALL_samples.txt: NTC-IR-1_1
Column name in DESeq2_norm_count_ALL_sample.csv: NTC-IR-1_1

value: Head

value: nSyb>mCherry IR

value: 3 day old


title: D425_PP2A_WT_RT_rep2

description:
Library name: WT_RT_rep2
Column name in FPKM_All_samples.txt: WT_RT_2


title: longissimus cervicis, female, 10-5489-S1-HiRUN42

description: Library name: 10__longissimus_cervicis__5489__female__S1__HiRUN42

value: skeletal muscle

value: female


description: Library name: ENU43040B6G2RN419_E1_neuro2222_S53_R1_2367729123


title: D425_PP2A_WT_RT_rep1

description:
Library name: WT_RT_rep1
Column name in FPKM_All_samples.txt: WT_RT_1

value: Medulloblastoma group 3

value: WT


description: Library name: ENU29013Inpp5dB6G2RN69_G1_neuro2008rep_S39_R1_2367729695

value: Inpp5d S308X


title: RNA-seq for GS76

city: Shenzhen

first: Zhe

state: Guangdong

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

country: China

institute: Shenzhen Bay Laboratory

description: Library name: 76R

library_source: genomic

data_processing:
All the relevant scripts can be found at zenodo (doi: 10.5281/zenodo.19430452). A standard bioinformatic pipeline was implemented to process the sequencing data. Briefly, adapter sequences were trimmed from the raw reads using Cutadapt. To ensure the stringent removal of the short adapter sequences flanking our library constructs, the Cutadapt-processed reads were further filtered with a custom script. This step involved removing the last 5 nucleotides from all reads longer than 113 nt. The resulting high-quality paired-end reads were then aligned to the UCSC human reference genome (hg38) using Bowtie2 in the --very-sensitive mode. The subsequent SAM file was processed to retain only uniquely mapped, properly paired reads with a MAPQ score of 30 or higher. Finally, the alignment data for each read was converted into cleavage site information, and all potential sites were statistically tallied and ranked. Cleavage sites that appeared only once were filtered out, retaining only those sites with a read count of at least two. Noise reduction was then performed using a custom script. This method functions by analyzing the signal intensity ratios within sequencing reads of a defined window size. All potential cleavage sites within a defined genomic window (50nt) are removed if more than one site is present and the signal intensity ratio between them is less than 10. Each potential cleavage site was subsequently assigned a score calculated as (N_5OH + 1) × (N_3P + 1), where N_5OH and N_3P represent the number of occurrences of the site in the 3P-seq sequencing library and the 5OH-seq sequencing library, respectively. For experimental validation, we selected a final candidate pool comprising the 96 highest-scoring sequences that were identified in both independent screening libraries. Sequencing data from mutational scanning experiments were processed similarly to previously described methods with minor modifications. Briefly, variant counts from the DNA‑seq (input) and RNA‑seq (selected) libraries were obtained by mapping the associated barcodes. The relative activity (RA) for each variant was then calculated using the following equation: RA(var)=N_cleaved (var)〖(N〗_cleaved (wt)〖+N〗_uncleaved (wt))/〖(N〗_cleaved (var)+N_uncleaved (var))N_cleaved (wt), where Ncleaved and Nuncleaved represent read counts of the cleaved and uncleaved fractions, respectively, and “wt” denotes the wild‑type sequence. Finally, a fitness score for each variant was defined as the natural logarithm of its RA value.
Assembly: hg38
Supplementary files format and content: All processed data files can be opened as plain txt. The file named "merged_final.txt" contains the genomic locations of ribozyme candidates. The files named with ".ra" contain the relative activity of the ribozyme mutants.

molecule: genomic DNA

source_name: hela

extract_protocol:
HeLa genomic DNA purchased from NEB, no. N4006S
Experimental process for ribozyme identification. HeLa genomic DNA libraries were constructed using the tagmentation method, which simultaneously fragments genomic DNA (NEB, no. N4006S) and incorporates adapter sequences via the Tn5 transposase. The process was performed using the Nextera XT DNA Library Preparation Kit (Illumina, no. FC-131-1024), following the manufacturer′s guidelines. PCR amplification of the tagmentation product was carried out using primers T7p-s7 and T7t-s5. These primers were designed to anneal to the Nextera s7 and s5 adapter regions, respectively, and incorporated the T7 promoter sequence at the 5′ ends of the amplicons.  Sequences of all oligonucleotides used in this study are listed in Supplementary Table 1. Separation of the DNA library fragments (500-1000 bp) was achieved by agarose gel electrophoresis and subsequent gel purification. Purified DNA library was then used as the template for in vitro transcription by incubation with 100 U of T7 RNA Polymerase (NEB, no. M0251L) in 1×T7 RNA polymerase buffer (40 mM Tris-HCl pH 7.9, 6 mM MgCl2, 1 mM DTT, 2 mM spermidine) with 2 mM NTP mix (NEB, no. N0466S) and 20 U Murine RNase Inhibitor (NEB, no. M0314S) in a 30 µl reaction volume for 5 h at 37 °C. DNA templates were removed by incubation with 2 U of DNase I (NEB, no. M0303S) and 1× DNase I reaction buffer in a 100 µl volume at 37 °C for 15 min, followed by purification with  RNA Clean & Concentrator-5 kit (Zymo Research, no. R1016). 2.5 µg purified RNA were incubated with 100 pmol linker (rM13F_3desBio for 3P-seq, rM13R_5desBio_3P for 5OH-seq) in 1× RtcB reaction buffer with 22.5 pmol RtcB ligase (NEB, no. M0458S), 0.1 mM GTP and 1 mM MnCl2 in 30 µl at 37 °C for 1 h. Ligation products were purified with Sera-Mag Streptavidin-Coated Magnetic Beads (Cytiva, no. 30152103010150) and eluted in 20 µl TNB buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 4 mM biotin). Before reverse transcription, ligation products were exchanged into H2O by column purification. Ligation products were reversed transcribed using primer (RT1_m13f_adp1 for 3P-seq, RT1_Tn5ME_adp1 for 5OH-seq) and the ProtoScript II Reverse Transcriptase (NEB, no. M0368S). Ligation product was first denatured at 65 °C for 5 min in a 19.5 µl volume containing 1 µl of 100 µM primer and 1.5 µl of 10 mM dNTP mix, followed by rapid snap-cooling on ice for 2 min. Then, 6 µl of 5 × ProtoScript II Reverse Transcriptase buffer, 3 µl of 0.1 M DTT, 0.5 µl of Murine RNase Inhibitor (NEB, no. M0314S) and 1 µl of ProtoScript II Reverse Transcriptase were added and incubated at 42 °C for 1 h and then 65 °C for 20 minutes to inactivate the enzyme, followed by enrichment with Sera-Mag Streptavidin-Coated Magnetic Beads (Cytiva, no. 30152103010150) and clean-up by using RNA Clean & Concentrator-5 kit (Zymo Research, no. R1016). Purified cDNA was amplified by touch-up PCR using primers (P7R2_Tn5ME/P5R1_adp1 for 3P-seq, P7R2_m13r/P5R1_adp1 for 5OH-seq) with Q5 Hot Start High-Fidelity DNA Polymerase (NEB, no. M0493S) to construct the high-throughput sequencing library. The PCR products were purified with a homemade magnetic bead mix and sequenced on an Illumina HiSeq X sequencer with 20% PhiX control by Novogene Technology Co., Ltd.  Mutational profiling of four identified ribozymes. Shorter versions of the identified ribozymes were defined by sequential truncation of terminal regions that did not significantly reduce cleavage activity. These truncated sequences were used for subsequent mutational‑scanning experiments. A random mutagenesis library was generated using a commercial Random Mutagenesis Kit (Biosharp, no. BL1668A). Barcode sequences were appended to the library in three PCR cycles. Approximately 10⁶ barcoded molecules were used as template to amplify the final mutant DNA library. The final mutant DNA library served as template for constructing the DNA‑seq library. The barcoded DNA library was transcribed with T7 RNA Polymerase (Beyotime, cat. no. R7012L) for 4 h at 37 °C. After transcription, the DNA template was removed by treatment with DNase I (New England Biolabs, no. M0303S). The purified RNA was incubated in 1× TKMS buffer (50 mM Tris‑HCl pH 8.0, 25 mM KCl, 10 mM MgCl₂, 2 mM spermidine) at 37 °C for 2 h to allow ribozyme cleavage, followed by purification with the RNA Clean & Concentrator‑5 kit (Zymo Research, cat. no. R1016). For reverse transcription, ~50 pmol of RNA was mixed with 50 pmol of RT primer and 200 pmol of template‑switch oligo (TSO), and reverse‑transcribed using M‑MLV (H‑) Reverse Transcriptase (Vazyme, no. R021) at 42 °C for 1 h. The purified cDNA was used as the template for NGS library amplification. PCR was performed with Q5 High-Fidelity DNA Polymerase (New England Biolabs, no. M0491L) for 12 cycles. The PCR products were purified with a homemade magnetic bead mix and sequenced on a Salus EVO sequencer by Shenzhen Salus BioMed Co., Ltd as the RNA-seq library.

value: hela


title: D425_PP2A_WT_NT_rep3

description:
Library name: WT_NT_rep3
Column name in FPKM_All_samples.txt: WT_NT_3

value: control


description: Library name: ENU29013Inpp5dB6G2RN68_F12_neuro2008rep_S38_R1_2367728838

value: m/m


title: POF 6

city: Guangzhou

first: Jiaqiong

last: Lin

address: Guangzhou dadaobei 1838

institute: South medical university

data_processing:
The raw reads underwent processing in a local Perl script to filter out reads containing connectors, unknown base N content exceeding 10%, and low-quality reads.
Bowtie was used for comparing the clean reads with databases such as Silva, GtRNAdb, Rfam, and Repbase. These comparisons filtered out rRNA, tRNA, snRNA, snoRNA, and other ncRNAs and repetitive sequences.
The remaining reads were used for identifying known miRNAs by comparing them with miRbase and the human genome (GRCh38), as well as predicting new miRNAs.
By comparing, the number of reads per miRNA was obtained, and the expression TPM was calculated.
Assembly: GRCh38
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Peripheral blood

extract_protocol:
Total exosomal RNA was extracted by miRNeasy Mini kit (Qiagen, cat. No. 217004).
RNA-sequencing libraries were constructed using QIAseq miRNA Library Kit (Qiagen, Frederick, MD).

value: Peripheral blood

tag: patient

value: premature ovarian failure


title: Healthy control 4

value: healthy


title: D425_PP2A_WT_NT_rep2

description:
Library name: WT_NT_rep2
Column name in FPKM_All_samples.txt: WT_NT_2


description: Library name: ENU29013Inpp5dB6G2RN67_F11_neuro2008rep_S38_R1_2367728766


title: RNA-seq for GS69

description: Library name: 69R


title: D425_PP2A_WT_NT_rep1

description:
Library name: WT_NT_rep1
Column name in FPKM_All_samples.txt: WT_NT_1


title: RNA-seq for GS46

description: Library name: 46R


description: Library name: ENU29013Inpp5dB6G2RN66_F10_neuro2008rep_S38_R1_2367729125


title: Healthy control 3


title: RNA-seq for GS59

description: Library name: 59R


title: D425_PP2A_KO_RT_rep3

description:
Library name: PP2A_KO_RT_rep3
Column name in FPKM_All_samples.txt: PP2A_KO_RT_3

value: PP2Ac KO

value: RT


title: D425_PP2A_KO_RT_rep2

description:
Library name: PP2A_KO_RT_rep2
Column name in FPKM_All_samples.txt: PP2A_KO_RT_2


title: Healthy control 2


title: POF 5


title: POF 4


title: D425_PP2A_KO_RT_rep1

description:
Library name: PP2A_KO_RT_rep1
Column name in FPKM_All_samples.txt: PP2A_KO_RT_1


title: DNA-seq for GS76

description: Library name: 76D


title: DNA-seq for GS59

description: Library name: 59D


description: Library name: ENU29013Inpp5dB6G2RN63_F7_neuro2008rep_S38_R1_2367729157

value: Whole brain

value: TRUE


title: D425_PP2A_KO_NT_rep3

description:
Library name: PP2A_KO_NT_rep3
Column name in FPKM_All_samples.txt: PP2A_KO_NT_3


description: Library name: ENU29013Inpp5dB6G2RN65_F9_neuro2008rep_S38_R1_2367729881


title: DNA-seq for GS69

description: Library name: 69D


title: DNA-seq for GS46

description: Library name: 46D


title: POF 3


description: Library name: ENU29013Inpp5dB6G2RN64_F8_neuro2008rep_S38_R1_2367728937


description: Library name: ENU29013Inpp5dB6G2RN62_F6_neuro2008rep_S38_R1_2367729318


title: Healthy control 1


description: Library name: ENU29013Inpp5dB6G2RN61_F5_neuro2008rep_S38_R1_2367729389


title: D425_PP2A_KO_NT_rep1

description:
Library name: PP2A_KO_NT_rep1
Column name in FPKM_All_samples.txt: PP2A_KO_NT_1


title: D425_PP2A_KO_NT_rep2

description:
Library name: PP2A_KO_NT_rep2
Column name in FPKM_All_samples.txt: PP2A_KO_NT_2


title: Capture RNA with 5′-hydroxyl ends

description: Library name: 5OH


title: Capture RNA with 2′,3′-cyclic phosphate or 3′-phosphate ends

description: Library name: 3P


title: POF 1


title: POF 2