title: RNA-Seq of nothobranchius furzeri: adult female gut from fish P1B3

description:
Library name: GutF77_P_1B_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H2_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1A6

status: Public on Jan 04 2026

type: SRA

city: Stanford

first: Jingxun

last: Chen

state: CA

address: 290 Jane Stanford Way, Room E365

department: Genetics

country: USA

institute: Stanford University - Stanford, CA

description:
Library name: MuscleM133_P_1A_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H14_1

library_source: transcriptomic

data_processing:
Combine the sequencing data from all the sequencing batches (1-4) for each sample
Raw sequencing data (FASTQ files) were merged for each library pool (2 lanes for the pooled library 1 and 3 lanes for the pooled library 2) and checked for quality using Trim-galore v0.5.0.
The processed reads were aligned to the African turquoise killifish reference genome downloaded from NCBI (Nfu_20140520, GCF_001465895.1) using STAR v2.7.10b83 with the default parameters. Out of all the sequenced samples, 14 samples had >90% of reads mapped to the genome; 252 samples, 80–90% reads mapped; and 178 samples, 75–80% mapped. Samtools v1.16.184, with the parameters of MAPQ < 255 (‘samtools view -q255 -b’), was used to remove the reads mapped to multiple genomic regions. Next, we input the uniquely mapped reads into the ‘featureCounts’ program (with the default parameters) from subread v2.0.685 to generate the read counts for each gene.
We detected three samples as outliers, which were removed from subsequent analyses: J6 (a liver sample), L21 (a testis sample), and H19 (a skin sample). Two samples (J6 and L21) were excluded because they had low total raw counts. One sample (H19) was excluded because it had low mapping performance. As a separate method, we used gene expression connectivity to detect outliers from the WGCNA package v1.73. This method computes sample-to-sample correlations and derives network connectivity for each sample, then standardizes the connectivity scores, and finally identifies samples with Z-scores below -2 as outliers. Through this method, we verified these same three samples (J6, L21, and H19) as ‘outliers,’ validating their removal.
Assembly: NCBI African turquoise killifish reference genome (Nfu_20140520, GCF_001465895.1).
Supplementary files format and content: Comma-separated text files include the transcript per million (TPM) for all files in a matrix.

molecule: total RNA

organism: Nothobranchius furzeri

source_name: muscle

growth_protocol: All experiments used the GRZ strain of the African turquoise killifish species Nothobranchius furzeri. Fish were housed in a 26°C circulating water system kept at a conductivity between 3500 and 4500 μS/cm and a pH between 6.5 and 7.5, with a daily water exchange of 10% with reverse-osmosis-treated water. All animals were kept on a 12 h/12 h day/night cycle. The detailed protocol for embryo collection and husbandry of juvenile fish before sexual maturity can be found in the associated publication. The atlas cohort began at the 5th week post-hatching, each fish was transferred to a 2.8 L tank and sexed by caudal fin color: males exhibit vivid colors, but females do not. Fish with severe gill defects, curved spines, and an inability to float (‘belly sliders’) were excluded. A random subset of individuals from each cohort were designated as ‘Lifespan’ animals, and these animals were not selected for harvest. Any other unharvested animals that died from natural causes were also plotted in the lifespan analysis. Cohort 1 fish were enrolled in two batches, 2 weeks apart. Cohort 2 fish were enrolled as an independent cohort, 6 months apart from Cohort 1. All fish from each cohort were randomly assigned to tank locations using the ‘Randomize Range’ function in Google Sheets. Cohort 1 (1A, first enrollment) fish were fed using an automated feeder22 under the ad libitum regimen (5 mg per feeding and fed 7 times a day for a total of 35 mg of Otohime fish pellets). Cohort 1 (1B, second enrollment) and Cohort 2 were fed using a custom-made manual feeder twice a day, 18 mg per feeding, for a total of 36 mg of Otohime fish pellets. The core design of the custom feeder has the same precision as the automated feeder.

extract_protocol:
The RNA isolation protocol was based on the RNeasy Mini RNA extraction protocol from QIAGEN and largely kept consistent between tissues, except for when stated otherwise. Please see the associated publication for the full details of the RNA extraction protocol. To reduce within-tissue batch effects, we processed all samples of the same tissue type on the same day unless otherwise noted. Due to the large number of samples, RNA extraction was performed in 2-3 batches for each tissue, with the order of samples randomized and a roughly equal assignment of age and sex combinations to each batch. The processing order of each sample within a tissue type was randomized using the “Randomize Range” option in Google Sheets. After randomization, tissue samples were assigned unique numerical “RNA_IDs” and split into batches of 12-24 samples for processing.
cDNA libraries were prepared using a SmartSeq-based in-house protocol. Briefly, RNA samples were thawed on ice, and the concentration was measured. RNA sample concentrations were normalized to 25 ng/µL, and 2 µL of each sample was used as input into the cDNA first-strand synthesis reaction. The resulting single-stranded library was amplified using 9 cycles. A portion of the full cDNA library volume (6 µL) was cleaned using Agencourt AMPure XP beads at a 0.7X ratio following the manufacturer’s guidelines. Next, sequencing libraries were made using the Nextera XT DNA Library Preparation Kit and the IDT for Illumina DNA/RNA UD Index Sets A-D (Illumina, 20027213, 20027214, 20042666, 20042667), following the manufacturer’s instructions except for reducing all the reactions by half. Two library pools were ultimately generated, one of 322 samples and the other of 358 samples, with all the samples from the same tissue type assigned unique dual indices in the same library pool to reduce any batch effects. For tagmentation, 0.5 ng of the cDNA (2.5 µL total) was mixed with 5 µL TD buffer and then 2.5 µL ATM buffer from the Nextera kit, incubated at 55°C for 5 min and cooled to 10°C. To stop the tagmentation reaction, we added 2.5 µL of NT buffer for 5 min at room temperature. The cDNA library was indexed and amplified for 12 cycles in a PCR reaction containing 10 µL of tagmented DNA, 5 µL of dual indices, and 7.5 µL NPM buffer. The amplified cDNA library (25 µL total) was split into two 12.5 µL aliquots, each purified using 22.5 µL of AMPure XP beads. The aliquots were re-pooled after the first was eluted in 11 µL of Buffer EB, such that the total elution volume was 10 µL. We performed most pipetting steps using the Dragonfly or Mosquito HV robotic liquid handlers to accelerate sample processing and maintain high pipetting accuracy. Each pooled library was sequenced by Novogene on 2 (pooled library 1, which included 322 tissues) or 3 lanes (pooled library 2, which included 358 tissues) of an Illumina NovaSeq X 25B flow cell (2x150 bp paired-end) with 10% PhiX spike-in control for each lane, at a target sequencing depth of >40 million paired-end reads (20 million single-end) per sample. Novogene performed base calling, demultiplexing, and FASTQ file generation.

treatment_protocol: The harvest dates were randomly assigned to each fish within each cohort. On a harvest day, each fish was fed 18 mg of Otohime fish pellets 7:30 - 8 AM. At ~10:30 AM, the fish were transported from the animal facility to the lab space in their own tanks. Typically, 4 fish (2 males and 2 females) were dissected on each harvest day (~30 min to dissect each fish). Dissection began with perfusion (detailed protocol and sample description can be found in the associated publication) and then tissue collections on top of ice-cold Sylgard-coated Petri dishes. Dissected tissues were placed in 1.5 mL tubes, snap-frozen in liquid nitrogen, and stored at -80°C until RNA extraction. The same operator dissected the same tissues for all fish in this study. Muscle samples were collected from a ~1 cm region immediately anterior to the caudal fin, with skin removed and cuts made above and below the horizontal septum to remove the spinal cord and vertebrae. The spinal cord was collected by dissecting out the vertebrae and gently pulling the spinal cord from the vertebral foramen. Skin samples corresponded to the caudal fin's most posterior ~0.5 cm portion. The retina and retinal pigment epithelium (RPE) were dissected from the eye together. In some cases, the retina/RPE samples were dissected from individual eyes from the same animal, and in other cases, samples were pooled between animals. Only the head kidney was collected for the kidney samples. For the liver samples, the pale green gallbladder was removed whenever it was visible. Total visceral fat was collected (without regional distinction). All oocytes were collected for ovaries, including those that had fallen out of the organ during dissection.

tag: tissue

value: muscle

tag: genotype

value: GRZ wild type

tag: Sex

value: male

tag: age days


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish A01

description:
Library name: LiverM78_A01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H5_1

source_name: liver

value: liver


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish J1A17

description:
Library name: LiverM47_J_1A_17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H6_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish J1B18

description:
Library name: KidneyF133_J_1B_18
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: I10_1

source_name: kidney

value: kidney

value: female


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1B11

description:
Library name: MuscleM147_P_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: J15_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish J1A1

description:
Library name: TestisM152_J_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H23_1

source_name: testis

value: testis


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish I06

description:
Library name: KidneyF78_I06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G9_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish J1B4

description:
Library name: LiverM161_J_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G8_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish E04

description:
Library name: TestisM102_E04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H21_1


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish P1A1

description:
Library name: LiverF47_P_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G7_1


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish P1B3

description:
Library name: OvaryF77_P_1B_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G23_1

source_name: ovary

value: ovary


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish E1

description:
Library name: KidneyM52_E_01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H11_1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish J1B6

description:
Library name: GutF133_J_1B_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G3_1

source_name: gut

value: gut


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish E02

description:
Library name: LiverF78_E02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G5_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish H2

description:
Library name: SkinM52_H_02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H17_1

source_name: skin

value: skin


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish J1B12

description:
Library name: MuscleM49_J_1B_12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H15_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish P1B8

description:
Library name: SkinM147_P_1B_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G20_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish D6

description:
Library name: MuscleF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H13_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish P1B9

description:
Library name: MuscleF49_P_1B_9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G15_1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish P1A2

description:
Library name: GutF103_P_1A_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G2_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish H2

description:
Library name: TestisM52_H_02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G21_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish J1B20

description:
Library name: MuscleM77_J_1B_20
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G16_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish P1B11

description:
Library name: TestisM147_P_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G24_1


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish J1A24

description:
Library name: LiverF47_J_1A_24
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G6_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1B12

description:
Library name: SkinM49_J_1B_12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G19_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish H2

description:
Library name: GutM52_H_02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H1_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish D05

description:
Library name: GutM162_D05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F3_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish J1A17

description:
Library name: TestisM47_J_1A_17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F23_1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish P1A1

description:
Library name: GutF47_P_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G4_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish P1B11

description:
Library name: GutM147_P_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F2_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish P1A8

description:
Library name: KidneyF75_P_1A_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: H10_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish I05

description:
Library name: SkinF134_I05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G17_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish P1A1

description:
Library name: SkinF47_P_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F20_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish B01

description:
Library name: SkinM134_B01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F17_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish P1A8

description:
Library name: MuscleF75_P_1A_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G14_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish P1A3

description:
Library name: SkinM152_P_1A_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F19_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish P1B4

description:
Library name: SkinF147_P_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F18_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1A25

description:
Library name: KidneyM103_J_1A_25
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G12_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish D6

description:
Library name: KidneyF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G11_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish J9

description:
Library name: KidneyF155_J9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F9_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish I03

description:
Library name: GutM162_I03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G1_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish J1B11

description:
Library name: LiverM161_J_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F7_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish P1A3

description:
Library name: KidneyM152_P_1A_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G10_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish E04

description:
Library name: LiverM102_E04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F6_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish J05

description:
Library name: MuscleF102_J05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G13_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish J1B5

description:
Library name: MuscleF49_J_1B_5
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F16_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish P1B9

description:
Library name: KidneyF49_P_1B_9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F10_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish P1A6

description:
Library name: SkinM133_P_1A_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: G18_1


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish C04

description:
Library name: LiverF134_C04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E6_1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish I06

description:
Library name: GutF78_I06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E3_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish J1A14

description:
Library name: GutM75_J_1A_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F4_1


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish J1B5

description:
Library name: OvaryF49_J_1B_5
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F24_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish J1A1

description:
Library name: GutM152_J_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E4_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish H2

description:
Library name: LiverM52_H_02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F5_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1B10

description:
Library name: MuscleM133_P_1B_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F15_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1A22

description:
Library name: SkinM47_J_1A_22
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E20_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish C03

description:
Library name: MuscleM162_C03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F13_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish J1B7

description:
Library name: MuscleF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F14_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish P1B11

description:
Library name: LiverM147_P_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F8_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish P1B8

description:
Library name: LiverM147_P_1B_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E7_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish J1A1

description:
Library name: MuscleM152_J_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E16_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish B01

description:
Library name: TestisM134_B01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E21_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish A01

description:
Library name: KidneyM78_A01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E9_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish A17

description:
Library name: SkinM78_A17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E17_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish P1A10

description:
Library name: KidneyM103_P_1A_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F12_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish J1B7

description:
Library name: KidneyF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E12_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish P1A6

description:
Library name: TestisM133_P_1A_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E24_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish I03

description:
Library name: LiverM162_I03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E5_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish C03

description:
Library name: KidneyM162_C03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F11_1


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish J1B7

description:
Library name: LiverF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E8_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish A01

description:
Library name: GutM78_A01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E1_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish C03

description:
Library name: GutM162_C03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: F1_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish B01

description:
Library name: KidneyM134_B01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D9_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish J1A25

description:
Library name: TestisM103_J_1A_25
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E23_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1B20

description:
Library name: SkinM77_J_1B_20
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E19_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish P1A3

description:
Library name: LiverM152_P_1A_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D8_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish A01

description:
Library name: MuscleM78_A01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E13_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish P1B4

description:
Library name: MuscleF147_P_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E14_1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish J1B7

description:
Library name: GutF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E2_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish A17

description:
Library name: MuscleM78_A17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E15_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish P1A12

description:
Library name: SkinF75_P_1A_12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E18_1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish P1B4

description:
Library name: GutF147_P_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D4_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish P1B2

description:
Library name: TestisM133_P_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D24_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish D05

description:
Library name: LiverM162_D05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D6_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1A25

description:
Library name: SkinM103_J_1A_25
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D19_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish J1B4

description:
Library name: GutM161_J_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D2_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish J04

description:
Library name: GutM162_J04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D3_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish A06

description:
Library name: KidneyF102_A06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E11_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish P1A2

description:
Library name: SkinF103_P_1A_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D18_1


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish P1A2

description:
Library name: KidneyF103_P_1A_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: E10_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish F05

description:
Library name: LiverM102_F05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D5_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish P1A10

description:
Library name: TestisM103_P_1A_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D23_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1A3

description:
Library name: MuscleM152_P_1A_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D16_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1A14

description:
Library name: SkinM75_J_1A_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D20_1


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish I06

description:
Library name: OvaryF78_I06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D21_1


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish P1B4

description:
Library name: LiverF147_P_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D7_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish A06

description:
Library name: MuscleF102_A06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D13_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish P1B2

description:
Library name: KidneyM133_P_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D10_1


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1A10

description:
Library name: MuscleM103_P_1A_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D14_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish I06

description:
Library name: MuscleF78_I06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D15_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1A13

description:
Library name: KidneyM75_J_1A_13
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D11_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1A17

description:
Library name: KidneyM47_J_1A_17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D12_1


title: lipid Barcodes

city: Clermont-Ferrand

first: Felipe

last: Maurelia

address: 28, place Henri Dunant - BP 38

country: France

institute: iGRED

description:
Library name: LMO2
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
We used the protocol of the BD Rhaspody without any modifications.
FASTQ files were processed using the standard Rhapsody analysis pipeline (BD Biosciences) on Seven Bridges (https://www.sevenbridges.com), following the manufacturer’s recommendations. The resulting unique molecular identifier (UMI) count matrices were imported into R (v3.6.2) and analyzed using the MULTI-seq package (https://github.com/chris-mcginnis-ucsf/MULTI-seq). To account for differences in LMO tagging, tables were manually curated so that each LMO-assigned cell expressed at least 2/3 of a specific LMO relative to the total LMOs identified for that cell.
Since encapsulation and sequencing were performed on the same lane, all conditions were bioinformatically processed together, as we did not expect sequencing depth differences across cells. RNA UMI count matrices were prepared for analysis using the Seurat R package, following the recommendations at https://satijalab.org.
Assembly: The reads were aligned against the genome of gallus gallus galgal7
Supplementary files format and content: sbc_arranged_CG.xlsx postfiltering of the LMO barcode such as each cell has a unique LMO and more than 100 LMO tag
Supplementary files format and content: _1_Lane2LMO1_EKDL220010577-1A_H5HJVDSX5_L1_1_RSEC_MolsPerCell.csv final expression matrix

molecule: polyA RNA

organism: Gallus gallus

source_name: posterior chicken end

growth_protocol: Chick embryonic tissue at 72h post incubations are dissected, briefly rinsed in cold HBSS and incubated in Accutase (Gibco) for 15 min at 37°C followed by mechanical dissociation. The cell suspension was analyzed with a hemocytometer to assess the quality of the dissociation and evaluate cell density. Dissociated cells were centrifuged at 350 g for 10 min at 4°C and resuspended in 0.25% BSA in PBS and labelled with LMO barcode: Cells (250 000) coming from a specific tissue are incubated with PBS1X supplemented with 200nM of Anchor and 200nM of specific Sample BarCode oligonucleotide. This SBC is labelled with a dedicated tag and must be only used with the cells from a specific tissue. The tag will allow after bioinformatic analysis the identification of tissue where cells are coming from. After a slight agitation and 5 min on ice, 200nM of Co-Anchor are added to the cells and left again for 5 additional min on ice. Cells are then washed twice thanks to centrifugation at 500g during 10min.

extract_protocol:
For single-cell dissociation, the dissected tissue was briefly rinsed in cold HBSS and incubated in Accutase (Gibco) for 15 min at 37°C followed by mechanical dissociation. The cell suspension was analyzed with a hemocytometer to assess the quality of the dissociation and evaluate cell density. Dissociated cells were centrifuged at 350 g for 5 min at 4°C and resuspended in 0.25% BSA in PBS.
We adapt this protocol with the help of Rhapsody Team to replace “AbSeq” methodology by LMOs identification. We performed a first PCR on the supernatant of BD Rhaspody cell capture beads. The total data depth was of 600GB  for WTA72h1207 and of 12GB for LMO72h1207.

treatment_protocol: Homocysteine treatment with 20 uL of 19 mM for high-dose and 0.5 mM for low-dose

value: posterior chicken end

value: WT


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish D05

description:
Library name: KidneyM162_D05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C9_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish E1

description:
Library name: GutM52_E_01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D1_1


title: Whole trancriptome

description:
Library name: WTA2
BD Rhapsody


title: GBC-SD-CASE

city: Shanghai

first: Yijie

last: Li

address: No. 160 Lanxi Road, Putuo District

department: Putuo Hospital

country: China

institute: Shanghai University of Traditional Chinese Medicine

description:
Library name: sample 4
GBC, drug treatment

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

organism: Homo sapiens

source_name: cell culture

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish I06

description:
Library name: SkinF78_I06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: D17_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish J1A1

description:
Library name: LiverM152_J_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C7_1


title: HIF-1 alpha KO2 in vivo day1

city: Tokyo

first: Takatsune

last: Shimizu

address: 2-4-41, Ebara, Shinagawa-ku

department: Pathophysiology

country: Japan

institute: Hoshi University

description: Library name: Sample 4

data_processing:
The quality of raw paired-end sequence reads was assessed using FastQC (v0.11.7). Low-quality bases (< Q20) and adapter sequences were removed with Trimmomatic (v0.38). The filtered reads were aligned to the reference genome using HISAT2 (v2.1.0). SAM files were converted to BAM format with Samtools (v1.9). Gene-level counts were obtained from uniquely mapped reads using featureCounts (v1.6.3).
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The .bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
Assembly: GRCm38
Supplementary files format and content: Processed data are provided as tab-delimited text files containing annotated gene-level read counts. Each row corresponds to a gene, annotated with gene identifiers (Ensembl GeneID, gene symbol, gene biotype, EntrezGeneID), genomic coordinates (chromosome, start, end, strand), and functional annotations (description, GO terms for cellular component, molecular function, and biological process). Columns corresponding to samples (e.g., mock, c11, c15, c22) contain raw read counts obtained from uniquely mapped reads using featureCounts (v1.6.3).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: osreosarcoma cells

growth_protocol: Mock AXT cells and HIF-1α-knockout AXT cells were cultured under 5% CO2 at 37°C in IMDM.

extract_protocol:
Tumors were disrupted using a BioMasher (Nippi, Tokyo, Japan) and total RNA was extracted using Nucleospin RNA spin colum kit (Takara).
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and  NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: 2x10^6 Mock control cells and HIF-1alpha KO cells emmbedded in matrigel were inoculated into C57BL/6scid mice and harvested tumors next day.

value: osreosarcoma cells

tag: cell line

value: HIF-1alphaKO AXT2

tag: cell type

value: HIF-1alpha KO

tag: treatment

value: Injected into a C57BL/6scid mouse


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish P1A6

description:
Library name: GutM133_P_1A_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C4_1


title: HIF-1alpha KO1-1 in vivo day1

description: Library name: Sample 2

value: HIF-1alphaKO AXT1-1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish J04

description:
Library name: LiverM162_J04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C5_1

value: GRZ wild type


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish D14

description:
Library name: LiverF52_D_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C6_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish P1B2

description:
Library name: LiverM133_P_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C8_1

value: male


title: HFL-1 cells, vec3

city: Guangzhou

first: Zehao

last: Guo

state: Guangdong

address: zhongshan 2 road

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: Sample 6
HFL1_WT3

data_processing:
Raw sequencing reads were first assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed with Trimmomatic.
Clean reads were then aligned to the human reference genome (GRCh38/hg38) using HISAT2.
Gene-level read counts were quantified with featureCounts.
Differential expression analysis between treatment groups was performed using DESeq2 in R.
Assembly: Homo sapiens reference genome GRCh38 (hg38).
Supplementary files format and content: Read count matrix in .xlsx format, where rows represent genes and columns represent samples.

growth_protocol: HFL-1 human lung fibroblast cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with extracellular vesicles (EVs) isolated from oelncOSLMT-overexpressing osteosarcoma cells or vector control osteosarcoma cells. After 24 hours of EV incubation, cells were harvested for downstream RNA extraction.


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish A06

description:
Library name: GutF102_A06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C3_1


title: NOZ-CASE

description:
Library name: sample 2
NOZ, drug treatment


title: GBC-SD-CON

description:
Library name: sample 3
GBC, control


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish D12

description:
Library name: TestisM134_D12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C21_1


title: HFL-1 cells, vec2

description:
Library name: Sample 5
HFL1_WT2


title: HIF-1alpha KO1-2 in vivo day1

description: Library name: Sample 3

value: HIF-1alphaKO AXT1-2


title: Mock control in vivo day1

description: Library name: Sample 1

value: Mock AXT


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish P1A4

description:
Library name: GutM133_P_1A_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C2_1


title: NOZ-CON

description:
Library name: sample 1
NOZ, control


title: CKO-AA scRNA-seq

first: Yi

address: 320 Yueyang Road

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

description:
Library name: CKO-AA
10x Genomics

data_processing:
Each scRNA-seq data set was processed by CellRanger (v6.1.1) pipeline to perform the alignment against the modified mouse reference genome mm10, filter the alignment and count barcodes and UMIs
Assembly: mm10
Supplementary files format and content: gz format, contained barcodes, features and matrix

source_name: aortic arch

extract_protocol:
The mice were perfused with 4℃ PBS, and then the tissues were collected, dissected in PBS to remove excess hair and blood. Then the aorta were finely minced and transferred to 5ml digestion mix (HBSS, 2U/µl Collagenase type I (17100017, Gibco), 2U/µl Collagenase type II (LS004177, Worthington)). The digestion mix included tissue were incubated at 37℃ for 15 minutes. The cell suspension was filtered through 40μm cell strainer and then pelleted by centrifugation at 500g for 5 minutes. Next the cells were incubated in red-blood-cell lysis buffer (1ml, eBioscience, 00-4333-57) at room temperature for 1 min. Add ten times the volume of cold PBS, centrifuged and resuspended with cold PBS. At last, the cells were pelleted by centrifugation at 300g for 5 minutes and resuspended with 100 µl cold PBS.
The cell suspense was loaded in 10x Chromium controller to generate GEMs, which were further processed into single cell 5ʹ gene expression libraries using Chromium Single Cell 5ʹ Library Kit (v2 Chemistry).

value: aortic arch

value: isolated aortic cells

value: aortic cells

tag: batch

value: single


title: HFL-1 cells, vec1

description:
Library name: Sample 4
HFL1_WT1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish J1B6

description:
Library name: SkinF133_J_1B_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C19_1

value: skin

value: female


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish P1B8

description:
Library name: TestisM147_P_1B_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C24_1

value: testis


title: mthfd1-1, leaf, highCO2, biorep3, RNAseq

city: Neuherberg

first: Martin

last: Groth

address: Ingolstädter Landstr. 1

department: Institute of Functional Epigenetics

country: Germany

institute: Helmholtz Munich

description:
Library name: RNAseq_m_h_3
m_h_3

data_processing:
BS-seq: Raw reads were pre-processed with trimmomatic using the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:1:30:12:3:true CROP:150 HEADCROP:3 (for standard)/12 (for PBAT libraries) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 for PE150 reads and ILLUMINACLIP:TruSeq3-SE.fa:1:30:10 CROP:50 HEADCROP:2 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 for SE50 reads. Pre-processed reads were mapped to TAIR10 using Bismark (v0.23.1) with parameters N set to 1 (allowing 1 mismatch in seed alignments) and X (maximum insert size for valid paired-end alignments) set to 700. Duplicated reads and reads flagged as unconverted due to three or more consecutive methylated CHH sites were discarded. Methylation ratios were calculated separately for CG, CHG, and CHH sites as #C/(#C+#T). Non-conversion ratios were calculated from chloroplast cytosine methylation ratios. Genome browser tracks showing CG, CHG, and CHH methylation ratios at single cytosine resolution were generated from Bismark genome-wide cytosine methylation output files for cytosine sites with at least 4 reads.
mRNA-seq: mRNA-seq reads were processed using the nf-core/rnaseq pipeline (v3.10.1) in Nextflow  (v22.10.6) executed using singularity containers on the high-performance computing cluster at Helmholtz Munich. Default parameters were used for read trimming/filtering, alignment, and quantification with Trim Galore!, STAR, and Salmon, respectively, except as stated below. TEs and genes were analyzed separately. For TEs, reads were aligned to the TAIR10 reference genome using a transcript-based TE annotation and extra STAR alignment arguments “--outMultimapperOrder Random --outFilterMultimapNmax 50 --alignIntronMax 10000 --alignSJoverhangMin 3”, whereas Araport11 gene models and extra STAR alignment arguments “--outFilterMultimapNmax 50 --alignIntronMax 10000 --alignSJoverhangMin 3” were used for genes. Transcript abundance estimates from Salmon were used to generate TE/gene-level count matrices for visualization and differential expression analysis with DESeq2 (v1.38.3). TEs/genes with less than 6 counts across all samples were removed.
Assembly: TAIR10/Araport11
Supplementary files format and content: BS-seq: wig or bigWig files showing single cytosine methylation ratios for each sequence context.
Supplementary files format and content: mRNA-seq: tab-separated text file containing TPM per gene/TE for all samples of the experiment.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were cultivated in growth chambers (Weiss Technik & Vötsch) at 23/20 °C (day/night), 65 % relative humidity and 100 μmol m-2 s-1 photosynthetically active radiation (PAR, 400–700 nm) under long day (LD), i.e. 16h light, and short day (SD), i.e. 10h light, 24h cycles. Plants were germinated and grown on soil consisting of 4 parts multiplication substrate (Floragard) and 1 part quartz sand.

extract_protocol:
Samples consisted of rosette leave tissue that was harvested 21 and 28 days after germination for LD and SD conditions, respectively. Genomic DNA was isolated from 100 mg (fresh weight) of rosette leave tissue pooled from 3-4 plants per sample using DNeasy Plant Mini Kit (Qiagen), except for comparison of DNA methylation under SD and LD conditions, where 14 days old seedlings grown on Phyto agar (RPI Corp.) with half-strength Murashige and Skoog (MS) basal salt mixture (MP Biomedicals) were used. Total RNA was isolated from 100 mg (fresh weight) of rosette leave tissue pooled from 3-4 plants per sample using RNeasy Plant Mini Kit (Qiagen) followed by DNA digestion with amplification grade DNase I (Thermo Fisher Scientific).
BS-seq: The isolated DNA was sheared into 200-400bp fragments by ultrasonication (Covaris S2/S220/E220). WGBS of wild type, mthfd1, thfs single and mt double mutants was performed by BGI TECH Solutions (Hong Kong), proceeding with end repair of the sheared DNA, deoxyadenylation, and ligation of methylated sequencing adaptors, followed by bisulfite conversion using EZ DNA Methylation-Gold kit (ZYMO Research), size selection, PCR amplification and final size selection of libraries. Libraries for WGBS of seedlings grown under SD and LD conditions and CRISPR-Cas9 lines were prepared the same way, except using KAPA HyperPrep Kit (Roche), TruSeq DNA LT (Illumina)/NEBNext Multiplex Oligos (New England Biolabs) methylated adaptors, and EpiTect Bisulfite Kit (Qiagen), and sequenced at Novogene. WGBS of wild type and mthfd1 plants grown under cCO2 and hCO2 was performed by Novogene using post-bisulfite adaptor tagging (PBAT) with Accel-NGS Methyl-Seq DNA Library Kit for Illumina (Swift Biosciences).
mRNA-seq: Library construction and sequencing was performed by Novogene. For preparation of non-directional libraries, messenger RNA (mRNA) was purified from total RNA using oligo-dT-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: For analysis of methylome and transcriptome changes upon suppression of photorespiration, plants were grown in a sun simulator climate chamber at the Research Unit for Environmental Simulation, Helmholtz Munich. Growth conditions were controlled with light intensity of 130 µmol m⁻² s⁻¹ (PAR) at plant height, day/night temperature cycle of 23°C (16 h) and 21°C (8 h), and relative humidity of 65%. Plants were grown in two Plexiglas cuvettes of dimensions 55 × 28 × 110 cm (W × D × H). One cuvette was flushed with 60 m³ h⁻¹ of air containing ambient CO₂ concentrations (cCO2), while the other was flushed with air and continuously fumigated with CO₂ (Air Liquide) at ~3000 ppm final concentration (hCO2). Airflows were controlled using a 1L mass flow controller (MKS Instruments GmbH), calibrated with a mass flow meter (ADM 3000, Agilent).

value: leaf


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish J1B7

description:
Library name: OvaryF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C23_1

value: ovary


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish J1A22

description:
Library name: MuscleM47_J_1A_22
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C16_1

value: muscle


title: HFL-1 cells, oe3

description:
Library name: Sample 3
HFL1_OE3


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish J1B2

description:
Library name: MuscleM49_J_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C14_1


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish C04

description:
Library name: MuscleF134_C04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C15_1


title: mthfd1-1, leaf, highCO2, biorep1, RNAseq

description:
Library name: RNAseq_m_h_1
m_h_1


title: HFL-1 cells, oe2

description:
Library name: Sample 2
HFL1_OE2


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish B01

description:
Library name: MuscleM134_B01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C13_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1B2

description:
Library name: SkinM49_J_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C18_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish D14

description:
Library name: SkinF52_D_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C17_1


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish P1B9

description:
Library name: SkinF49_P_1B_9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C20_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1A14

description:
Library name: KidneyM75_J_1A_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C12_1

value: kidney


title: Col0, leaf, highCO2, biorep3, RNAseq

description:
Library name: RNAseq_wt_h_3
wt_h_3

value: wild type


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish P1A4

description:
Library name: KidneyM133_P_1A_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C10_1


title: HFL-1 cells, oe1

description:
Library name: Sample 1
HFL1_OE1


title: Col0, leaf, highCO2, biorep2, RNAseq

description:
Library name: RNAseq_wt_h_2
wt_h_2


title: KO2

city: Jinan

first: Huirui

last: Wang

state: -- None selected --

address: 44 Wenhuaxi Road

institute: Shandong University

description: Library name: KO2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HFL1 cells

extract_protocol:
Cells were lysed in TRIzol reagent, and total RNA was extracted by using a Rapid RNA Extraction Kit per the manufacturer’s protocol. The integrity of the RNA was verified via agarose gel electrophoresis, and the RNA concentrations were quantified with a NanoDrop spectrophotometer.
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq 6000. The index of the reference genome was built by using HISAT2 (v2.0.5), and paired-end clean reads were aligned to the reference genome.

value: HFL1 cells

value: KO


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish I05

description:
Library name: KidneyF134_I05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B9_1

value: GRZ wild type


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1B20

description:
Library name: KidneyM77_J_1B_20
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C11_1

value: male


title: KO1

description: Library name: KO1


title: Col0, leaf, highCO2, biorep1, RNAseq

description:
Library name: RNAseq_wt_h_1
wt_h_1


title: mthfd1-1, leaf, highCO2, biorep2, RNAseq

description:
Library name: RNAseq_m_h_2
m_h_2


title: mthfd1-1, leaf, controlCO2, biorep3, RNAseq

description:
Library name: RNAseq_m_c_3
m_c_3


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish I05

description:
Library name: LiverF134_I05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B6_1

value: liver


title: WT2

description: Library name: WT2

value: WT


title: mthfd1-1, leaf, controlCO2, biorep2, RNAseq

description:
Library name: RNAseq_m_c_2
m_c_2


title: WT1

description: Library name: WT1


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish J05

description:
Library name: LiverF102_J05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B5_1


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish P1B10

description:
Library name: LiverM133_P_1B_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B7_1


title: L7851

city: Leiden

first: Debora

last: Meijer

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: 105372-001-057

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

source_name: tumor

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

tag: disease

value: Con. Central CS

tag: grade

value: tumor


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish D6

description:
Library name: GutF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B3_1

value: gut


title: mthfd1-1, leaf, controlCO2, biorep1, RNAseq

description:
Library name: RNAseq_m_c_1
m_c_1


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish P1A8

description:
Library name: OvaryF75_P_1A_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B24_1


title: Col0, leaf, controlCO2, biorep3, RNAseq

description:
Library name: RNAseq_wt_c_3
wt_c_3


title: Col0, leaf, controlCO2, biorep2, RNAseq

description:
Library name: RNAseq_wt_c_2
wt_c_2


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish D14

description:
Library name: GutF52_D_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: C1_1


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish P1B10

description:
Library name: TestisM133_P_1B_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B22_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1A17

description:
Library name: SkinM47_J_1A_17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B20_1

value: skin


title: L7570

description: Library name: 105372-001-054


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish C03

description:
Library name: TestisM162_C03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B23_1


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish P1A10

description:
Library name: GutM103_P_1A_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B2_1


title: Col0, leaf, controlCO2, biorep1, RNAseq

description:
Library name: RNAseq_wt_c_1
wt_c_1


title: L7754

description: Library name: 105372-001-056


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish J1B7

description:
Library name: SkinF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B18_1

value: female


title: L7714

description: Library name: 105372-001-055


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish J9

description:
Library name: OvaryF155_J9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B21_1


title: CC9_23, leaf, LD, biorep2, BSseq

description: Library name: BSseq_CC9_23_rep2

library_source: genomic

molecule: genomic DNA

value: long day


title: PacBio_AAV_p152

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description:
Library name: PacBio_AAV_p152
sequenced on the benchtop Vega system
Long-read PacBio data from packaged AAV (direct). Library p152, PHP.eB serotype, standard input dose

library_source: other

data_processing:
Creation of oBC-enhancer-mBC association dictionary for scQer constructs
To generate the dictionary connecting the oBC, enhancer, and mBC, the intermediate plasmid library without reporter insert (see section above) was used as a template for PCR to append P5 and P7 Illumina adapters with primers oJBL425 and oJBL884 with 12 cycles (PCR products ranging from 724 bp to 1313 bp in expected size). While the upper bound is starting to be long for clustering on the Illumina flow cells, we still obtained sufficient read coverage for appropriate barcode assignment. The library was sequenced on a NS2000, with the following sequencing primers and read architecture: read1: oJBL371 15 cycles mBC, index1: oJBL432 6 cycles sample index; index2: oJBL433 16 cycles oBC, read2: oJBL775 101 cycles. Sequencing data was analyzed as follows: the enhancer read was aligned to the list of CRE in the constructs using bowtie2. Aligned reads were then combined with the barcode reads and piled up to counts using custom scripts. Given the high coverage of the library, the following downstream processing was performed. First, triplets were processed separately for different enhancers. Then a low count threshold on the triplet was applied and oBC/mBC were error corrected using a graph-based Hamming distance of 1 approach on a per-enhancer basis. The resulting re-summed triplet (from the error corrected set) was then filtered with a more stringent threshold, leading to a set of n=3614 unique oBC-enhancer-mBC triplets in the library.
PacBio AAV library analysis
In order to analyze the different class of reads in the data identified by initial inspection of the read length distribution (Fig. S8a), we first selected reads within the expected size range for ssAAV and scAAV (p151:mid-hom ssAAV 2350-2650 bp, scAAV-like 4750-5000 bp; p152:mid-non-hom ssAAV 2300-2700 bp, scAAV-like 4750-5200 bp). For the ssAAV reads (putatively generated by annealing prior to SMRTbell ligation), analysis proceeded as before for the ONT data. For the scAAV-like reads (from extension), in order to analyze the BC sets on both halves of the reads separately, reads were split in two at 2500 nt. The ‘left’ and ‘right’ halves were then analyzed using the same pipeline as the other reads. Tn5 mosaic end snapback molecules (which corresponded to a distinct population of a definite size, see Fig. S8a) were analyzed using another pipeline given the different barcode architecture. Specifically, reads of the expected size (between 3800 and 3900 bp for p151 and 3800-4000 bp for p152) with two mapped ITRs were extracted.  Then signposts surrounding BC2 (up: GATCCGTCGATCGACTGAGT, down: TAGCGCGCCATTAGGCATGA) were scanned in both orientation using function matchPattern from Biostrings with option max.mismatch=2. BC2s from reads with 4 hits (up/down, forward/reverse) were selected based on whether both BC2 reads were in the starting BC1-BC2 dictionaries and concordance assessed.
Assembly: Custom constructs, N/A.
Supplementary files format and content: see: supplementary_file_readme.txt

molecule: other

organism: synthetic construct

source_name: AAV-293 cells for AAV packaging, PHP.eB serotype

extract_protocol:
Plasmids were purified with Zymo MidiPrep kit. AAV samples were sequenced by Plasmidsaurus (ONT) or locally on a PacBio Vega.
See manuscript for details on cloning of scQer-AAV libraries and other BC1-BC2 libraries used in the manuscript.
AAV preps were submitted to Plasmidsaurus for direct sequencing (which involves an annealing step, end-repair and adapter ligation) with Oxford Nanopore.
To generate libraries of barcoded insert by PCR from the AAV packaged DNA, we first extracted DNA by performing proteinase K treatment (3 μL crude AAV prep, 6 μL 10 mM Tris 8, 1 μL proteinase K [Thermo Scientific EO0491], 60 min at 50C, 5 min at 70C, then placed on ice), followed by phenol/chloroform extraction (add 190 μL 10 mM Tris 8, add 200 μLphenol-chloroform-isoamyl alcohol [Invitrogen 15593-031], vortex 30 s, spin at 16,000 g at room temperature for 5 min, take aqueous layer) and isopropanol precipitation (add 1 μL glycoblue, 50 μLNaOAc 3M, 250 μLisopropanol 100%, vortex, 45 min at -80C, 45 min at 21,000 g at 4C, 80% EtOH wash, air dry pellet, resuspend in 10 μL 10 mM Tris 8). 2 μL of the precipitated DNA was taken as template for PCR.
Amplicons for the oBC-CRE-mBC association in scQer library were generated by PCR.


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish J1B6

description:
Library name: LiverF133_J_1B_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B8_1


title: PacBio_AAV_p151

description:
Library name: PacBio_AAV_p151
sequenced on the benchtop Vega system
Long-read PacBio data from packaged AAV (direct). Library p151, PHP.eB serotype, standard input dose

value: AAV-293 cells for AAV packaging, PHP.eB serotype


title: L6991

description: Library name: 105372-001-052


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish J1A22

description:
Library name: GutM47_J_1A_22
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B4_1


title: CC9_20, leaf, LD, biorep2, BSseq

description: Library name: BSseq_CC9_20_rep2

value: leaf

value: mthfd1-1 thfs


title: L7147

description: Library name: 105372-001-053


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish C03

description:
Library name: SkinM162_C03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B19_1


title: L6807

description: Library name: 105372-001-050


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1A4

description:
Library name: MuscleM133_P_1A_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B16_1

value: muscle


title: ONT_scQer_plasmid_digested_v2

description:
Library name: ONT_scQer_plasmid_digested_v2
Long-read ONT data of scQer library with oBC-enhance-mBC (AAV adapted version), plasmid digested (rep 2)


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish C1

description:
Library name: SkinF155_C1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B17_1


title: L6648

description: Library name: 105372-001-049


title: ONT_scQer_plasmid_PCR_11cycles

description:
Library name: ONT_scQer_plasmid_PCR_11cycles
Long-read ONT data of scQer library with oBC-enhance-mBC (AAV adapted version), PCR from plasmid library (11 cycles)


title: ONT_scQer_plasmid_PCR_14cycles

description:
Library name: ONT_scQer_plasmid_PCR_14cycles
Long-read ONT data of scQer library with oBC-enhance-mBC (AAV adapted version), PCR from plasmid library (14 cycles)


title: L6544

description: Library name: 105372-001-048


title: CC9_20, leaf, LD, biorep1, BSseq

description: Library name: BSseq_CC9_20_rep1


title: CC9_23, leaf, LD, biorep1, BSseq

description: Library name: BSseq_CC9_23_rep1


title: L6480

description: Library name: 104320-001-013

value: Dediff. Central CS

value: Dedifferentiated


title: L6479

description: Library name: 105372-001-047


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish E04

description:
Library name: MuscleM102_E04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B15_1


title: nucleus pulposus cells, SOD1-K123R-1

city: Chongqing

first: Yuyao

last: Zhang

address: No.83, Xinqiao Zhengjie, Shapingba District

institute: Xiqiao hospital

description:
Library name: Sample 5
L1MKH0409318-L_1

data_processing:
Significantly differentially expressed genes (DEGs) were filtered with the thresholds of |log2 (fold change, FC)| > 2 and P value < 0.05 using the R package DESeq2
Transcription factor prediction was performed using the STRING database, CHEA3 database or Cytoscape software
Data from transcription factor prediction were filtered using the cytoHubba plugin
Assembly: GRCr8
Supplementary files format and content: Gene expression count matrix: Format is TSV/CSV; content includes gene IDs and read count values of each experimental sample

organism: Rattus norvegicus

source_name: nucleus pulposus

extract_protocol:
Total RNA from NPCs was isolated using TRIzol, and quantified using a NanoDrop 2000 (NanoDrop, U.S.A.)
cDNA libraries were constructed with SuperScript™ II reverse transcriptase; 2 × 150 bp paired-end RNA-seq was performed using the Illumina NovaSeq platform

value: nucleus pulposus

value: nucleus pulposus cells

value: lactate


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish P1B4

description:
Library name: KidneyF147_P_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B11_1

value: kidney

value: GRZ wild type


title: nucleus pulposus cells, SOD1-K123R-4

description:
Library name: Sample 8
L1MKH0409321-L_4


title: nucleus pulposus cells, SOD1-K123R-2

description:
Library name: Sample 6
L1MKH0409319-L_2


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish P1B3

description:
Library name: MuscleF77_P_1B_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B14_1


title: ONT_scQer_plasmid_digested_v1

description:
Library name: ONT_scQer_plasmid_digested_v1
Long-read ONT data of scQer library with oBC-enhance-mBC (AAV adapted version), plasmid digested (rep 1)


title: L6431

description: Library name: 105372-001-046

value: Con. Central CS


title: ONT_scQer_AAV_PCR_17cycles

description:
Library name: ONT_scQer_AAV_PCR_17cycles
Long-read ONT data of scQer library with oBC-enhance-mBC (AAV adapted version), PCR from AAV encapsidated DNA (17 cycles)


title: nucleus pulposus cells, SOD1-K123R-3

description:
Library name: Sample 7
L1MKH0409320-L_3


title: L6255

description: Library name: 105372-001-045

value: tumor


title: ONT_AAV_direct_p152_100%_dosage_input

description:
Library name: ONT_AAV_direct_p152_100__dosage_input
Long-read ONT data from packaged AAV (direct). Library p152, PHP.eB serotype, standard input dose


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish J1B5

description:
Library name: KidneyF49_J_1B_5
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B12_1


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish P1B8

description:
Library name: KidneyM147_P_1B_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B10_1

value: male


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish J9

description:
Library name: MuscleF155_J9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B13_1


title: nucleus pulposus cells, Ctrl-3

description:
Library name: Sample 3
L1MKH0409308-Ctrl_3

value: WT


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish B01

description:
Library name: GutM134_B01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: B1_1

value: gut


title: L5432

description: Library name: 105372-001-032


title: L7264

description: Library name: 104320-001-061


title: nucleus pulposus cells, Ctrl-2

description:
Library name: Sample 2
L1MKH0409307-Ctrl_2


title: ONT_AAV_direct_p151_1%_dosage_input

description:
Library name: ONT_AAV_direct_p151_1__dosage_input
Long-read ONT data from packaged AAV (direct). Library p151, PHP.eB serotype, input dose 1% from standard


title: nucleus pulposus cells, Ctrl-4

description:
Library name: Sample 4
L1MKH0409309-Ctrl_4


title: ONT_AAV_direct_p151_10%_dosage_input

description:
Library name: ONT_AAV_direct_p151_10__dosage_input
Long-read ONT data from packaged AAV (direct). Library p151, PHP.eB serotype, input dose 10% from standard


title: RNA-Seq of nothobranchius furzeri: adult female kidney from fish E02

description:
Library name: KidneyF78_E02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A9_1

value: female


title: nucleus pulposus cells, Ctrl-1

description:
Library name: Sample 1
L1MKH0409306-Ctrl_1


title: ONT_AAV_direct_p151_0.1%_dosage_input

description:
Library name: ONT_AAV_direct_p151_0.1__dosage_input
Long-read ONT data from packaged AAV (direct). Library p151, PHP.eB serotype, input dose 0.1% from standard

value: AAV-293 cells for AAV packaging, PHP.eB serotype


title: L6065

description: Library name: 105372-001-044


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish P1A6

description:
Library name: LiverM133_P_1A_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A8_1

value: liver


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish J1B18

description:
Library name: LiverF133_J_1B_18
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A7_1


title: ONT_AAV_direct_p151_100%_dosage_input

description:
Library name: ONT_AAV_direct_p151_100__dosage_input
Long-read ONT data from packaged AAV (direct). Library p151, PHP.eB serotype, standard input dose


description:
Library name: scQer_AAV_oBC_CRE_mBC_dictionary_generation
Mapping barcode pairs in scQer library used for in vivo AAV delivery

source_name: Escherichia coli (for plasmid amplification)


title: L6634

description: Library name: 104320-001-053


title: RNA-Seq of nothobranchius furzeri: adult female liver from fish D6

description:
Library name: LiverF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A6_1


title: U3054_3D_2

type: RNA

city: Lund

first: Mattias

last: Belting

address: Barngatan 4

department: Department of Clinical Sciences, Division of Oncology

country: Sweden

institute: Lund University

description: Replicate 2

hyb_protocol: 5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45°C to Affymetrix Clariom S human arrays according to standard protocol. Washing and staining were performed using Affymetrix Fluidics Station 450

scan_protocol: The arrays were scanned using an Affymetrix Gene Chip Scanner 3000 7G.

data_processing: Gene array data was processed using the R statistical language (v4.4.2) within Rstudio. Using oligo (v1.70.0) package, raw CEL files were loaded into R (oligo::read.celfiles), then Robust Multichip Average (RMA)-based background correction and quantile normalization were performed (oligo::rma). Annotation of probe IDs was performed with affycoretools (v1.78.0) package (affycoretools::annotateEset) with the clariomdhumantranscriptcluster.db (c8.8.0) ChipDb reference package. Analysis of differentially expressed genes was performed with limma (v3.62.1) package in R according to best practices, such as design matrix was built (stats::model.matrix), a linear model was fitted (limma::lmFit), a contrast matrix was constructed (limma::makeContrast), coefficients and errors were estimated (limma::contrast.fit), empirical Bayes statistics moderation was applied (limma::eBayes), and finally DEGs were extracted using limma::topTable.

label: Biotin

source_name: U3054MG glioblastoma cells cultured for 14 days in 3D

label_protocol: Sense target cDNA was prepared from 150 ng of total RNA using the Affymetrix GeneChip WT Plus Kit (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

growth_protocol: Cells were routinely cultured  in a humidified atmosphere of 5% CO2 at 37°C on precoated poly-L-ornithine- and laminin- surfaces in Neurobasal:DMEM/F12 (1:1) medium supplemented with EGF (10 ng/mL), FGF2 (10 ng/mL), and stem cell supplements N2 (1%) and B27 (2%) and PEST (1%). For 3D spheroid cultures, GBM cells were cultured in poly-hema coated dishes on an orbital shaker at 90 rpm.

extract_protocol: All samples were dissolved in 350 μl lysis solution provided by the AllPrep DNA/RNA Micro Kit (Qiagen) for RNA isolation according to the manufacturer’s instructions. Total RNA quality was assessed by Agilent Technologies 2200 Tapestation and concentrations were measured by NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Cells were grown at pH 7.4 in routine culture medium (see above). 2D cultures were lysed 72 h after seeding. For 3D spheroid cultures, cells were cultured in poly-hema coated dishes at 2 x 10^5 cells/mL for 14 days prior to lysis, with medium exchanged every 4th day. 3D spheroid were collected by centrifugation and washed twice with PBS prior to lysis.

value: Brain

value: 14 days in 3D


title: HU74_OLIG2

city: JERUSALEM

first: Serafima

last: Dubnov

address: The Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: Sample 79

data_processing:
Quality control was re-assessed using FastQC version 0.11.8, with Cutadapt for removing the adaptor sequences.
Assembly: Alignment to tRFs was done using MINTmap to MINTbase v2.0 and to microRNA using miRDeep2 to miRbase 22.1.
Supplementary files format and content: Tab-limited csv files with microRNA, tRNA fragments and tRNA fragment family raw counts for each sample.

source_name: Cerebral Cortex

extract_protocol:
Neurosurgery-obtained fresh human brain specimens were lightly fixed with formalin and broken down to single nuclei with cytoplasmatic fractions. The cell suspensions were next stained cell-type-specific antibodies (NeuN for neurons, Iba1 for microglia, Gfap for astrocytes, Olig2 for oligodendrocytes) and FACS-sorted to distinct cell type populations. RNA from FACS-sorted cell populations was extracted using the RNeasy FFPE kit (Qiagen, 73504), according to the manufacturer’s instructions.
Libraries were constructed using the D-Plex Small RNA-seq Kit from Illumina (Diagenode, C05030001), using 500 and 1000 pg/sample in Batch 1 and Batch 2, respectively.

value: Cerebral Cortex

value: Oligodendrocytes

value: FACS-sorted with OLIG2 antibody

value: Batch 2

value: M

tag: age

tag: hemisphere and_lobe

value: Left frontal


title: HU71_OLIG2

description: Library name: Sample 80

value: Right occipital


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish P1A8

description:
Library name: GutF75_P_1A_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A4_1

value: GRZ wild type


title: L5837

description: Library name: 105372-001-041

value: Con. Central CS

value: tumor


title: HU66_OLIG2

description: Library name: Sample 77

value: F


title: U3054_3D_3

description: Replicate 3


title: L5976

description: Library name: 105372-001-043


title: U3054_3D_1

description: Replicate 1


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish I05

description:
Library name: GutF134_I05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A3_1

value: gut


title: HU64_OLIG2

description: Library name: Sample 78

value: Biilateral parietal


title: HU57_OLIG2

description: Library name: Sample 76

value: Left temporal


title: L5717

description: Library name: 105372-001-039


title: U3054_2D_3

description: Replicate 3

source_name: U3054MG glioblastoma cells cultured for 72 h in 2D

value: 72 h in 2D


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish J1A13

description:
Library name: TestisM75_J_1A_13
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A24_1

source_name: testis

value: testis

value: male


title: U3054_2D_2

description: Replicate 2

value: Brain


title: L5812

description: Library name: 105372-001-040


title: HU67_OLIG2

description: Library name: Sample 75

value: Cerebral Cortex

value: Oligodendrocytes

value: Right frontal


title: RNA-Seq of nothobranchius furzeri: adult male liver from fish B01

description:
Library name: LiverM134_B01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A5_1

source_name: liver

value: liver


title: RNA-Seq of nothobranchius furzeri: adult female ovary from fish E02

description:
Library name: OvaryF78_E02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A23_1

source_name: ovary

value: ovary

value: female


title: U3054_2D_1

description: Replicate 1


title: L5850

description: Library name: 105372-001-042


title: HU68_OLIG2

description: Library name: Sample 74

value: FACS-sorted with OLIG2 antibody

value: Batch 2

value: M


title: L5692

description: Library name: 105372-001-038

value: Con. Central CS

value: tumor


title: RNA-Seq of nothobranchius furzeri: adult male testis from fish A01

description:
Library name: TestisM78_A01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A21_1

value: GRZ wild type


title: L5688

description: Library name: 105372-001-037


title: U3047_3D_3

description: Replicate 3

source_name: U3047MG glioblastoma cells cultured for 14 days in 3D

value: 14 days in 3D


title: L5670

description: Library name: 105372-001-036


title: U3047_3D_2

description: Replicate 2


title: L5574

description: Library name: 105372-001-035


title: HU73_OLIG2

description: Library name: Sample 73

value: Left frontal


title: RNA-Seq of nothobranchius furzeri: adult male gut from fish P1B2

description:
Library name: GutM133_P_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A2_1

source_name: gut

value: gut


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1B11

description:
Library name: SkinM161_J_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A20_1

source_name: skin

value: skin

value: male


title: L5546

description: Library name: 105372-001-034


title: HU61_OLIG2

description: Library name: Sample 72

value: Cerebral Cortex

value: F

value: Bilateral frontal


title: HU78_OLIG2

description: Library name: Sample 70

value: Oligodendrocytes

value: Right parietal


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish I03

description:
Library name: SkinM162_I03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A19_1


title: RNA-Seq of nothobranchius furzeri: adult male skin from fish J1B4

description:
Library name: SkinM161_J_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A18_1


title: HU79_OLIG2

description: Library name: Sample 71

value: Left temporal


title: U3047_2D_2

description: Replicate 2

source_name: U3047MG glioblastoma cells cultured for 72 h in 2D

value: Brain

value: 72 h in 2D


title: HU77_OLIG2

description: Library name: Sample 69

value: FACS-sorted with OLIG2 antibody

value: Batch 2

value: M

value: Right temporal


title: L5380

description: Library name: 104320-001-005

value: Con. Central CS

value: tumor


title: U3047_3D_1

description: Replicate 1

value: 14 days in 3D


title: RNA-Seq of nothobranchius furzeri: adult female skin from fish C04

description:
Library name: SkinF134_C04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A17_1

value: skin

value: GRZ wild type

value: female


title: U3047_2D_1

description: Replicate 1


title: L5540

description: Library name: 105372-001-033


title: RNA-Seq of nothobranchius furzeri: adult female muscle from fish P1A2

description:
Library name: MuscleF103_P_1A_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A16_1

source_name: muscle

value: muscle


title: U3047_2D_3

description: Replicate 3


title: HU75_OLIG2

description: Library name: Sample 67

value: Cerebral Cortex

value: Left parietal


title: L5364

description: Library name: 104320-001-074


title: HU76_OLIG2

description: Library name: Sample 68

value: Oligodendrocytes

value: Left frontal


title: L7262

description: Library name: 104320-001-059


title: U3017_3D_1

description: Replicate 1

source_name: U3017MG glioblastoma cells cultured for 14 days in 3D

value: Brain


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish E1

description:
Library name: MuscleM52_E_01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A15_1

value: male


title: L5213

description: Library name: 105372-001-029

value: ACT


title: U3017_3D_3

description: Replicate 3


title: U3017_3D_2

description: Replicate 2


title: HU23_NEUN

description: Library name: Sample 65

value: Neurons

value: FACS-sorted with NEUN antibody

value: Batch 1

value: F


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish D12

description:
Library name: MuscleM134_D12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A13_1


title: L5206

description: Library name: 105372-001-028

value: Con. Central CS

value: tumor


title: RNA-Seq of nothobranchius furzeri: adult male muscle from fish P1B8

description:
Library name: MuscleM147_P_1B_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A14_1


title: HU39_NEUN

description: Library name: Sample 66

value: Batch 2

value: M


title: U3017_2D_3

description: Replicate 3

source_name: U3017MG glioblastoma cells cultured for 72 h in 2D

value: 72 h in 2D


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1A22

description:
Library name: KidneyM47_J_1A_22
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A11_1

source_name: kidney

value: kidney

value: GRZ wild type


title: U3017_2D_2

description: Replicate 2


title: L5037

description: Library name: 105372-001-025

source_name: tumor


title: HU54_NEUN

description: Library name: Sample 63

value: Cerebral Cortex

value: Right parietal


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish J1B4

description:
Library name: KidneyM161_J_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A12_1


title: HU16_NEUN

description: Library name: Sample 62

value: Right occipital


title: L5205

description: Library name: 104320-001-116


title: L4937

description: Library name: 105372-001-023


title: PANC1_NA3

description: Replicate 3

hyb_protocol: 5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45°C to Affymetrix Clariom S human arrays according to standard protocol. Washing and staining were performed using Affymetrix Fluidics Station 450.

source_name: PANC1 pancreatic cancer, non-adapted control cancer cells

growth_protocol: Cells were routinely cultured in high-glucose DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37°C. To investigate the effects of acidosis, cells were cultured in pH 6.4 medium (or pH 7.4 = Ctrl) supplemented with HEPES (20 mM), MES sodium salt (20 mM) and MOPS (20 mM). Medium pH was adjusted using 1 M HCl and/or 1 M NaOH, and sterile filtered prior to usage.

extract_protocol: All samples were dissolved in 250 μl lysis solution provided by the RNAeasy mini kit (Qiagen) for RNA isolation according to the manufacturer’s instructions.

treatment_protocol: For acidosis-adapted, cells were chronically cultured at pH 6.4 for 10 weeks. Control, non-adapted cells were grown under the same conditions but at physiological pH 7.4.

value: Pancreas; Duct

value: Neutral pH (pH 7.4) 10 weeks


title: HU17_NEUN

description: Library name: Sample 61

value: Left occipital


title: RNA-Seq of nothobranchius furzeri: adult male kidney from fish P1B10

description:
Library name: KidneyM133_P_1B_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A10_1

value: male


title: RNA-Seq of nothobranchius furzeri: adult female gut from fish J9

description:
Library name: GutF155_J9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: A1_1

value: gut

value: female


title: PANC1_NA1

description: Replicate 1


title: HU15_NEUN

description: Library name: Sample 64

value: Neurons

value: FACS-sorted with NEUN antibody

value: Batch 1

value: Left frontal


title: PANC1_AA3

description: Replicate 3

source_name: PANC1 pancreatic cancer, acidosis-adapted cancer cells

value: Acidosis (pH 6.4) 10 weeks


title: PANC1_NA2

description: Replicate 2


title: BV2 microglial cells, overexpress TDP43-NLS, rep3

first: Shenrui

address: Kongjiang Road 1665, Yangpu District

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: NLS3

data_processing:
ZTRON(Version:22.0.5)
Data filtering: removal of adapter-contaminated reads, removal of low-quality reads, and removal of reads containing an excessive proportion of undetermined bases (N).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Mus_Musculus.GRCm39.chr
Supplementary files format and content: txt files include FPKM values for each sample
Supplementary files format and content: txt files include raws counts for each sample

source_name: BV2 microglial cells

growth_protocol: BV2 microglial cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum and 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent. A total of 2 µg RNA per sample was used as the input material for library preparation.
Sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s instructions, and unique index codes were added to each sample for multiplexing. Briefly, mRNA was isolated from total RNA using poly-T oligonucleotide-attached magnetic beads. The mRNA was fragmented in NEBNext First Strand Synthesis Reaction Buffer (5X) at elevated temperature in the presence of divalent cations. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis with DNA polymerase I, dNTPs, and RNase H. The cDNA fragments were purified using QiaQuick PCR purification kits and eluted in EB buffer. The purified products were subsequently subjected to end repair, A-tailing, and adapter ligation. Finally, target-sized fragments were selected and PCR-amplified to complete the library construction.

value: BV2 microglial cells

value: overexpress TDP43-NLS


title: BV2 microglial cells, overexpress TDP43-NLS, rep2

description: Library name: NLS2


title: L7261

description: Library name: 104320-001-109

value: Dediff. Central CS

value: Dedifferentiated

value: tumor


title: L4872

description: Library name: 105372-001-021

value: Con. Central CS


title: L4893

description: Library name: 105372-001-022


title: U3017_2D_1

description: Replicate 1

value: Brain

value: 72 h in 2D


title: L4714

description: Library name: 105372-001-019


title: PANC1_AA1

description: Replicate 1

value: Pancreas; Duct


title: HU47_NEUN

description: Library name: Sample 59

source_name: Cerebral Cortex

value: Cerebral Cortex

value: Batch 2

value: M


title: HU20_NEUN

description: Library name: Sample 58

value: Neurons

value: Left frontal tip


title: BV2 microglial cells, overexpress TDP43-NLS, rep1

description: Library name: NLS1


title: HU19_NEUN

description: Library name: Sample 60

value: FACS-sorted with NEUN antibody

value: Batch 1

value: Right frontal suprasylvian


title: HU14_NEUN

description: Library name: Sample 57

value: F

value: Right frontal


title: HU8_NEUN

description: Library name: Sample 54

value: Left parietal


title: CC_LD

description: RNA extracted from brain tissue areas high in lipid droplets, LD+ cancer cell.

hyb_protocol: 5.2 µg of fragmented and labeled sscDNA target was hybridized to Clariom™ D Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific). Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific).

data_processing: Gene array data was processed using the R statistical language (v4.4.2) within Rstudio. Using oligo (v1.70.0) package, raw CEL files were loaded into R (oligo::read.celfiles), then Robust Multichip Average (RMA)-based background correction and quantile normalization were performed (oligo::rma). Annotation of probe IDs was performed with affycoretools (v1.78.0) package (affycoretools::annotateEset) with the clariomdhumantranscriptcluster.db (c8.8.0) ChipDb reference package. Differentially gene expression was determined as a difference of lognormalized intesity values recorded in LD+ and LD- tissue samples.

source_name: Microdissected GBM regions, LD+ cancer cells. No CD68 positive cells , with lipid droplets.

label_protocol: Fragmentation and labeling were performed with the GeneChip® WT Pico Labeling Kit according to the manufacturer’s instructions. The sample volume was 15ul at 30ng/ul out of which 200 ng of total RNA was used to generate amplified sense strand cDNA targets using GeneChip® WT Pico Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling of 5.5 ug sscDNA.

extract_protocol: LD+ cancer cell and LD- cancer cell areas (N = 5 patients with a total area of approximately 10 mm^2) were dissolved in 50 μl lysis solution provided by the AllPrep DNA/RNA Micro Kit (Qiagen) for RNA isolation according to the manufacturer’s instructions. Total RNA quality was assessed by Agilent Technologies 2200 Tapestation and concentrations were measured by NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Human glioblastoma tumor cryosections (10 μm) were mounted on DNase and RNase-free membranes (FrameSlidePET), rapidly stained for nuclei with cresyl violet and dehydrated in ice-cold ethanol. Adjacent sections were mounted on poly-lysine coated slides and stained for nuclei (Hoechst), CD68, and LipidTox to identify areas of interest. LD+ cancer cell and LD- cancer cell areas were isolated by LCM using the Zeiss PALM system.


title: L4595

description: Library name: 105372-001-017


title: L4543

description: Library name: 105372-001-016


title: PANC1_AA2

description: Replicate 2

value: Acidosis (pH 6.4) 10 weeks


title: HU22_NEUN

description: Library name: Sample 56

value: Right frontal pericentral


title: L4513

description: Library name: 105372-001-014R

value: Con. Central CS

value: N/A (phalanx)

value: tumor


title: HU64_NEUN

description: Library name: Sample 53

value: Biilateral parietal


title: L4348

description: Library name: 105372-001-013


title: CC_noLD

description: RNA extracted from brain tissue areas low in lipid droplets, LD- cancer cell.

source_name: Microdissected GBM regions, LD- cancer cells. No CD68 positive cells , no lipid droplets.

value: Brain