title: CRC0267PRX0B01201, 201868500022_R05C01, qc_ok

value: COLON


title: Mouse, embryos, cell-GasbE751056

status: Public on Jan 31 2023

type: SRA

city: Beijing

first: Menghan

last: Liu

address: Yiheyuan Road

country: China

institute: Peking University

library_source: genomic

data_processing:
For in silico isolation of RNA from DNA reads, we used Cutadapt (version 3.5) to identify  and extract RNA reads which contained a specific sequence  (GGTTGAGGTAGTATTGCGCAATG) within the GAT5-RT primer from the 5-prime end of  5 Read 2. The RNA reads and DNA reads were then processed separately as two files.
We preprocessed Hi-C part of HiRES data as previously described with custom scripts. Briefly, reads were mapped to the GRCm38 reference genome with BWA-mem2 in “5SP” mode. Contacts and 3D genome structures were generated with Hickit software using default parameters. To remove potential contamination from RNA reads, we cleaned contacts between 10 two exons from the same transcript, which counted for ~0.04% of all contacts. For quality control of reconstructed 3D genome structures, five replicates were generated with random seeds, and median RMSD for each combination of 3 replicates was calculated. The first replicate in the combination with the minimum median RMSD value (if < 1.5) were used for downstream analysis. 3D proximity and 3D distance maps were generated as previously descried with custom codes.
For RNA data, we first removed reads containing no poly-A sequence following GAT5-RT primer sequence. We then aligned Read 1 to the GRCm38 reference genome using STAR. Duplications were removed based on UMIs with UMI-tools. RNA count matrix was generated by FeatureCounts with parameters “-O -M --fraction”. We used RNAsnpSplit for phasing of  allele-specific RNA counts.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

organism: Mus musculus

source_name: Embryos

extract_protocol:
All animal maintenance and experimental procedures were carried out in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) of Peking University. Cast/Eij male and C57BL/6J female mice were purchased from Jackson Laboratory and raised under 12h brightness and 12h darkness. 8-week-old mice were naturally mated and females were transferred on the next morning (considered as E0.5). Post-implantation embryos were collected in PBS containing 10%FBS between E7.0 and E11.5. For brain tissues, left cortex was dissected from 8 to 9-week-old F1 hybrid mice in ice-cold PBS.
Mouse Embryos. For E7.0 - E8.5 embryos, all embryos from one mouse were collected and dissociated in 100 μL TrypLE™ Express (Gibco 12604013) for 5 min. For E9.5 - E11.5 embryos, one or two embryos from one mouse were collected and dissociated in 200 μL TrypLE™ Express for 10 min. TrypLE™ Express was inactivated by adding 5-fold volume of  PBS. The cell suspension was then filtered with a 40 μm cell strainer (Falcon 352340) and centrifuged at 100 g fro 5 min at 4 C. The pellet was washed once with 500 μL PBS and the cell number was adjusted to ~100 k in 200 μL PBS.
Mouse Brains. Cortex was dissected in ice-cold PBS and transferred to a 1 mL Dounce homogenizer (Wheaton 357538) containing 1mL ice-cold Homogenization Buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 μM DTT, 0.1% Igepal CA 630) with 10 μL Recombinant RNase Inhibitor (TaKaRa 2313B), 10 μL SUPERaseIn (Invitrogen AM2694) and 100 μL protease inhibitor (Sigma P8340). Dissected tissues were homogenized with five strokes of the loose pestle, followed by 15 strokes of the tight pestle. The homogenate was filtered through a 40 μm cell strainer and centrifuged at 300 g for 5 min at 4 C. The pellet was washed in 500 μL Nuclei Storage Buffer (166.5 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0) with 5 μL Recombinant RNase Inhibitor and 50 μL protease inhibitor and centrifuged at 300 g for 5 min at 4 °C. The pellet was resuspended with 500 μL of Nuclei Storage Buffer to estimate the number of intact nuclei. Then the number of nuclei was adjusted to ~250 k in 500 μL Nuclei Storage Buffer.
The single-cell preamplification product was diluted for 15 folds and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C × 2 min 45 and repeat Step 3 for an additional 5 times; Step 4: 4 °C hold on. Then 2 μL 5 μM i7 UD index was added and incubated with: Step 1: 4 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C × 2 min and repeat Step 3 for an additional 5 times; Step 4: 72 °C × 5 min. The sequence of RNA-P7 primer was GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGTTGAGGTAGTATTGCGCAATG. The barcoded single-cell libraries were then pooled and purified with 0.6 × and 0.15 × AMPure XP Beads (Beckman, A63881). The final libraries were sequenced with paired end 150-bp reads on a NovaSeq 6000 (Illumina) platform according to the manufacturer’s instructions.

tag: tissue

value: Embryos

tag: strain

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, embryos, cell-GasbE751054


title: CRC0288PRH0000000, 201869680085_R05C01, qc_ok

type: genomic

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

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

scan_protocol: GenomeStudio Illumina standard acquisition protocols.

data_processing:
processed with minfi package (v1.32.0), intensities were preprocessed with preprocessRaw() function, beta values were generated after preprocessNoob() function
Matrix_Processed.txt: Average Beta
Matrix_Signal.txt: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Colorectal Cancer

label_protocol: Standard Illumina protocols

growth_protocol: Standard LMX/PRX growth xenografts protocols

extract_protocol: genomic DNA was extracted and purified using Promega Maxwell RSC Blood DNA, according to standard instructions

tag: disease state

value: CRC

tag: gender

value: Male

value: PR

tag: subtypes

value: H

tag: xenografts recist

tag: age

tag: tnm

tag: Stage

value: I

tag: location

value: RETTO


title: Mouse, embryos, cell-GasbE751053


title: CRC0264LMX0A02201, 201868500046_R06C01, qc_ok

value: LM

value: X

value: SD

value: IV


title: CRC0263PRX0A01201, 201503670141_R07C01, qc_ok

value: IIIB


title: CRC0262LMX0A02201, 201985320161_R01C01, qc_ok

value: OR


title: Mouse, embryos, cell-GasbE751052


title: CRC0259PRX0A01201, 201868500022_R04C01, qc_ok

value: Female

value: II


title: Mouse, embryos, cell-GasbE751050


title: CRC0257LMX0A02204, 201868500027_R05C01, qc_ok


title: CRC0261LMX0A02201, 201858500245_R06C01, qc_ok

value: PD

value: IVA


title: Mouse, embryos, cell-GasbE751051

value: Embryos

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, embryos, cell-GasbE751049


title: Mouse, embryos, cell-GasbE751107


title: CRC0256PRX0A01201, 201868500021_R08C01, qc_ok

value: CRC

value: COLON


title: CRC0269PRX0A01201, 201868500022_R06C01, qc_ok

value: PR


title: CRC0253LMX0A02201, 201868500077_R03C01, qc_ok

value: Male

value: III


title: CRC0254LMX0A01201, 201868500022_R03C01, qc_ok

value: LM


title: CRC0246LMX0B01201, 201868500021_R03C01, qc_ok

value: X


title: Mouse, embryos, cell-GasbE751048


title: Mouse, embryos, cell-GasbE751047


title: Mouse, embryos, cell-GasbE751043


title: Mouse, embryos, cell-GasbE751045


title: Mouse, embryos, cell-GasbE751044


title: Mouse, embryos, cell-GasbE751046


title: CRC0252LMX0A02204, 201870620137_R08C01, qc_ok

value: IIa


title: CRC0240PRX0A01201, 201496850100_R04C01, qc_ok


title: Mouse, embryos, cell-GasbE751041


title: CRC0243LMX0A02204, 201868500127_R07C01, qc_ok

value: SD

value: IIIb

value: RETTO


title: CRC0242LMX0B02201, 201868500163_R01C01, qc_ok

value: Female

value: IV


title: CRC0238PRX0B01201, 201496850086_R01C01, qc_ok


title: CRC0234PRX0A01201, 201868500021_R07C01, qc_ok


title: Mouse, embryos, cell-GasbE751039


title: Mouse, embryos, cell-GasbE751040


title: Mouse, embryos, cell-GasbE751042


title: CRC0231LMX0A02204, 201858500154_R04C01, qc_ok

value: PD


title: CRC0223PRX0A01201, 201496850086_R03C01, qc_ok


title: Mouse, embryos, cell-GasbE751037


title: CRC0221LMX0B02204, 201858500154_R02C01, qc_ok


title: Mouse, embryos, cell-GasbE751036


title: Mouse, embryos, cell-GasbE751035


title: CRC0229LMX0A02201, 201858500154_R03C01, qc_ok


title: Mouse, embryos, cell-GasbE751034


title: Mouse, embryos, cell-GasbE751038


title: Mouse, embryos, cell-GasbE751033


title: CRC0218LMX0A02204, 201533550057_R03C01, qc_ok


title: CRC0219LMX0A02201, 201496850132_R07C01, qc_ok

value: OR


title: CRC0217LMX0A02204, 201858500154_R01C01, qc_ok


title: CRC0216LMX0A02204, 201496850132_R05C01, qc_ok


title: Mouse, embryos, cell-GasbE751032

value: Embryos


title: CRC0214LMX0A02204, 201858500050_R08C01, qc_ok


title: Mouse, embryos, cell-GasbE751031

value: C57BI6/J(female)x CAST/EiJ(male)


title: CRC0207LMX0A02201, 201858500050_R07C01, qc_ok

value: CRC


title: Mouse, embryos, cell-GasbE751029


title: CRC0207LMH0000000, 201533540005_R02C01, qc_ok

value: H

value: COLON


title: CRC0204LMX0A02204, 201858500050_R06C01, qc_ok


title: CRC0202LMX0B02204, 201858500050_R05C01, qc_ok

value: Male


title: Mouse, embryos, cell-GasbE751027


title: CRC0199LMX0A02201, 201533550057_R01C01, qc_ok


title: Mouse, embryos, cell-GasbE751026


title: Mouse, embryos, cell-GasbE751025


title: CRC0223PRH0000000, 201868500030_R06C01, qc_ok

value: PR

value: III


title: Mouse, embryos, cell-GasbE751024


title: CRC0198LMX0A02204, 201858500050_R04C01, qc_ok

value: LM

value: X


title: CRC0197LMX0A02204, 201870620137_R02C01, qc_ok

value: IVA


title: Mouse, embryos, cell-GasbE751023


title: CRC0196LMX0B02201, 201858500245_R05C01, qc_ok

value: IIA


title: Mouse, embryos, cell-GasbE751022


title: Mouse, embryos, cell-GasbE751021


title: CRC0190LMX0A02204, 201870620137_R01C01, qc_ok

value: SD

value: RETTO


title: Mouse, embryos, cell-GasbE751020


title: Mouse, embryos, cell-GasbE751019


title: CRC0188LMX0A01201, 201868500021_R05C01, qc_ok


title: CRC0187LMX0A02204, 201858500050_R03C01, qc_ok

value: IV


title: Mouse, embryos, cell-GasbE751030


title: CRC0186LMX0B02204, 201870620093_R08C01, qc_ok

value: Female

value: PD

value: IIa


title: Mouse, embryos, cell-GasbE751018

value: Embryos

value: C57BI6/J(female)x CAST/EiJ(male)


title: CRC0185LMX0B01201, 201868500021_R04C01, qc_ok

value: CRC

value: OR


title: Mouse, embryos, cell-GasbE751017


title: Mouse, embryos, cell-GasbE751028


title: CRC0180LMX0A02204, 201870620093_R06C01, qc_ok

value: COLON


title: CRC0179LMX0B02204, 201858500050_R02C01, qc_ok

value: Male


title: CRC0178LMX0A02204, 201870620093_R05C01, qc_ok


title: CRC0177LMX0A02204, 201858500050_R01C01, qc_ok


title: CRC0195PRX0A01201, 201868500021_R06C01, qc_ok

value: PR

value: I


title: Mouse, embryos, cell-GasbE751015


title: Mouse, embryos, cell-GasbE751013


title: Mouse, embryos, cell-GasbE751011


title: CRC0175LMX0A02204, 201869690204_R03C01, qc_ok

value: LM

value: X


title: Mouse, embryos, cell-GasbE751010


title: Mouse, embryos, cell-GasbE751009


title: Mouse, embryos, cell-GasbE751016


title: Mouse, embryos, cell-GasaE751384


title: CRC0174LMX0A01201, 201868500021_R01C01, qc_ok


title: CRC0171LMX0B02204, 201869690204_R02C01, qc_ok


title: Mouse, embryos, cell-GasaE751383


title: CRC0170LMX0A02204, 201870620144_R07C01, qc_ok

value: III


title: CRC0169LMX0B02204, 201870620144_R06C01, qc_ok


title: CRC0184LMX0A02204, 201870620093_R07C01, qc_ok


title: Mouse, embryos, cell-GasaE751380


title: CRC0169LMH0000000, 201868500046_R08C01, qc_ok

value: H


title: Mouse, embryos, cell-GasbE751014


title: CRC0168LMX0A02204, 201870620144_R05C01, qc_ok

value: II


title: Mouse, embryos, cell-GasaE751378


title: CRC0167LMX0B02204, 201868500014_R02C01, qc_ok

value: IV


title: Mouse, embryos, cell-GasaE751379


title: Mouse, embryos, cell-GasaE751377


title: CRC0166LMX0B02203, 201870620144_R04C01, qc_ok


title: Mouse, embryos, cell-GasbE751012


title: CRC0176LMX0A02201, 201869690204_R04C01, qc_ok

value: Female


title: Mouse, embryos, cell-GasaE751376


title: CRC0165LMH0000000, 201868500035_R02C01, qc_ok

value: PD


title: CRC0165LMX0B02203, 201858500245_R04C01, qc_ok


title: CRC0163LMX0B01201, 201869680085_R07C01, qc_ok


title: Mouse, embryos, cell-GasaE751375


title: CRC0164LMX0B02201, 201869690204_R01C01, qc_failed


title: Mouse, embryos, cell-GasaE751382


title: CRC0162LMX0B02204, 201870620144_R03C01, qc_ok


title: Mouse, embryos, cell-GasaE751373


title: Mouse, embryos, cell-GasaE751372


title: Mouse, embryos, cell-GasaE751370


title: Mouse, embryos, cell-GasaE751371


title: Mouse, embryos, cell-GasaE751369


title: Mouse, embryos, cell-GasaE751381


title: CRC0161LMX0A02202, 201870620144_R02C01, qc_ok


title: CRC0159LMX0A02201, 201870620144_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751368


title: Mouse, embryos, cell-GasaE751367


title: CRC0155LMX0A01201, 201858500245_R03C01, qc_ok

value: RETTO


title: CRC0154LMX0A01201, 201868500014_R07C01, qc_ok


title: CRC0158LMX0A02204, 201870620093_R04C01, qc_ok


title: Mouse, embryos, cell-GasaE751366

value: Embryos


title: Mouse, embryos, cell-GasaE751365

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, embryos, cell-GasaE751363


title: CRC0153LMX0A02201, 201869690114_R07C01, qc_ok

value: CRC

value: SD


title: CRC0151LMX0B02204, 201869690114_R06C01, qc_ok

value: IIIb

value: COLON


title: Mouse, embryos, cell-GasaE751362


title: CRC0152LMX0B02204, 201870620093_R03C01, qc_ok

value: Male

value: IVA


title: Mouse, embryos, cell-GasaE751361


title: Mouse, embryos, cell-GasaE751374


title: Mouse, embryos, cell-GasaE751360


title: CRC0162LMH0000000, 201868500035_R01C01, qc_ok

value: LM


title: CRC0150LMH0000000, 201868500030_R08C01, qc_ok


title: CRC0149LMX0A02204, 201858500245_R01C01, qc_ok

value: X


title: CRC0148LMX0A02201, 201858500245_R02C01, qc_ok

value: III


title: Mouse, embryos, cell-GasaE751358


title: Mouse, embryos, cell-GasaE751359


title: CRC0160LMX0B01201, 201868500014_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751357


title: CRC0146LMX0A02204, 201870620093_R02C01, qc_ok


title: CRC0145LMX0A02204, 201869690114_R04C01, qc_ok


title: Mouse, embryos, cell-GasaE751356


title: CRC0143LMX0B02201, 201870620137_R07C01, qc_ok


title: CRC0144LMX0A01201, 201868500081_R01C01, qc_ok


title: Mouse, embryos, cell-GasaE751351


title: Mouse, embryos, cell-GasaE751352


title: Mouse, embryos, cell-GasaE751354


title: Mouse, embryos, cell-GasaE751353


title: CRC0140LMX0A02201, 201870620093_R01C01, qc_ok


title: Mouse, embryos, cell-GasaE751350


title: Mouse, embryos, cell-GasaE751349


title: CRC0139LMX0A02204, 201870620137_R06C01, qc_ok


title: CRC0138LMX0A02201, 201870620137_R05C01, qc_ok


title: CRC0150LMX0A02204, 201869690114_R05C01, qc_ok


title: CRC0137LMX0A01201, 201868500022_R02C01, qc_ok

value: IIa


title: Mouse, embryos, cell-GasaE751348


title: Mouse, embryos, cell-GasaE751347


title: Mouse, embryos, cell-GasaE751345


title: Mouse, embryos, cell-GasaE751346


title: CRC0147LMX0A02204, 201869690114_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751355


title: Mouse, embryos, cell-GasaE751343


title: Mouse, embryos, cell-GasaE751342


title: CRC0131LMX0A02201, 201870620144_R01C01, qc_ok


title: CRC0133LMX0A02201, 201858500154_R08C01, qc_ok


title: CRC0134LMX0A02204, 201869690204_R07C01, qc_ok


title: CRC0130LMX0A02202, 201869690204_R08C01, qc_ok


title: CRC0136LMX0B02201, 201869690114_R02C01, qc_ok


title: Mouse, embryos, cell-GasaE751341


title: CRC0141LMX0A02204, 201869690114_R03C01, qc_ok


title: CRC0129LMX0A02204, 201858500154_R07C01, qc_ok


title: Mouse, embryos, cell-GasaE751340


title: CRC0127LMX0A02204, 201870620137_R04C01, qc_ok


title: CRC0128LMX0A02204, 201876940031_R07C01, qc_ok


title: Mouse, embryos, cell-GasaE751339


title: Mouse, embryos, cell-GasaE751338


title: CRC0125LMX0A02204, 201876940031_R06C01, qc_ok


title: CRC0124LMX0A02201, 201876940031_R01C01, qc_ok


title: Mouse, embryos, cell-GasaE751337


title: CRC0123LMX0A02204, 201868500196_R03C01, qc_ok

value: II


title: CRC0121LMX0A02202, 201869680211_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751336


title: Mouse, embryos, cell-GasaE751335


title: Mouse, embryos, cell-GasaE751334


title: CRC0135LMX0A02204, 201533580058_R07C01, qc_ok

value: IV


title: Mouse, embryos, cell-GasaE751333


title: Mouse, embryos, cell-GasaE751344


title: CRC0120LMX0A02204, 201869690114_R01C01, qc_ok


title: Mouse, embryos, cell-GasaE751332


title: CRC0119LMX0A02202, 201876940031_R05C01, qc_ok


title: CRC0118LMX0A02204, 201870620137_R03C01, qc_ok


title: Mouse, embryos, cell-GasaE751331


title: CRC0117LMX0A02204, 201868500196_R02C01, qc_ok


title: CRC0116LMX0A02201, 201858500154_R06C01, qc_ok

value: OR


title: Mouse, embryos, cell-GasaE751327


title: CRC0115LMH0000000, 201868500030_R04C01, qc_ok

value: H


title: CRC0114LMX0A01201, 201868500022_R01C01, qc_ok

value: Female


title: CRC0115LMX0A02201, 201858500154_R05C01, qc_ok

value: RETTO


title: Mouse, embryos, cell-GasaE751326

value: Embryos

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, embryos, cell-GasaE751329


title: Mouse, embryos, cell-GasaE751328


title: Mouse, embryos, cell-GasaE751325


title: Mouse, embryos, cell-GasaE751324


title: Mouse, embryos, cell-GasaE751323


title: CRC0112LMX0A02201, 201533580027_R02C01, qc_ok

value: CRC

value: PD


title: CRC0113LMX0B02201, 201876940031_R08C01, qc_ok

value: COLON


title: CRC0109LMX0A02203, 201868500160_R04C01, qc_ok

value: Male

value: SD


title: Mouse, embryos, cell-GasaE751322


title: CRC0108LMX0A02204, 201876940031_R04C01, qc_ok

value: LM


title: CRC0106LMX0B02204, 201868500014_R01C01, qc_ok

value: X


title: CRC0105LMX0A02204, 201868500111_R08C01, qc_ok

value: IIIc


title: CRC0104LMX0A02204, 201868500196_R01C01, qc_ok


title: Mouse, embryos, cell-GasaE751317


title: Mouse, embryos, cell-GasaE751319


title: CRC0110LMX0A02204, 201868500127_R01C01, qc_ok

value: III


title: CRC0103LMX0B02202, 201876940031_R03C01, qc_ok

value: IIA


title: CRC0101LMX0A02201, 201869690204_R06C01, qc_ok

value: II


title: Mouse, embryos, cell-GasaE751315


title: Mouse, embryos, cell-GasaE751318


title: Mouse, embryos, cell-GasaE751330


title: Mouse, embryos, cell-GasaE751321


title: CRC0099LMX0A02204, 201868500160_R03C01, qc_ok

value: IIa


title: CRC0099LMH0000000, 201868500046_R01C01, qc_ok

value: H


title: Mouse, embryos, cell-GasaE751313


title: Mouse, embryos, cell-GasaE751311


title: CRC0098LMH0000000, 201868500035_R08C01, qc_ok

value: OR

value: IV


title: Mouse, embryos, cell-GasaE751314

value: Embryos


title: Mouse, embryos, cell-GasaE751312

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, embryos, cell-GasaE751310


title: CRC0097LMX0B02202, 201869690204_R05C01, qc_ok

value: CRC

value: Female


title: CRC0098LMX0A02204, 201868500160_R02C01, qc_ok

value: RETTO


title: Mouse, embryos, cell-GasaE751309


title: CRC0100LMX0A02204, 201869680211_R07C01, qc_ok

value: PD

value: IIIb

value: COLON


title: Mouse, embryos, cell-GasaE751307


title: CRC0094LMX0A02201, 201868500111_R04C01, qc_ok

value: LM

value: X


title: CRC0095LMX0A02204, 201868500111_R07C01, qc_ok

value: Male

value: SD


title: Mouse, embryos, cell-GasaE751305


title: Mouse, embryos, cell-GasaE751308


title: Mouse, embryos, cell-GasaE751316


title: CRC0086LMX0A02201, 201868500035_R07C01, qc_ok

value: III


title: Mouse, embryos, cell-GasaE751304


title: CRC0086LMH0000000, 201868500163_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751303


title: Mouse, embryos, cell-GasaE751302


title: CRC0085LMX0A02204, 201868500163_R06C01, qc_ok


title: Mouse, embryos, cell-GasaE751301


title: CRC0082LMX0A02201, 201869680211_R05C01, qc_ok


title: Mouse, embryos, cell-GasaE751300


title: CRC0081LMH0000000, 201868500035_R06C01, qc_ok


title: Mouse, embryos, cell-GasaE751299


title: CRC0081LMX0A02202, 201868500163_R07C01, qc_ok


title: CRC0080LMX0A02204, 201869680211_R06C01, qc_ok


title: Mouse, embryos, cell-GasaE751298


title: CRC0096LMX0A02204, 201868500160_R01C01, qc_ok


title: CRC0079LMH0000000, 201868500035_R05C01, qc_ok

value: IIIA


title: Mouse, embryos, cell-GasaE751297


title: Mouse, embryos, cell-GasaE751306


title: Mouse, embryos, cell-GasaE751295


title: Mouse, embryos, cell-GasaE751294


title: CRC0079LMX0A02204, 201868500127_R06C01, qc_ok


title: CRC0077LMX0A02203, 201868500111_R03C01, qc_ok


title: CRC0094PRX0A01201, 201868500021_R02C01, qc_ok

value: PR


title: CRC0076LMX0B02203, 201868500163_R05C01, qc_ok

value: OR


title: CRC0072LMH0000000, 201868500030_R07C01, qc_ok

value: H

value: IV


title: Mouse, embryos, cell-GasaE751291

value: Embryos

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, embryos, cell-GasaE751290


title: CRC0071LMX0A02204, 201869680211_R03C01, qc_ok

value: CRC


title: Mouse, embryos, cell-GasaE751293


title: Mouse, embryos, cell-GasaE751292


title: Mouse, embryos, cell-GasaE751289


title: Mouse, embryos, cell-GasaE751288


title: CRC0071PRX0A01201, 201868500046_R07C01, qc_ok


title: CRC0068LMX0A02203, 201868500196_R08C01, qc_ok

value: Female


title: CRC0070LMX0A02204, 201868500160_R08C01, qc_ok

value: PD


title: CRC0067LMX0B02204, 201868500163_R04C01, qc_ok

value: RETTO


title: Mouse, embryos, cell-GasaE751287


title: Mouse, embryos, cell-GasaE751284


title: Mouse, embryos, cell-GasaE751296


title: Mouse, embryos, cell-GasaE751283


title: CRC0065LMX0B01201, 201869680085_R01C01, qc_ok


title: CRC0066LMX0A02204, 201868500127_R05C01, qc_ok

value: COLON


title: CRC0072LMX0A02203, 201869680211_R04C01, qc_ok

value: LM


title: Mouse, embryos, cell-GasaE751281


title: CRC0065PRX0A01201, 201868500014_R05C01, qc_ok

value: X


title: CRC0064LMX0A02204, 201868500160_R07C01, qc_ok


title: CRC0063LMX0A02204, 201858500245_R07C01, qc_ok

value: Male


title: Mouse, embryos, cell-GasaE751280


title: Mouse, embryos, cell-GasaE751279


title: CRC0073LMX0A02201, 201868500111_R06C01, qc_ok


title: Mouse, embryos, cell-GasaE751278


title: Mouse, embryos, cell-GasaE751277


title: CRC0062LMH0000000, 201869680085_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751276


title: CRC0062LMX0A02201, 202093120031_R08C01, qc_ok


title: CRC0061LMX0A02203, 201868500127_R04C01, qc_ok


title: Mouse, embryos, cell-GasaE751275


title: CRC0059LMX0A02204, 201868500127_R03C01, qc_ok

value: II


title: CRC0058LMX0A02201, 201868500111_R02C01, qc_ok


title: CRC0057LMX0A02201, 201868500160_R06C01, qc_ok


title: Mouse, embryos, cell-GasaE751273


title: CRC0057LMH0000000, 201868500030_R03C01, qc_ok


title: CRC0056LMX0A02201, 201868500111_R05C01, qc_ok

value: SD


title: Mouse, embryos, cell-GasaE751282


title: Mouse, embryos, cell-GasaE751271


title: Mouse, embryos, cell-GasaE751272


title: Mouse, embryos, cell-GasaE751270


title: Mouse, embryos, cell-GasaE751269


title: Mouse, embryos, cell-GasaE751268


title: Mouse, embryos, cell-GasaE751266


title: Mouse, embryos, cell-GasaE751265


title: CRC0051LMX0A02204, 202093120031_R05C01, qc_ok

value: IIIb


title: Mouse, embryos, cell-GasaE751264


title: CRC0054LMX0B02202, 201868500127_R02C01, qc_ok

value: IIa


title: CRC0054LMH0000000, 201868500030_R02C01, qc_ok


title: CRC0053PRX0A01201, 201868500014_R03C01, qc_ok

value: PR


title: CRC0053LMX0A02204, 202093120031_R06C01, qc_ok


title: CRC0055LMX0A02201, 202093120031_R07C01, qc_ok


title: CRC0050PRX0A02201, 202093120031_R04C01, qc_ok


title: CRC0050LMX0A02201, 202093120031_R03C01, qc_ok


title: CRC0032LMX0A02201, 201868500127_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751262


title: Mouse, embryos, cell-GasaE751274


title: Mouse, embryos, cell-GasaE751263


title: CRC0030LMX0B02203, 201868500163_R03C01, qc_ok


title: CRC0031LMX0A02203, 201868500196_R07C01, qc_ok


title: Mouse, embryos, cell-GasaE751260


title: Mouse, embryos, cell-GasaE751261


title: Mouse, embryos, cell-GasaE751259


title: CRC0029LMX0A02204, 201869680211_R02C01, qc_ok


title: CRC0028LMX0A02204, 201868500196_R06C01, qc_ok


title: Mouse, embryos, cell-GasaE751258


title: CRC0027LMX0A02201, 201868500111_R01C01, qc_ok

value: III


title: Mouse, embryos, cell-GasaE751255


title: Mouse, embryos, cell-GasaE751256


title: Mouse, embryos, cell-GasaE751267


title: CRC0024LMX0A02204, 201868500196_R05C01, qc_ok

value: IV


title: CRC0025LMX0B02204, 201858500245_R08C01, qc_ok


title: Mouse, embryos, cell-GasaE751254

value: Embryos


title: Mouse, embryos, cell-GasaE751253

value: C57BI6/J(female)x CAST/EiJ(male)


title: CRC0021LMX0B02204, 201868500014_R06C01, qc_ok

value: CRC


title: Mouse, embryos, cell-GasaE751249


title: Mouse, embryos, cell-GasaE751250


title: CRC0018LMX0B02201, 201868500196_R04C01, qc_ok

value: Female


title: CRC0019LMX0A01201, 201868500014_R04C01, qc_ok

value: PD


title: Mouse, embryos, cell-GasaE751252


title: CRC0022LMX0A02204, 201868500160_R05C01, qc_ok


title: Mouse, embryos, cell-GasaE751248


title: Mouse, embryos, cell-GasaE751245


title: Mouse, embryos, cell-GasaE751247


title: Mouse, embryos, cell-GasaE751251


title: CRC0014LMX0A02201, 201868500046_R02C01, qc_ok

value: RETTO


title: CRC0017LMX0A02201, 201868500046_R03C01, qc_ok


title: Mouse, embryos, cell-GasaE751246


title: Mouse, embryos, cell-GasaE751242


title: Mouse, embryos, cell-GasaE751243


title: Mouse, embryos, cell-GasaE751240


title: Mouse, embryos, cell-GasaE751239


title: pool 1C pool number 1

city: London

first: Goran

last: Tomic

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
We quantified each of the shRNAs by aligning the reads to the target library using bwa-0.5.9
For any given pool, all samples "targeting" that pool were run within the same lane and so we applied a "pool" level normalisation, i.e. raw read counts were scaled such that the total number of reads targeting a pool were the same across all samples in that lane. "Off target" read, i.e. those mapping to a target in a pool other than the intended pool are filtered prior to normalisation in this approach.
Supplementary files format and content: The normalised counts files are tab delimited text files containing the following columns. Column 1 an shRNA feature_id, Column 2 a target_id or gene symbol, Column 3 a refseq_id, Column 4 the pool, and Column 5 the normalised_count value.

source_name: PDA530 Met

growth_protocol: Virus for each pool was generated and used to infect target PDA530 Met cells at an MOI of 0.3. Cells were selected for 4 days with puromycin (3 µg/ml) and then 5 x 105 cells were injected via tail vein into mice (3 mice per pool). A cell pellet was also generated to provide a Day 0 sample of each pool. After 28 days, lung samples were harvested and all tumours within the same mouse were pooled to generate a pooled lung DNA sample. In parallel, cells were cultured in vitro in triplicate over the same time-frame.

extract_protocol:
Genomic DNA extraction of Day 0, in vitro and in vivo samples was carried out using Qiagen Gentra Puregene Tissue Kit.
A two-step PCR was carried out to amplify shRNA sequences from the genomic DNA samples. Sequencing adapters and multiplexing barcodes were incorporated into the PCR primer. PCR products were purified using Qiagen MiniElute PCR Purification Kit and DNA concentration was determined using Bioanalyser.

tag: pool

tag: cell line

value: PDA530 Met

tag: cell type

value: pancreatic cancer adenocarcinoma, liver metastasis

tag: day


title: pool Cells 1/2 A pool number 1


title: pool 2A pool number 2


title: pool 2B pool number 2


title: pool 2C pool number 2


title: pool 1B pool number 1


title: Mouse, embryos, cell-GasaE751237


title: pool Cells 1/2 C pool number 1


title: Mouse, embryos, cell-GasaE751236


title: Mouse, embryos, cell-GasaE751238


title: pool Cells 1/2 A Technical Replicate pool number 1


title: pool Cells 1/2 B pool number 1


title: Mouse, embryos, cell-GasaE751235


title: pool 1A Technical Replicate pool number 1


title: pool Lungs 2C pool number 2


title: pool Lungs 2B pool number 2


title: Mouse, embryos, cell-GasaE751233


title: Mouse, embryos, cell-GasaE751232


title: Mouse, embryos, cell-GasaE751231


title: pool Lungs 2A pool number 2


title: pool Lungs 1C pool number 1


title: Mouse, embryos, cell-GasaE751230


title: Mouse, embryos, cell-GasaE751229


title: pool Lungs 1B pool number 1


title: Mouse, embryos, cell-GasaE751227


title: pool 1A pool number 1


title: Mouse, embryos, cell-GasaE751228


title: pool 9A pool number 9


title: Mouse, embryos, cell-GasaE751225


title: pool Lungs 7B pool number 7


title: pool Lungs 7A pool number 7


title: pool Lungs 6C pool number 6


title: pool Lungs 7C pool number 7


title: Mouse, embryos, cell-GasaE751226


title: Mouse, embryos, cell-GasaE751222


title: Mouse, embryos, cell-GasaE751223


title: Mouse, embryos, cell-GasaE751234


title: Mouse, embryos, cell-GasaE751221


title: pool Lungs 6B pool number 6


title: pool Lungs 6A pool number 6


title: pool Cells 6/7B pool number 6


title: Mouse, embryos, cell-GasaE751219


title: pool Cells 6/7C pool number 6


title: Mouse, embryos, cell-GasaE751220


title: pool Lungs 1A pool number 1


title: pool Cells 6/7A pool number 6


title: pool Cells 3C pool number 3


title: pool 7C pool number 7


title: Mouse, embryos, cell-GasaE751217


title: Mouse, embryos, cell-GasaE751216


title: Mouse, embryos, cell-GasaE751214


title: pool 7A pool number 7


title: Mouse, embryos, cell-GasaE751224


title: Mouse, embryos, cell-GasaE751213


title: pool 6C pool number 6


title: Mouse, embryos, cell-GasaE751212


title: Mouse, embryos, cell-GasaE751210


title: pool 6B pool number 6


title: Mouse, embryos, cell-GasaE751208


title: Mouse, embryos, cell-GasaE751209


title: pool 6A pool number 6


title: Mouse, embryos, cell-GasaE751207


title: pool Lungs 17C pool number 17


title: Mouse, embryos, cell-GasaE751218


title: Mouse, embryos, cell-GasaE751206


title: pool Lungs 17B pool number 17


title: pool Cells 3B pool number 3


title: Mouse, embryos, cell-GasaE751205


title: Mouse, embryos, cell-GasaE751215


title: pool Lungs 16D pool number 16


title: pool Lungs 16E pool number 16


title: Mouse, embryos, cell-GasaE751202


title: Mouse, embryos, cell-GasaE751203


title: pool Lungs 1A Technical Replicate pool number 1


title: pool Cells 16E pool number 16


title: pool Cells 16D pool number 16


title: pool 7B pool number 7


title: Mouse, embryos, cell-GasaE751201


title: pool Cells 16/17C pool number 16


title: Mouse, embryos, cell-GasaE751200


title: pool Cells 16/17B pool number 16


title: Mouse, embryos, cell-GasaE751199


title: Mouse, embryos, cell-GasaE751198


title: pool Cells 16/17A pool number 16


title: pool 17B pool number 17


title: pool Lungs 17A pool number 17


title: Mouse, embryos, cell-GasaE751204


title: Mouse, embryos, cell-GasaE751195


title: pool 16E pool number 16


title: pool 16D pool number 16


title: pool 17A pool number 17


title: Mouse, embryos, cell-GasaE751193


title: pool Cells 3A pool number 3


title: Mouse, embryos, cell-GasaE751194


title: pool 16A pool number 16


title: pool Lungs 15D pool number 15


title: Mouse, embryos, cell-GasaE751192


title: pool Lungs 15B pool number 15


title: Mouse, embryos, cell-GasaE751191


title: Mouse, embryos, cell-GasaE751189


title: pool Lungs 15C pool number 15


title: Mouse, embryos, cell-GasaE751187


title: pool Lungs 14C pool number 14


title: pool Lungs 14B pool number 14


title: pool Lungs 14A pool number 14


title: Mouse, embryos, cell-GasaE751186


title: Mouse, embryos, cell-GasaE751197


title: Mouse, embryos, cell-GasaE751196


title: Mouse, embryos, cell-GasaE751185


title: pool 17C pool number 17


title: Mouse, embryos, cell-GasaE751183


title: Mouse, embryos, cell-GasaE751184


title: pool Cells 14/15C pool number 14


title: pool Cells 14/15B pool number 14


title: Mouse, embryos, cell-GasaE751181


title: pool Cells 14/15A pool number 14


title: Mouse, embryos, cell-GasaE751180


title: pool Cells 15D pool number 15


title: Mouse, embryos, cell-GasaE751179


title: Mouse, embryos, cell-GasaE751190


title: Mouse, embryos, cell-GasaE751188


title: pool 15B pool number 15


title: Mouse, embryos, cell-GasaE751178


title: Mouse, embryos, cell-GasaE751175


title: Mouse, embryos, cell-GasaE751176


title: Mouse, embryos, cell-GasaE751174


title: pool 14C pool number 14


title: pool 15D pool number 15


title: Mouse, embryos, cell-GasaE751177


title: pool 14A pool number 14


title: pool 14B pool number 14


title: pool 13B pool number 13


title: pool 13C pool number 13


title: Mouse, embryos, cell-GasaE751171


title: Mouse, embryos, cell-GasaE751170


title: pool Lungs 19B pool number 19


title: pool Lungs 19A pool number 19


title: pool Lungs 19D pool number 19


title: Mouse, embryos, cell-GasaE751169


title: pool Lungs 18C pool number 18


title: Mouse, embryos, cell-GasaE751166


title: Mouse, embryos, cell-GasaE751167


title: Mouse, embryos, cell-GasaE751168


title: pool Lungs 18A pool number 18


title: pool Lungs 18B pool number 18


title: pool Cells 19D pool number 19


title: Mouse, embryos, cell-GasaE751165


title: pool 15C pool number 15


title: pool Cells 18/19B pool number 18


title: pool Cells 18/19C pool number 18


title: Mouse, embryos, cell-GasaE751164


title: Mouse, embryos, cell-GasaE751162


title: pool Cells 18/19A pool number 18


title: Mouse, embryos, cell-GasaE751163


title: pool 13A pool number 13


title: Mouse, embryos, cell-GasaE751173


title: pool 19B pool number 19


title: pool 19D pool number 19


title: Mouse, embryos, cell-GasaE751160


title: Mouse, embryos, cell-GasaE751159


title: Mouse, embryos, cell-GasaE751172


title: pool 19A pool number 19


title: Mouse, embryos, cell-GasaE751161


title: Mouse, embryos, cell-GasaE751158


title: Mouse, embryos, cell-GasaE751156


title: Mouse, embryos, cell-GasaE751157


title: pool 18C pool number 18


title: Mouse, embryos, cell-GasaE751154


title: Mouse, embryos, cell-GasaE751153


title: Mouse, embryos, cell-GasaE751155


title: pool Lungs 5B pool number 5


title: pool 18B pool number 18


title: pool Lungs 5C pool number 5


title: Mouse, embryos, cell-GasaE751152


title: pool Lungs 5A pool number 5


title: pool Lungs 4C pool number 4


title: Mouse, embryos, cell-GasaE751151


title: pool 3C pool number 3


title: Mouse, embryos, cell-GasaE751150


title: pool Lungs 4B pool number 4


title: Mouse, embryos, cell-GasaE751147


title: pool Cells 4/5C pool number 4


title: Mouse, embryos, cell-GasaE751149


title: Mouse, embryos, cell-GasaE751148


title: pool Cells 4/5B pool number 4


title: pool Cells 4/5A pool number 4


title: Mouse, embryos, cell-GasaE751146


title: pool 18A pool number 18


title: pool 5C pool number 5


title: Mouse, embryos, cell-GasaE751144


title: Mouse, embryos, cell-GasaE751145


title: pool 5B pool number 5


title: pool 5A pool number 5


title: Mouse, embryos, cell-GasaE751143


title: Mouse, embryos, cell-GasaE751141


title: pool 4C pool number 4


title: Mouse, embryos, cell-GasaE751142


title: Mouse, embryos, cell-GasaE751140


title: pool 4B pool number 4


title: Mouse, embryos, cell-GasaE751139


title: Mouse, embryos, cell-GasaE751137


title: pool 3B pool number 3


title: pool 4A pool number 4


title: pool Lungs 4A pool number 4


title: Mouse, embryos, cell-GasaE751138


title: pool Lungs 13C pool number 13


title: Mouse, embryos, cell-GasaE751135


title: pool Lungs 13B pool number 13


title: Mouse, embryos, cell-GasaE751136


title: pool Lungs 3C pool number 3


title: Mouse, embryos, cell-GasaE751134


title: Mouse, embryos, cell-GasaE751133


title: pool Lungs 13A pool number 13


title: pool 8A replicate pool number 8


title: Mouse, embryos, cell-GasaE751131


title: Mouse, embryos, cell-GasaE751132


title: pool Lungs 3B pool number 3


title: Mouse, embryos, cell-GasaE751130


title: pool Lungs 8C pool number 8


title: pool Lungs 8B pool number 8


title: Mouse, embryos, cell-GasaE751128


title: Mouse, embryos, cell-GasaE751126


title: pool Cells 8/9C pool number 8


title: Mouse, embryos, cell-GasaE751127


title: Mouse, embryos, cell-GasaE751125


title: Mouse, embryos, cell-GasaE751124


title: pool Cells 8/9A pool number 8


title: pool 8C pool number 8


title: Mouse, embryos, cell-GasaE751122


title: pool 8A pool number 8


title: pool Lungs 8A replicate pool number 8


title: pool 8B pool number 8


title: Mouse, embryos, cell-GasaE751123


title: Mouse, embryos, cell-GasaE751120


title: pool Cells 8/9A replicate pool number 8


title: Mouse, embryos, cell-GasaE751121


title: Mouse, embryos, cell-GasaE751119


title: pool Lungs 12B pool number 12


title: pool Lungs 12C pool number 12


title: pool Lungs 3A pool number 3


title: Mouse, embryos, cell-GasaE751129


title: pool Lungs 12A pool number 12


title: Mouse, embryos, cell-GasaE751117


title: pool Lungs 11C pool number 11


title: pool Lungs 11B pool number 11


title: pool Lungs 8A pool number 8


title: Mouse, embryos, cell-GasaE751116


title: Mouse, embryos, cell-GasaE751115


title: pool Cells 8/9B pool number 8


title: pool Lungs 11A pool number 11


title: Mouse, embryos, cell-GasaE751114


title: Mouse, embryos, cell-GasaE751113


title: pool Cells 12B pool number 12


title: pool Cells 12A pool number 12


title: Mouse, embryos, cell-GasaE751112


title: Mouse, embryos, cell-GasaE751111


title: Mouse, embryos, cell-GasaE751110


title: pool Cells 10/11C pool number 10


title: Mouse, embryos, cell-GasaE751109


title: pool Cells 10/11B pool number 10


title: Mouse, embryos, cell-GasaE751108


title: pool Cells 13C pool number 13


title: Mouse, embryos, cell-GasaE751118


title: Nos mutant, metabolic stress

city: Hannover

first: Halyna

last: Shcherbata

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Cell Biochemistry

country: Germany

institute: Medical School Hannover

library_source: transcriptomic

data_processing:
Reads were mapped to the reference genome using STAR: ultrafast universal RNA-seq aligner. Subsequent analyses were performed in R statistical software using packages from the Bioconductor project.
BAM alignment files were used to generate counts on individual transcripts using transcript database from the GTF file (Drosophila_melanogaster.BDGP6.84) via Rsamtools and GenomicFeatures packages and "summarizeOverlaps" function in "Union" mode via GenomicAlignments package.
Counts were analyzed and genotype and condition comparisons were performed through built-in statistical models in the DESeq2 package. For data visualization, gplots and RColorBrewer packages were used.
Assembly: BDGP6

molecule: total RNA

organism: Drosophila melanogaster

source_name: whole flies

extract_protocol:
Approximately 10 male flies per genotype and condition were homogenized together in Trizol, and total RNA was extracted using Direct-zol RNA mini-prep with an additional on-column DNAse digestion step.
RNA-seq libraries were prepared by RNA poly-A purification, fragmentation, random primed cDNA synthesis, linker ligation, and PCR enrichment. The samples were used to make a random-primed cDNA library.
100 bp reads

value: whole flies

tag: Sex

value: male

value: 1 week

tag: genotype

tag: treatment

value: 4 days on yeast paste only; no sugar

tag: treatment type

value: metabolic stress (no sugar)


title: Nos mutant, temperature stress

tag: tissue

value: 5 days at 33C

value: temperature stress (33C)


title: Nos mutant, control genotype

value: 5 days at 25C

value: control treatment


title: Syn1 mutant, metabolic stress


title: Mouse, embryos, cell-GasaE751107

value: Embryos

tag: strain


title: pool Cells 10/11A pool number 10


title: Mouse, embryos, cell-GasaE751105

value: C57BI6/J(female)x CAST/EiJ(male)


title: pool 12C pool number 12


title: Mouse, embryos, cell-GasaE751106


title: pool 12B pool number 12


title: Syn1 mutant, temperature stress


title: Mouse, embryos, cell-GasaE751104


title: Syn1 mutant, control genotype


title: pool Cells 12C pool number 12


title: pool 11C pool number 11


title: pool 12A pool number 12


title: Mouse, embryos, cell-GasaE751103


title: Mouse, embryos, cell-GasaE751102


title: pool 11B pool number 11


title: pool 11A pool number 11


title: Dys mutant, temperature stress


title: pool Lungs 10C pool number 10


title: Dys mutant, control genotype


title: Dg mutant, metabolic stress


title: Mouse, embryos, cell-GasaE751100


title: Mouse, embryos, cell-GasaE751099


title: Mouse, embryos, cell-GasaE751098


title: Mouse, embryos, cell-GasaE751097


title: Dg mutant, temperature stress


title: pool Lungs 10A pool number 10


title: Dg mutant, control treatment


title: pool Lungs 9C pool number 9


title: pool Cells 13B pool number 13


title: pool Lungs 10B pool number 10


title: Mouse, embryos, cell-GasaE751096


title: control genotype, metabolic stress


title: control genotype, temperature stress


title: pool Lungs 9A pool number 9


title: Mouse, embryos, cell-GasaE751092


title: Mouse, embryos, cell-GasaE751093


title: Mouse, embryos, cell-GasaE751094


title: control genotype, control treatment


title: Mouse, embryos, cell-GasaE751090


title: Mouse, embryos, cell-GasaE751101


title: pool Cells 9/10B pool number 9


title: pool Cells 9/10A pool number 9


title: pool 10B pool number 10


title: Mouse, embryos, cell-GasaE751095


title: Dys mutant, metabolic stress


title: pool 10C pool number 10


title: pool Cells 9/10C pool number 9


title: pool 10A pool number 10


title: pool 9C pool number 9


title: Mouse, embryos, cell-GasaE751088


title: Mouse, embryos, cell-GasaE751086


title: pool 9B pool number 9


title: Mouse, embryos, cell-GasaE751085


title: pool 3A pool number 3


title: pool Cells 13A pool number 13


title: Mouse, embryos, cell-GasaE751081


title: Mouse, embryos, cell-GasaE751087


title: Mouse, embryos, cell-GasaE751083


title: Mouse, embryos, cell-GasaE751082


title: Mouse, embryos, cell-GasaE751084


title: Mouse, embryos, cell-GasaE751080


title: abundance not1 degron vs control strain replicate 3

type: RNA

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Biological replicate 3 of 3.

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on mean fluorescence signal (background fluorescence substraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards E. coli tRNALys2, yeast tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios.

organism: Saccharomyces cerevisiae

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNALys2, E. coli tRNATyr2, human tRNAHis1, human tRNASer3) were added to 2 µg extracted total RNA prior to deacetylation.
2. For  abundance arrays total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9); For tRNA charging arrays total RNA  was oxidized with periodate and thereafter treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation; tRNA standards were added prior the deacylation step.
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
Cells were cultivated in glucose rich medium (YPD),grown over night until OD600 0.8, then treated
Cell were grown independently for each biological experiment

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich) and for arrays to determine the charged fraction with acidic phenol (pH 4.5) according to manufacturer's protocol

treatment_protocol: Cells were treated with auxin (3-indoleacetic acid, Sigma-Aldrich I2886, stock solution at 250 mM in EtOH) at 1mM final for 15 min to exponentially growing cells diluted to OD600 0.3

value: MY13523  MATa leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 not1::NOT1-AID-Myc6-NATMX4

value: MY13472 MATa leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100


title: RC43T cells, Vector, treat 3

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

country: USA

institute: Cedars-Sinai Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Read count extraction and normalization were performed featureCounts and an edgeR workflow in R
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: All cells were maintained at 37oC and 5.0% CO2 (Sanyo); HPr1AR, RC43N, RC43T,  cells were maintained in keratinocyte serum free media (supplemented with 25mg of Bovine pituitary extract, 10ug EGF and 10% FBS); LNCaP cells were maintained in RPMI 1640 containing 10% FBS. All media contained 100 U/mL Penicillin-Streptomycin. 1α,25(OH)2D3 was kept as 10mM EtOH stocks. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Total RNA was isolated via TRIzol® reagent
Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

treatment_protocol: Cells were grown to 70% confluence and treated with 1α,25(OH)2D3 (100nM, 8hr) or EtOH in biological triplicate samples and analyzed by RNA-Seq.

tag: vector

value: Vector

value: African American prostate cancer

value: Vehicle


title: Mouse, embryos, cell-GasaE751089


title: RC43T cells, Vector, treat 1


title: Mouse, embryos, cell-GasaE751077


title: RC43T cells, Vector, veh control 3


title: Mouse, embryos, cell-GasaE751078


title: Mouse, embryos, cell-GasaE751079


title: Mouse, embryos, cell-GasaE751076


title: abundance not1 degron vs control strain replicate 2

description: Biological replicate 2 of 3.


title: RC43T cells, Vector, treat 2


title: Mouse, embryos, cell-GasaE751075


title: control strain charging replicate 3

description: Biological replicate 3 of 3.


title: abundance not1 degron vs control strain replicate 1

description: Biological replicate 1 of 3.


title: control strain charging replicate 2

description: Biological replicate 2 of 3.


title: RC43T cells, Vector, veh control 2


title: RC43T cells, Vector, veh control 1


title: Mouse, embryos, cell-GasaE751074


title: RC43T cells, BAZ1A, treat 3

value: BAZ1A trans


title: not1 degron charging replicate 2

description: Biological replicate 2 of 3.


title: Mouse, embryos, cell-GasaE751073


title: RC43T cells, BAZ1A, treat 2


title: RC43T cells, BAZ1A, veh control 3


title: not1 degron charging replicate 3

description: Biological replicate 3 of 3.


title: not1 degron charging replicate 1

description: Biological replicate 1 of 3.


title: Mouse, embryos, cell-GasaE751071


title: RC43T cells, BAZ1A, treat 1


title: Dpp4 KO : Chow : k851

city: Ottawa

first: Erin

last: Mulvihill

state: On

address: 40 Ruskin Street

country: Canada

institute: UOHI

hyb_protocol: 100ng of total RNA was used for NanoString hybridization, reaction was incubated for 16 hours before being processed on the NanoString nCounter Analysis System

scan_protocol: Raw mRNA counts were determined using the NanoString nCounter Analysis System at max quality

data_processing: The raw data were log2 normalized to housekeeping genes shared across all diet and genotypes (10 in total)

source_name: Isolated F4/80+ cells from liver

extract_protocol: F4/80+ cells were isolated from whole liver using the liver dissocition kit from Miltenyi Biotech, total RNA was extracted using Trizol Reagent, following manufacturer's protocol.

value: Dpp4-/- (Dpp4 whole body knockout)

tag: diet

value: Standard laboratory diet (SLD)


title: Mouse, embryos, cell-GasaE751070


title: RC43T cells, BAZ1A, veh control 2


title: Dpp4 hep-/- : HFD : 1467

value: Dpp4hep-/- (Dpp4 hepatocyte specific knockout)

value: High fat high cholesterol diet (HFHC)


title: Dpp4 hep-/- : HFD : 1526


title: RC43T cells, BAZ1A, veh control 1


title: RC43N cells, Vector, treat 3

value: African American non-malignant prostate


title: control strain charging replicate 1

description: Biological replicate 1 of 3.


title: Mouse, embryos, cell-GasaE751069


title: Dpp4 KO : Chow : k863


title: Mouse, embryos, cell-GasaE751067


title: Mouse, embryos, cell-GasaE751066


title: Dpp4 KO : HFD : k858


title: Dpp4 GFP : HFD : 1559


title: RC43N cells, Vector, treat 1


title: Mouse, embryos, cell-GasaE751068


title: Mouse, embryos, cell-GasaE751064


title: Mouse, embryos, cell-GasaE751072


title: Dpp4 KO : HFD : k856


title: RC43N cells, Vector, veh control 2


title: RC43N cells, Vector, treat 2


title: Mouse, embryos, cell-GasaE751065


title: WT : Chow : k848

value: Wildtype (WT)


title: RC43N cells, Vector, veh control 1


title: Dpp4 KO : Chow : k850


title: Mouse, embryos, cell-GasaE751062


title: RC43N cells, BAZ1A, treat 3


title: Dpp4 KO : Chow : k866


title: WT : HFD : of3


title: Mouse, embryos, cell-GasaE751060


title: Dpp4 hep-/- : HFD : 1544


title: RC43N cells, BAZ1A, treat 1


title: RC43N cells, BAZ1A, veh control 3


title: WT : HFD : k841


title: RC43N cells, Vector, veh control 3


title: RC43N cells, BAZ1A, veh control 2


title: Mouse, embryos, cell-GasaE751057


title: Mouse, embryos, cell-GasaE751058


title: Dpp4 hep-/- : HFD : 1466


title: Dpp4 KO : HFD : k859


title: Mouse, embryos, cell-GasaE751063


title: WT : Chow : k861


title: RC43N cells, BAZ1A, veh control 1


title: LNCaP cells, Vector, treat 2

source_name: LNCaP

value: LNCaP

value: European American prostate cancer


title: LNCaP cells, Vector, treat 3


title: Mouse, embryos, cell-GasaE751056


title: Mouse, embryos, cell-GasaE751054


title: Dpp4 hep-/- : HFD : 1525


title: LNCaP cells, Vector, treat 1


title: Dpp4 KO : Chow : k862


title: Mouse, embryos, cell-GasaE751053


title: LNCaP cells, Vector, veh control 3


title: Mouse, embryos, cell-GasaE751061


title: Mouse, embryos, cell-GasaE751055


title: RC43N cells, BAZ1A, treat 2


title: LNCaP cells, Vector, veh control 2


title: Dpp4 KO : Chow : k867


title: Dpp4 GFP : HFD : 1558


title: Mouse, embryos, cell-GasaE751059


title: Mouse, embryos, cell-GasaE751052


title: Mouse, embryos, cell-GasaE751051


title: WT : HFD : k911


title: WT : Chow : K884


title: LNCaP cells, BAZ1A, treat 3


title: Mouse, embryos, cell-GasaE751049


title: WT : Chow : OF6


title: Dpp4hepKO : HFD : 1531


title: Mouse, embryos, cell-GasaE751048


title: LNCaP cells, BAZ1A, treat 1


title: LNCaP cells, BAZ1A, veh control 3


title: LNCaP cells, BAZ1A, veh control 2


title: Mouse, embryos, cell-GasaE751046


title: Dpp4 GFP : HFD : a592


title: WT : Chow : OF5

value: Standard chow diet (chow)


title: LNCaP cells, BAZ1A, veh control 1


title: Mouse, embryos, cell-GasaE751045

value: Embryos


title: HPr1-AR cells, Vector, treat 3

value: European American non-malignant prostate


title: WT : HFD : k853


title: Mouse, embryos, cell-GasaE751044

value: C57BI6/J(female)x CAST/EiJ(male)


title: WT : HFD : OF1


title: LNCaP cells, Vector, veh control 1


title: Mouse, embryos, cell-GasaE751042


title: HPr1-AR cells, Vector, treat 2


title: Mouse, embryos, cell-GasaE751043


title: Dpp4hepKO : HFD : 1527


title: HPr1-AR cells, Vector, treat 1


title: HPr1-AR cells, Vector, veh control 3


title: Mouse, embryos, cell-GasaE751041


title: Mouse, embryos, cell-GasaE751050


title: LNCaP cells, BAZ1A, treat 2


title: WT : Chow :OF7


title: HPr1-AR cells, Vector, veh control 2


title: Mouse, embryos, cell-GasaE751047


title: Mouse, embryos, cell-GasaE751040


title: k867 : Dpp4KO : Chow

data_processing: The raw data were log2 normalized to housekeeping genes shared across all diet and genotypes (9 in total)

source_name: Liver

extract_protocol: ~100-150 mg of whole liver tissue was homogenized using Trizol Reagent, following manufacturer's protocol.

value: Liver


title: HPr1-AR cells, Vector, veh control 1

value: Vector


title: k866 : Dpp4KO : Chow


title: Dpp4 KO : HFD : k885


title: Mouse, embryos, cell-GasaE751038


title: Mouse, embryos, cell-GasaE751039


title: HPr1-AR cells, BAZ1A, treat 3


title: k862 : Dpp4KO : Chow


title: k850 : Dpp4KO : Chow


title: HPr1-AR cells, BAZ1A, treat 1


title: Mouse, embryos, cell-GasaE751035


title: OF8 : WT : Chow


title: HPr1-AR cells, BAZ1A, veh control 3


title: OF7 : WT : Chow


title: HPr1-AR cells, BAZ1A, veh control 2


title: Mouse, embryos, cell-GasaE751033


title: OF6 : WT : how


title: HPr1-AR cells, BAZ1A, veh control 1


title: Mouse, embryos, cell-GasaE751031


title: Mouse, embryos, cell-GasaE751034


title: OF5 : WT : Chow


title: Mouse, embryos, cell-GasaE751030


title: k848 : WT : Chow


title: Mouse, embryos, cell-GasaE751028


title: HPr1-AR cells, BAZ1A, treat 2


title: k884 : WT : Chow


title: Mouse, embryos, cell-GasaE751026


title: Mouse, embryos, cell-GasaE751029


title: Mouse, embryos, cell-GasaE751025


title: a591 : Dpp4hepKO : HFD


title: k863 : Dpp4KO : Chow


title: Mouse, embryos, cell-GasaE751024


title: Mouse, embryos, cell-GasaE751036


title: 1556 : Dpp4hepKO : HFD


title: 1557 : Dpp4hepKO : HFD


title: Mouse, embryos, cell-GasaE751027


title: 1466 : Dpp4hepKO : HFD


title: Mouse, embryos, cell-GasaE751023


title: 1526 : Dpp4hepKO : HFD


title: Mouse, embryos, cell-GasaE751022


title: 1525 : Dpp4hepKO : HFD


title: 1531 : Dpp4hepKO : HFD


title: Mouse, embryos, cell-GasaE751020


title: k861 : WT : Chow


title: Mouse, embryos, cell-GasaE751021


title: Mouse, embryos, cell-GasaE751019


title: a592 : Dpp4GFP : HFD


title: 1468 : Dpp4GFP : HFD


title: Mouse, embryos, cell-GasaE751018


title: 1559 : Dpp4GFP : HFD


title: Mouse, embryos, cell-GasaE751017


title: 1544 : Dpp4hepKO : HFD


title: a588 : Dpp4hepKO : HFD


title: Mouse, embryos, cell-GasaE751016


title: Mouse, embryos, cell-GasaE751015


title: Mouse, embryos, cell-GasaE751014


title: 1558 : Dpp4GFP : HFD


title: k859 : Dpp4KO : HFD


title: Mouse, embryos, cell-GasaE751013


title: 1527 : Dpp4hepKO : HFD


title: Mouse, embryos, cell-GasaE751012


title: Mouse, embryos, cell-GasaE751010


title: k858 : Dpp4KO : HFD


title: k856 : Dpp4KO : HFD


title: k843 : Dpp4KO : HFD


title: k847 : Dpp4KO : HFD


title: OF3 : WT : HFD


title: Mouse, embryos, cell-GasaE751009


title: Mouse, embryos, cell-GasaE751037


title: Mouse, embryos, cell-GasaE751008


title: HCT116 cells, ov-PBX1-3

city: Guangzhou

first: Yinan

state: Guangdong

address: no.58 Zhongshanerlu street

institute: The first affiliated hospital, Sun Yat-sen University

data_processing:
all reads were mapped to the human genome 19 using BWA tools
annotated using miRBase version 21 (https://www.mirbase.org) and miRDeep2 (https://www.mdc-berlin.de /8551903 /en /).
Assembly: hg 19
Supplementary files format and content: FPKM and Count excel files

source_name: colon

extract_protocol:
Cells were removed, and RNA was harvested using Trizol reagent. Intact mRNA was isolated from total RNA samples using an Arraystar Seq-StarTM poly(A) mRNA Isolation Kit (Aksomics, Shanghai, China).
A KAPA Stranded mRNA-seq Kit (F. Hoffmann-La Roche Ltd, Grenzacherstrasse, Basel, Switzerland) was used to create RNA-seq libraries. The prepared libraries were diluted to a final concentration of 8 pmol/L, and clusters were generated on an Illumina cBot using a HiSeq 3000/4000 PE Cluster Kit (#PE-410-1001, Illumina), followed by sequencing on an Illumina HiSeq 2500.

value: colon

value: colon cancer cells

value: PBX3 overexpression

value: no


title: Mouse, embryos, cell-GasaE751006


title: HCT116 cells, ov-PBX1-2

value: PBX2 overexpression


title: Mouse, embryos, cell-GasaE751007


title: OF2 : WT : HFD


title: K562 Essential DHS Tiling Plasmid

city: Palo Alto

first: David

last: Yao

state: CA California

address: Michael Bassik/Room 4300, 240 Pasteur Dr.,

institute: Stanford University Bassik Lab

description: sgRNA library sequencing

data_processing:
Reads are trimmed to 20 bases covering the sgRNA spacer sequence
Bowtie1 alignment, v1.2.2, 0 mismatches allowed
Supplementary files format and content: tab-delimited text files include Bowtie alignment counts for each sample

organism: Synthetic plasmid

source_name: plasmid

extract_protocol:
Genomic DNA was harvested using QIAgen DNA Blood & Tissue Maxi Kit; Plasmid DNA was extracted from bacterial cultures using the QIAgen Maxi Prep Kit
The sgRNA sequence present on the plasmid or integrated into genomic DNA was amplified and barcoded using PCR, from either 320 ug of genomic DNA per sample, or 5 ng of plasmid DNA

tag: sample type

value: plasmid


title: OF1 : WT : HFD

value: High fat high cholesterol diet (HFHC)


title: Mouse, embryos, cell-GasaE751005


title: HCT116 cells, ov-PBX1-1

value: PBX1 overexpression


title: k853 : WT : HFD

value: Wildtype (WT)


title: Mouse, embryos, cell-GasaE751011


title: k911 : WT : HFD


title: Mouse, embryos, cell-GasaE751003


title: k914 : WT :HFD


title: k841 : WT : HFD


title: Mouse, embryos, cell-GasaE751004


title: HCT116 cells, ovControl-3

value: WT


title: HCT116 cells, ovControl-1


title: Mouse, embryos, cell-GasaE751002


title: PV3

city: New Haven

first: Dongjoo

last: Kim

state: CT

address: 55 Prospect st.

department: BME

institute: Yale University

data_processing:
Sequencing data was generated on Illumina HiSeq 2500 instrument, same as GSE109535.
Casava 1.8.2 and bcl2fastq2 v2.19.0 were used for fastq generation.
Sequenced reads were trimmed for adaptor sequence, preprocessed for cell barcodes and unique molecular index, and  then mapped to hg19 genome(STAR v2.5.2b).
Genome_build: hg19
Supplementary_files_format_and_content: Text files of expression matrix used in analysis.  The Seurat package (V2.3.0) in R (V3.4.1) was applied to identify differentially expressed genes among 3817 single cells. Cells were considered in the analysis only if they met the following quality control criteria: low expression of mitochondrial genes (<10% of total counts in a cell). The name of each column indicates the batch and cell barcode. For example, the column name "CarT_ATGCAGCGCTGA" represents the mRNA expression data from the CAR-T control group, and from the cell "ATGCAGCGCTGA".

source_name: CD34+ hematopoietic stem cell

extract_protocol:
Mononuclear cells were purified using Ficoll-Qacque and CD34+ cells isolated using human CD34 MicroBeads and column filtration per the manufacturer's protocol.
The single cell mRNA libraries were prepared using the DropSeq protocol (GSE63473), tagged with Illumina nextera single indexes (N701, N702, N703, N704, N705, N706). We used the same protocol as in scFTD-seq(GSE109535), where each mRNA captured was end-paired with an unique molecular index(UMI) and a cell barcode.

value: CD34+ cells

value: Blood


title: PV1


title: PV2


title: ET2


title: MF1


title: ET1


title: D9, pool B, replicate 2

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

institute: TIGEM

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Foreskin

extract_protocol:
For each time-point, cells were detached using TrypLE-express (ThermoFisher, Gibco 12604). Harvested cells were then centrifuged at 300 g and resuspended at the final cell density of 100 cells/mL using a solution containing 40% KnockOut Serum Replacement (KSR, ThermoFisher, Gibco 10828) in DMEM. For each timepoint, two replicates were produced, each containing cells from 4 independent chips that were pooled together then divided in aliquots containing 5,000-80,000 cells. Samples were cryopreserved in DMEM supplemented with 40 % KSR and 15 % DMSO and stored in liquid nitrogen.
scRNA-seq libraries were generated using one or two samples for each replicate. Briefly, each cryopreserved aliquot was thawed at 37 °C until a tiny ice crystal remained in solution. Then each sample was diluted under gentle shaking by dropwise adding 10 volumes of DMEM supplemented with 40 % KSR. Cells were washed twice using a washing buffer containing 8 % MACS Running Buffer (Miltenyi, 130-091-221) in PBS. Cells were then resuspended in the washing buffer and filtered through a 40 µm cell strainer (Biosigma, 010198Z). Cell viability and concentration were checked by visual inspection using Trypan Blue (Logos Biosystems, L12002).
10X scRNA-seq 3' gene expression

value: Human Fibroblasts

value: Foreskin

value: BJ cells

value: mRNA transfections

tag: time

value: B


title: D15, pool B

description: 10x Genomics


title: D11, pool B, replicate 2

description: 10x Genomics


title: D13, pool A

description: 10x Genomics

value: A


title: D11, pool A

description: 10x Genomics


title: D13, pool B

description: 10x Genomics


title: D15, pool A

description: 10x Genomics


title: D9, pool B, replicate 1

description: 10x Genomics


title: D9, pool A, replicate 2

description: 10x Genomics


title: D7, pool B, replicate 2

description: 10x Genomics


title: D7, pool B, replicate 1

description: 10x Genomics


title: D5, pool B, replicate 1

description: 10x Genomics


title: HCT116 cells, ovControl-2

value: colon

value: colon cancer cells


title: D7, pool A

description: 10x Genomics


title: Ndp knockout +PBS (bulk RNA)

city: New York City

first: Lukas

last: Vlahos

state: New York

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

data_processing:
The sequencing libraries were multiplexed and clustered on a flowcell.
After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.
The samples were sequenced using a 2x150 Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
One mis-match was allowed for index sequence identification.
Assembly: mm10

source_name: retina endothelia cells

extract_protocol:
Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
RNA libraries for RNA-seq were prepared using NEB Next Ultra II DNA Library Prep Kit following manufacturer's protocols.

value: retina endothelia cells

value: Ndp knockout

value: PBS


title: Ndp knockout +L6-F4-2 (bulk RNA)


title: D5, pool A, replicate 1

description: 10x Genomics


title: D5, pool A, replicate 2

description: 10x Genomics


title: Mouse, embryos, cell-GasaE751001

value: Embryos

value: C57BI6/J(female)x CAST/EiJ(male)


title: D5, pool B, replicate 2

description: 10x Genomics


title: Ndp wild type +PBS (bulk RNA)

value: Ndp WT


title: D3, pool B

description: 10x Genomics


title: Normal3

city: guangzhou

first: wenbin

last: Chen

address: Industrial Avenue Central

department: zhujiang hospital

institute: Southern medical university

data_processing:
Use the sequenced reads to map with the known piRNA, and then use the unmap reads to make predictions. Otherwise, predict piRNA directly from the beginning
The expression of piRNA in each sample was counted, and the expression normalization treatment was carried out with TPM
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: testicle

extract_protocol:
Total RNA was extracted by Trizol (Invitrogen, USA).
RNA libraies were prepared for sequencing using standard illumina protocols.

value: testicle

value: control


title: D3, pool A

description: 10x Genomics


title: ET3

value: CD34+ cells

value: Blood


title: D0, pool B

description: 10x Genomics

value: Human Fibroblasts

value: Foreskin


title: Normal2


title: Normal1


title: D9, pool A, replicate 1

description: 10x Genomics

value: BJ cells

value: mRNA transfections


title: Heat2

value: testicular heat stress (43°C)


title: D11, pool B, replicate 1

description: 10x Genomics

value: B


title: Heat1


title: Heat3


title: D0, pool A

description: 10x Genomics

value: A


title: Tet1/3 cDKO TGFb+IL2 1

city: Iowa City

first: Priya

middle: Darshinee

last: Issuree

state: IA

address: 431 Newton Road

department: Department of Internal Medicine

institute: University of Iowa

data_processing:
Sequencing adapters were removed from paired-end reads using Trimmomatic version 0.39
Trimmed reads were aligned to mouse reference genome GRCm38 using Bowtie 2 version 2.4.1 with options --very-sensitive -X 2000. Following genome alignment, Picard was used to mark PCR duplicates, and samtools version 1.3.1 was used to remove PCR duplicates, discordant pairs, and alignments to the mitochondrial genome
Peak calling was performed using MACS2 version 2.2.7.1, cutoff q value of 0.05 and differential accessibility analyses of MACS2 peaks were performed using the R package DiffBind version 2.10.0
Differentially accessible peaks were annotated to genome regions of interest using the R package ChIPseeker version 1.18.0 and sequence motif enrichment analyses were performed using HOMER version 4.11.1
Assembly: mm10/GRCm38
Supplementary files format and content: narrow peaks

source_name: Spleen

growth_protocol: cells were seeded in complete T cell medium [RPMI 1640 (Gibco), 10% heat-inactivated FBS (Gibco Lot no. 2261598RP or Atlanta Lot no. A16003), 2 mM L-glutamine, 50 µg/ml gentamicin, 1% Penn/Strep, 50uM 2-mercaptoethanol (Gibco)] along with anti-CD3 (Tonbo, clone 17A2, 0.25ug/mL) and anti-CD28 (Tonbo, clone 37.51, 1ug/mL) antibodies

extract_protocol:
48hrs later T cells were harvested for ATAC-Seq processing.
ATAC-Seq was performed using 90,000 cells/sample. Cell nuclei were obtained and tagmented using the Active-Motif ATAC-Seq Prep Kit
DNA libraries for ATAC-seq were prepared using ActiveMotif ATAC-Seq Prep Kit following manufacturer's protocols.

treatment_protocol: Naïve CD4+ T cells were FACS sorted and activated with anti-CD3/CD28 and 20 ng/mL TGF-b +/- 100U IL-2

value: Spleen

value: CD4 T cells

value: Tet1/3 cDKO

value: induced Treg differentiation


title: control TGFb+ IL-2 2

value: WT


title: Tet1/3 cDKO TGFb+IL2 2


title: Tet1/3 cDKO TGFb only 2


title: control TGFb+ IL-2 1


title: Tet1/3 cDKO TGFb only 1


title: control TGFb only 2


title: control TGFb only 1


title: Ndp wild type +PBS

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Fresh retinas were minced and incubated in 5 ml DMEM containing 200 U/ml collagenase I (Invitrogen) for 45 mins at 37°C with occasional shaking followed by filtering through a 40 µm nylon mesh. The cells were then centrifuged at 94 x g for 5 mins at 4°C and resuspended in PBS with 0.1% BSA + 2 mM EDTA. Endothelial cells were labeled with PE-Cy7 rat anti-mouse CD31 (#25-0311-82, eBiosciences, CA). 7-AAD (Invitrogen, Waltham, MA) were added to exclude dead cells. Staining was performed for 1 h at 4°C. Retina ECs were sorted into DMEM medium with an Aria II sorter (BD) at the Stanford University Shared FACS Facility
scRNA-seq with the 10X Genomics Single Cell 3′ platform was performed per manufacturer’s protocol.

value: retina endothelia cells

value: Ndp WT

value: PBS


title: MGI2482_TWJG-S-005-G005,G-CSF,Healthy

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S. Euclid Avenue

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
For each sample, we obtained the unfiltered feature-barcode matrix per sample by passing the demultiplexed FASTQs to Cell Ranger v6.0.1 ‘count’ command using default parameters and the prebuilt GRCh38 genome reference (GRCh38-2020-A) and the Chemistry flag (Single Cell 5’ PE) for scRNA. Seurat 4.1.0 was used for all subsequent analyses.
Cells were further filtered to only maintain cells with: <20% human mitochondrial DNA content; minimum of at least 200 and maximum of 20000 genes expressed. We constructed a Seurat object using the unfiltered feature-barcode matrix for each sample. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c(“nCount_RNA”, “percent.mito”), variable.features n = 2000). Any merged analysis or subsequent subsetting of cells/samples underwent the same scaling and normalization method. Cells were clustered using the original Louvain algorithm and top 30 PCA dimensions via ‘FindNeighbors’ and ‘FindClusters’ (with parameters: resolution = 0.5) functions. The resulting merged and normalized matrix was used for the subsequent analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).

source_name: Apheresis Products

extract_protocol:
CD34+ HSPCs from N=12 patients with MM (placebo+G-CSF N=4, plerixafor+G-CSF N=4, motixafortide+G-CSF N=4) as well as N=6 healthy allogeneic HSPC donors (G-CSF N=2, plerixafor N=2, motixafortide N=2) were purified from apheresis products collected on the first day of apheresis via CD34 immunomagnetic selection.
Transcriptional profiling was performed by 10x, 5’ scRNA sequencing. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: HSPC

value: Apheresis Products


title: MGI2482_TWJG-D026-A026,Plerixafor,Healthy

description: 10x Genomics


title: MGI2482_TWJG-DIV29-A029,Plerixafor,Healthy

description: 10x Genomics


title: Ndp knockout +L6-F4-2

description: 10x Genomics

value: Ndp knockout


title: MGI2482_TWJG-S-009-G009,G-CSF,Healthy

description: 10x Genomics


title: Aged Wild-Type after ischemic insult

city: Tampa

first: Ji

last: Li

state: FL

address: 12901 Bruce B. Downs Blvd

department: Surgery

institute: University of South Florida

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, and gene counting  were done by the 10x Genomics Cell Ranger software v6.0.2
Assembly: Mm10 Mouse Reference Genome supplied from 10x Genomics: refdata-gex-mm10-2020-A
Supplementary files format and content: Sample separate barcode, matrix, and genes

molecule: nuclear RNA

source_name: Left Ventricle

extract_protocol:
Left ventricle tissue was collected after 24 hours for ischemic insult mice, Fresh left ventricle tissue was collected from healthy mice
Library constructed follwing manufacturer protocol for the 10x Genomics Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit

treatment_protocol: LAD surgery performed on both aged and young mice causing 45 minute ischemia then allowing 24 hours for reperfusion for ischemic insult mice.

value: Left Ventricle

value: Cardiomyocyte, Endothelial, Fibroblast, Macrophage

value: Male

tag: age

value: 24-26 Months Old

value: 45 minute ischemia/24 hour reperfusion


title: MGI2482_TWJG-BL010-BL010,Motixafortide,Healthy

description: 10x Genomics


title: MGI1150_TWJJ-012-049-B49,Motixafortide+G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-012-036-B36,Motixafortide+G-CSF,Myeloma

description: 10x Genomics


title: MGI2482_TWJG-BL011-BL011,Motixafortide,Healthy

description: 10x Genomics


title: Young Wild-Type after ischemic insult

description: 10x Genomics

value: 3-5 Months Old


title: MGI2482_TWJG-012-059-B012-059,Motixafortide+G-CSF,Myeloma

description: 10x Genomics


title: Young Wild-Type under sham conditions

description: 10x Genomics

value: Healthy (No Alteration)


title: MGI2482_TWJG-1100-A1100,Plerixafor+G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-1104-A1104,Plerixafor+G-CSF,Myeloma

description: 10x Genomics


title: Aged Wild-Tyoe under sham conditons

description: 10x Genomics


title: MGI2482_TWJG-1096-A1096,Plerixafor+G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-012-055-P55,G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-012-045-P45,G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-012-015-P15,G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-1102-A1102,Plerixafor+G-CSF,Myeloma

description: 10x Genomics


title: MGI1150_TWJJ-012-037-P37,G-CSF,Myeloma

description: 10x Genomics


title: Tric-b-KO Round

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

country: Japan

institute: Kyoto University

description: Gene expression data from round chondrocytes in femoral cartilage of embryonic E17.5 Tric-b-KO mice

hyb_protocol: The labeled cRNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Normakisation and data analyses were performed by using Affymetrix GeneChip Command Console Software 6.

label: biotin

source_name: Round chondrocytes, Tric-b-KO mice cartilage

label_protocol: cRNA labeling was performed according to the manufacturer’s instructions.

growth_protocol: Mice were housed under a 12-hr light–dark cycle and given regular chow.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cRNA.

treatment_protocol: Femoral cartilage plate sections enriched with round chondrocytes or columnar and hypertrophic chondrocytes were isolated from embryonic E17.5 Tric-b KO mice.

value: C57BL/6J, 129Sv, Tric-b-KO

value: Round chondrocytes

value: cartilage

tag: developmental stage

value: E17.5 embryo


title: Kidney, BALBc, rep2

city: Seoul

first: Hye Young

address: 103 Daehak-ro, Jongro-gu

country: South Korea

institute: Seoul National University

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(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Kidney, data, repstep
Kidney, data, repstep
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: Kidney, processed, repcontent

source_name: kidney

growth_protocol: Kidney, growth, repoptional

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Kidney, treatment, repoptional

value: kidney


title: Kidney, BALBc, rep3


title: Ndp knockout +PBS

description: 10x Genomics

value: retina endothelia cells


title: MGI2482_TWJG-012-052-B012-052,Motixafortide+G-CSF,Myeloma

description: 10x Genomics


title: Tric-b-KO Columnar.Hypertrophy

description: Gene expression data from columnar and hypertrophic chondrocytes in femoral cartilage of embryonic E17.5 Tric-b-KO mice

source_name: Columnar and hypertrophic chondrocytes, Tric-b-KO mice cartilage

value: Columnar and hypertrophic chondrocytes


title: Kidney, B6, rep3


title: Kidney, B6, rep2


title: CD49f-NGFR-  Sir Tubulin + cells rep1

first: Andreas

last: Wack

description: ALI t10 sorted

data_processing:
fastq files were processed with nf-core/rnaseq pipeline v  3.8.1
pipeline was run using STAR and RSEM for alignment and quantification
Differential expressed genes were obtained from DESeq2 v1.34.0 within an R 4.1.1 environment
Genes are considered significant when padj < 0.05
Assembly: Mus_musculus, ensembl,GRCm38,release-95
Supplementary files format and content: rsem output, counts and TPMs per gene per sample as tab separate file

source_name: primary epithelia

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Cells were collected at day 10 post air-exposure.

extract_protocol:
RNA was isolated from sorted cells  , using the Qiagen RNeasy mini kit
RNA (200 ng) was used to prepare cDNA libraries using the NEBNext_Low_Input_w_NEB_Ultra_II_FS Kit.

treatment_protocol: Cultures were trypsinized and sorted into  CD49f+NGFR+ (Basal Cells), CD49f-NGFR- SiRTubulin + (ciliated) and CD49f-NGFR- SiRTubulin - (secretory) subsets

value: airway epithelia

value: wt

value: ciliated


title: CD49f-NGFR-  Sir Tubulin + cells rep2

description: ALI t10 sorted


title: CD49f-NGFR-  Sir Tubulin - cells rep3

description: ALI t10 sorted

value: secretory


title: CD49f+NGFR+ cells rep 2

description: ALI t10 sorted

value: basal


title: Kidney, B6, rep1


title: CD49f+NGFR+ cells rep 1

description: ALI t10 sorted


title: CD49f-NGFR-  Sir Tubulin - cells rep2

description: ALI t10 sorted


title: Kidney, BALBc, rep1


title: 18 CD

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
Raw reads were trimmed and filtered using Trimmomatic v0.36
Gene level expression was quantified using Kallisto v0.44
Differential gene expression analysis was performed using R packaged edgeR v3.28
Assembly: GRCm38.p6 (GENCODE release M23)
Supplementary files format and content: raw count matrices

growth_protocol:
The mice were either on chow, ketogenic or high fat diet
The mice were on HFD or KD only for 3 days at the age of 12 weeks

extract_protocol: Total RNA was extracted from liver of mice fed a chow, KD or HFD for 3 days, using Trizol reagent

treatment_protocol: Short term  ketogenic diet

value: Liver

value: Chow diet


title: 15 CD


title: 17 CD


title: 19 CD


title: 10 HFD

value: High fat diet


title: K562, eNFE2 sgRNA, Biological Replicate 2

data_processing:
Raw data filtering: remove reads containing adapters, remove reads containing N > 10% (N represents bases that cannot be determined), remove reads containing low quality (Qscore <= 5) bases which is over 50% of the total bases
STAR alignment, v2.7.5b, two-pass alignment with default parameters
htseq-count, v0.6.0, default parameters
Assembly: hg38
Supplementary files format and content: tab-delimited text files include htseq-count values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
1.0 ug of total RNA was used for the construction of sequencing libraries. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Lymphoblast cells

value: Puromycin


title: 16 CD


title: 6 KD

value: ketogenic diet


title: 9 HFD


title: K562, eNFE2 sgRNA, Biological Replicate 3


title: 8 KD


title: K562, Safe sgRNA, Biological Replicate 3

value: WT; Safe-targeting negative control sgRNA


title: K562, eNFE2 sgRNA, Biological Replicate 1


title: CD49f-NGFR-  Sir Tubulin - cells rep1

city: London

address: 1 Midland Road

institute: The Francis Crick Institute

description: ALI t10 sorted


title: CD49f+NGFR+ cells rep 3

description: ALI t10 sorted


title: K562, Safe sgRNA, Biological Replicate 2


title: 3 KD


title: 4 KD


title: 2 KD


title: Hep3B_siRNA1_10nM_rep4

city: Cambridge

first: Joseph

last: Barry

state: MA

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

data_processing:
Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using the ea-utils software fastq-mcf.
Filtered reads were aligned to the Mus musculus (GRCm39/mm39), or Homo sapiens (hg38/GRCh38) genomes using STAR (ultrafast universal RNAseq aligner) v2.7.9a.
Differential gene expression analysis was performed by the R package DESeq2 v1.34.0 with the betaPrior parameter set to TRUE to shrink log2 fold-change estimates for noisy, low-count genes.
Assembly: GRCm39, GRCh38
Supplementary files format and content: tab-delimited raw count files
Supplementary files format and content: tab-delimited DESeq2 tables with differential expression metrics

growth_protocol: Primary Mouse Hepatocytes (BIOIVT, Cat # M005052-P, Lot GBW) were transfected in 384-well plates (5000 cells per well) with siRNA or DPBS (mock control) at a final concentration of 50 nM using Invitrogen Lipofectamine® RNAiMAX (Invitrogen, Carlsbad, CA, Catalog No. 13778-150). After 48 hours, cell were lysed in lysis buffer (Tris HCl pH 7.5 100mM, LiCl 500mM, EDTA pH 8.0 10mM, LiDS 1%, DTT 5mM supplemented with TURBO™ DNase,Thermofisher #AM2238) for 30 min. Hep3B cells followed an equivalent protocol at 10nM and 48hrs for dose and time respectively.

extract_protocol:
Dynabeads Oligo (dT)25 (Thermo Fisher Scientific 61005)
Whole transcriptome mRNA-enriched RNA-Seq libraries were constructed using a KAPA mRNA Capture Kit and mRNA HyperPrep Kit (Roche) from cell lysates as per protocol but in 5x miniaturized reagent scale (except mRNA capture beads were resuspended in water prior to mix with lysate).
RNA-Seq libraries were quantified by low depth sequencing on Illumina iSeq instrument . Equal amounts of each library/sample were pooled and sequenced on a Illumina NovaSeq instrument with 2x150bp paired-end settings, according to manufacturers’ instructions.

value: Hep3B Cells

tag: dose

value: transgene-regulator siRNA


title: Hep3B_siRNA1_10nM_rep2


title: Hep3B_siRNA1_10nM_rep1


title: K562, Safe sgRNA, Biological Replicate 1


title: 14 HFD


title: Hep3B_siRNA3_10nM_rep2


title: Hep3B_siRNA1_10nM_rep3


title: RNA-seq, CD36 HFD treatment fish-2

city: Zhunan

first: Chiou Hwa

last: Yuh

address: 35, Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

data_processing:
Raw data qulity contol by fastQC
Trimmomatic, those that meet the following conditions will be deleted: 1) Base quality <3 from either 3’ or 5’ end. 2) Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3) Read length <36.
Post-Trimming quality control
read alignmnet by HISAT2
Differential expression analysis by DESeq2 (with biological replicates)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: whole larvae

growth_protocol: CD36 transgenic zebrafish larvae feeding with normal diet (12%) or high-fat diet (24%) from 5dpf to 15dpf, feeding the larvae for diet and paramecium four times per day from 9:00~16:00. In this experiment we use CD36 normal diet (12%) as control.

extract_protocol:
RNA was harvested using NucleoSpin® RNA kit (MACHEREY-NAGEL). 5 ug of total RNA was used for the construction of sequencing libraries.
TruSeq® Stranded mRNA Library Prep

treatment_protocol: After the last meal, we move the larvae to a peri dish and treat them with or without CACF (40 μg/ml) in E3 buffer from 4 pm to 9 am tomorrow

value: whole larvae

value: CD36 overexpression

value: HFD


title: 11 HFD


title: 12 HFD


title: RNA-seq, CD36 HFD treatment fish-4


title: Hep3B_siRNA3_10nM_rep1


title: Hep3B_siRNA2_10nM_rep3


title: RNA-seq, CD36 HFD with CACF treatment fish-2

value: HFD+CACF


title: RNA-seq, CD36 HFD with CACF treatment fish-4


title: Hep3B_siRNA2_10nM_rep2


title: RNA-seq, CD36 normal diet fish-2

value: Normal diet


title: RNA-seq, CD36 normal diet fish-4


title: Hep3B_siRNA2_10nM_rep4


title: Hep3B_siRNA2_10nM_rep1


title: Hep3B_siRNA.ctrl_10nM_rep3

value: TMPRSS6 knockdown

value: noisy siRNA control


title: Hep3B_siRNA.ctrl_10nM_rep4


title: Hep3B_siRNA.ctrl_10nM_rep1


title: Hep3B_mock_rep4

value: no treatment

value: mock transfection control


title: Hep3B_siRNA.ctrl_10nM_rep2


title: Hep3B_siRNA3_10nM_rep3


title: Hep3B_mock_rep3


title: Hep3B_mock_rep2


title: Hep3B_mock_rep1


title: PMH_mock_rep4

source_name: PMH

value: PMH

value: Primary Mouse Hepatocytes


title: PMH_mock_rep3


title: OIR2

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description:
circular RNA
m6A-circRNA epitranscriptomic microarray data from sample of OIR mice.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Mouse circRNA Epitranscriptomic Arrays (8x15K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Captured array images were analyzed by Agilent Feature Extraction software (V11.0.1.1). Average log2-scaled spike-in RNA intensities were used for normalization of the raw intensities of IP and Sup. m6A quantities were calculated based on normalized IP amounts, and m6A methylation levels were calculated as the percentage of modification (IP normalized intensities) of the input (IP and Sup normalized intensities).

label: Cy3, Cy5

source_name: retinal tissues

label_protocol: "IP" and "Sup" RNAs were treated with RNase R, and then amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: The pups and the feeding mothers were maintained in cages in temperature-controlled rooms featuring a 12-h light/12-h dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs were immunoprecipitated with anti-N6-methyladenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs.

treatment_protocol: The pups were exposed to hypoxic conditions (75%) from postnatal day (P) 7, and returned to room air at P12. Pups in the control group were exposed to room air continuously. The retinas were collected at P17 in both groups.

tag: group

value: oxygen-induced retinopathy

value: retina

value: postnatal day 17


title: OIR1


title: OIR3


title: Con3

description:
circular RNA
m6A-circRNA epitranscriptomic microarray data from sample of room air control.

value: control


title: PMH_mock_rep2

tag: cell line


title: Con2


title: PMH_siRNA.ctrl_50nM_rep4

tag: cell type


title: Con1


title: PMH_siRNA.ctrl_50nM_rep3


title: PMH_siRNA.ctrl_50nM_rep2


title: PMH_mock_rep1


title: RNA-seq, CD36 normal diet fish-1


title: PMH_siRNA2_50nM_rep4


title: Telogen SHFs in March, female (bio rep 1)

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to goat (Capra hircus) transcriptomes (GCF_001704415.1_ARS1) using Kallisto (v.0.46.1) with parameters -b 100. The gene abundances were obtained by kallisto-sleuth (v.0.30.0) pipeline in TPM (transcripts per million) (Bray NL et al. 2016).
Assembly: GCF_001704415.1_ARS1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Capra hircus

source_name: Secondary hair follicles from goat skin

extract_protocol:
Total RNA was extracted from the secondary hair follicles using RNAiso Plus (TRIzol method, TaKaRa Bio, Dalian, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Secondary hair follicles from goat skin

value: female

value: 1.5 years

tag: month

value: March

tag: growth stage

value: Telogen


title: Telogen SHFs in February, male (bio rep 2)

tag: Sex

value: male

value: February


title: PMH_siRNA2_50nM_rep3

tag: genotype

value: transgene-regulator siRNA

tag: treatment


title: Catagen SHFs in December, male (bio rep 2)

tag: tissue

value: December

value: Catagen


title: PMH_siRNA.ctrl_50nM_rep1

value: TMPRSS6 knockdown

value: noisy siRNA control


title: PMH_siRNA2_50nM_rep2

value: PMH

value: Primary Mouse Hepatocytes


title: Telogen SHFs in February, female (bio rep 1)


title: Catagen SHFs in December, female (bio rep 1)


title: Catagen SHFs in November, male (bio rep 2)

value: November


title: PMH_siRNA3_50nM_rep4


title: Catagen SHFs in November, female (bio rep 1)


title: PMH_siRNA3_50nM_rep3


title: PMH_siRNA2_50nM_rep1


title: PMH_siRNA3_50nM_rep2


title: Anagen SHFs in September, female (bio rep 1)

value: September

value: Anagen


title: PMH_siRNA1_50nM_rep4


title: Telogen SHFs in March, male (bio rep 2)

value: Secondary hair follicles from goat skin


title: Anagen SHFs in May, female (bio rep 1)

value: female

value: May


title: PMH_siRNA1_50nM_rep3


title: PMH_siRNA1_50nM_rep2


title: Aged IR rep 2

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
Quality check on raw sequence data, FastQC.
Read mapping. Reads were mapped to the Mus musculus genome assembly GRCm38 (mm10) with HISAT2 on default parameters.
Read counting. Reads were counted into Ensembl annotation intervals using HTSeq-count.
Data normalization and differential analysis. Differential expressed genes were estimated using DESeq2 with default parameters.
Assembly: mm10
Supplementary files format and content: DESeq2 normalized count

source_name: spleen

growth_protocol: Female C57BL/6J mice were used for all the experiments and were maintained in pathogen-free conditions at the Experimental Medicine Centre (Bialystok, Poland).

extract_protocol:
For RNA sequencing, RPMs (live, single, CD45+, B220-, GR1-, F4/80-high, CD11b-dim, TREML4+) were sorted into Trizol-LS (Invitrogen, 10296010). RNA was isolated using Direct-zol RNA Microprep Kit (Zymo Research, R2062) according to the manufacturer's instructions.
To prepare libraries from FACS-sorted RPMs (at least 100 000 cells/sample) we used the previously described Smart-seq2 protocol {Picelli, 2013 #1236}, suitable for low-input total mRNA sequencing. The quality of RNA and material during the preparation of libraries was checked by Bioanalyzer. .
The samples were sequenced on NextSeq500 (Illumina) with 75 bp single-end reads, with ~50 million reads/sample. RNAseq was performed at GeneCore at EMBL (Heidelberg, Germany)

treatment_protocol: Starting with the age of 4 weeks mice were fed a diet with a standard iron content (200 mg/kg, SAFE #U8958v0177; for Young and Aged), as described before,{Kautz, 2008 #10;Pagani, 2011 #238} or reduced iron content [25 mg/kg; SAFE #U8958v0294; for Aged iron reduced (IR)]. Diets were from SAFE (Augy, France). Mice were analyzed at 8-10 weeks (Young) and 10-11 months (Aged and Aged IR) of age. For supplementation with N-Acetyl-L-cysteine (NAC), aging mice (Aged NAC) were supplied with NAC dissolved in drinking water from 8 weeks of age until 10-11 months of age. Mice were delivered to the local facility at the IIMCB and sacrificed after short acclimatization, or subjected to additional procedures, if applicable.

tag: strain

tag: organ

value: spleen

value: FACS-sorted red pulp macrophages

value: 10 months

value: reduced iron 25 ppm from the 5th week of life


title: Aged IR rep 3

tag: diet


title: Aged IR rep 4


title: PMH_siRNA3_50nM_rep1

value: transgene-regulator siRNA


title: Aged rep 4

value: standard 200 ppm Fe from the 5th week of life


title: Aged IR rep 1


title: Aged rep 3


title: Anagen SHFs in September, male (bio rep 2)

value: male

value: 1.5 years


title: Aged rep 2


title: Anagen SHFs in May, male (bio rep 2)


title: patient 6_Vermilion 6

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: human lip tissue

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: After centrifugation of the cells derived from vermilion and oral mucosa, the total RNA was extracted using a RNeasy mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

tag: subject id

value: patient 6

value: 8 months old

tag: gender

value: lip


title: PMH_siRNA1_50nM_rep1

value: PMH

value: Primary Mouse Hepatocytes

tag: time


title: patient 6_Oral mucosa 6

tag: age


title: Aged rep 1


title: human renal tubular epithelial cells -Input

city: Zhengzhou

first: Yanan

last: Gong

state: Henan

address: 1 Jianshe Road

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

source_name: human renal tubular epithelial cells

growth_protocol: Human renal tubular epithelial cells (HK-2) were kindly provided by Stem Cell Bank, Chinese Academy of Sciences. Cells were routinely cultured in Dulbecco's Modified Eagle Medium (DMEM) (1 g/L glucose) (Gibco, Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Thermo Fisher Scientific, USA), 100 UI/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: human renal tubular epithelial cells

tag: chip antibody

value: Rabbit(DA1E) mAb IgG XP Isotype Control (CST, #3900)


title: Young rep 4

value: female

value: 8 weeks


title: Young rep 3

value: spleen


title: patient 5_Vermilion 5

value: patient 5

value: 5 months old


title: patient 3_Skin ３

extract_protocol: After centrifugation of the cells derived from vermilion and skin, the total RNA was extracted using a RNeasy mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

value: patient 3

value: 7 months old


title: Young rep 1

value: FACS-sorted red pulp macrophages

value: standard 200 ppm Fe from the 5th week of life


title: patient 5_Oral mucosa 5


title: patient 2_Vermilion 2

value: patient 2

value: male


title: patient 3_Vermilion ３


title: patient 2_Skin ２


title: patient 1_Skin 1

value: patient 1

value: 3 months old


title: patient 4_Oral mucosa 4

value: patient 4

value: lip


title: human renal tubular epithelial cells -IP

value: human renal tubular epithelial cells

value: p300(D2X6N) Rabbit mAb (CST, #54062)