title: young_surgery_48h_hemisphere_2

description:
Library name: FACS81_HM
FACS81_HM

value: brain

value: hemisphere

value: 48 hours


title: rtgill.dmso.5.D11

status: Public on Jan 01 2025

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rtgill.dmso.5.D11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.D11.expression.values

library_source: transcriptomic

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: RTgill-W1 ctrl rep 27

growth_protocol: Cells were grown in Thermo Scientific™ BioLite™ Cell Culture Treated 100 mm Petri dishes containing 10 ml of complete culture medium (Leibovitz L-15 culture medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin), at 21°C.

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

tag: tissue

value: ctrl

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: Sample_UIC4_5_359_218

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

description:
PA_UC_4_5
nup107_mo_tpm_polyA.tsv.gz

data_processing:
Stranded paired-end polyA+ and ribozero 150 bp RNA-seq reads were aligned to the Xt9.1 genome combined with ERCC spikes using STAR and quantified as transcripts per million (TPM) for each gene with RSEM  using the RSEM-STAR pipeline, with additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --paired-end”.
Assembly: Xt9.1
Supplementary files format and content: Tab delimited file with transcripts per million quantifications for all genes. The gene models are the Xenopus tropicalis 9.1 Xenbase models from https://www.xenbase.org/ (a link to the GTF: https://download.xenbase.org/xenbase/Genomics/JGI/Xentr9.1/XENTR_9.1_Xenbase.gtf.gz).

organism: Xenopus tropicalis

source_name: Whole Embryo

growth_protocol: We induced ovulation, performed IVF, and raised embryos in 1/9xMR, We staged X. tropicalis embryos according to Nieuwkoop and Faber.

extract_protocol:
10 ml of an ERCC RNA Spike-In Mix (Thermo Fisher Scientific) was added to 860 ml of DEPC-treated water and then diluted 1:10 into Trizol. 10 embryos per timepoint and condition (UIC and MO) were homogenized in 100 ml of Trizol+Spike-In mixture. Each sample was frozen using ethanol and dry ice and then stored at -80 °C. All samples were processed for RNA extraction at the same time. Following isopropanol precipitation, RNA pellets were resuspended in DEPC-treated water and precipitated with 5M LiCl at 4 °C overnight. This solution was centrifuged at 4 °C, and RNA pellets were washed twice with 70% ethanol. Final RNA products were resuspended in DEPC-treated water (2 ml/embryo).
RNA libraries were prepared for Illumina sequencing using standard polyA+ and RiboZero Illumina protocols

treatment_protocol: Synchronized embryos were generated by IVF. Uninjected controls (UC) and embryos injected with 10ng of the ATG Nup107 morpholino oligo (MO) were raised in 1/9X MR at 25 °C and then 10 embryos were collected from each group at 30 min intervals from stage 6 until stage 12

value: Whole Embryo

tag: time

value: 4.5 hpf

value: UC

tag: fraction

value: PolyA+ RNA


title: young_ctrl_48h_hemisphere_2

city: Boston

first: Zhuoran

last: Yin

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

country: USA

institute: Brigham and Women's Hospital

description:
Library name: FACS82_HM
FACS82_HM

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
FASTQ files were quantified using the Bulk RNA-seq pipeline published by BCBio at Harvard Medical School (June 2022).
Differential expression analysis was conducted using R (v4.2.1) and DESeq2 (v1.36.0); for each dataset we quantified differential expression between young surgery and young control mice, and between old surgery and old control mice.
Adjusted p-values were determined using the Benjamini-Hochberg procedure and significance cutoffs were set at FDR <= 0.2, log2FC >= |0.58|
Assembly: mm10
Supplementary files format and content: matrix tables with raw gene counts for every sample, divided by brain region and timepoint

organism: Mus musculus

source_name: brain

extract_protocol:
1,000 isolated Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: region

value: microglia

tag: genotype

value: WT

tag: age

value: 3-5 months

value: control

tag: timepoint


title: rtgill.dmso.4.F10

description:
Library name: rtgill.dmso.4.F10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.F10.expression.values

source_name: RTgill-W1 ctrl rep 21


title: rtgill.dmso.5.C11

description:
Library name: rtgill.dmso.5.C11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.C11.expression.values

source_name: RTgill-W1 ctrl rep 26


title: rtgill.dmso.4.H10

description:
Library name: rtgill.dmso.4.H10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.H10.expression.values

source_name: RTgill-W1 ctrl rep 23


title: rtgill.dmso.4.G10

description:
Library name: rtgill.dmso.4.G10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.G10.expression.values

source_name: RTgill-W1 ctrl rep 22


title: dsGFP_chromatin_associated_(0-500bp_fraction) S21_B1S

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

country: Spain

institute: Universitat de València

description:
dsGFP_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in GFP-Control S2 cells. Replicate 2. This sample together with S13_B1L, correspond to B1_merged_chromatin_fractions column in each processed data file

data_processing:
Read file QC: Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering: Adapters were trimmed with cutadapt and trimmomatic
Genome alignment: Raw sequences were aligned to the Ensembl drosophila genome using TopHat
Read count extraction: Read counts per gene were extracted with featureCounts
Filtering by expression and normalization: DESeq2 outlier removal, low count filtering, and normalization.
Assembly: BDGP6 (dm6)
Supplementary files format and content: Tab-delimited text file containing the featureCounts raw read count matrix

organism: Drosophila melanogaster

source_name: S2 cell line

growth_protocol: Drosophila melanogaster Schneider 2 (S2) cells were cultured at 28 °C in Schneider’s medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 50 μg/ml streptomycin and 50 U/ml penicillin (Gibco).

extract_protocol:
Total RNA was extracted using Trizol (Ambion) and ethanol precipitated following standard procedures. For chromatin-associated RNA extraction,S2 cells were crosslinked with formaldehyde for 10 min at RT and the cross-linking was stopped by addition of 1 M glycine for 10 additional min. RNA was isolated with Trizol (Ambion) The cells were then collected and resuspended in Buffer 1 (50 mM Hepes pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0,25% Triton X100 and cOmplete protease inhibitors) and incubated for 10’ at 4 °C, followed by centrifugation at 4 °C and 500g. The pellet was resuspended in cold Buffer 2 (200 mM Nacl, 1 mM EDTA, 0,5 mM EGTA, 10 mM Tris pH 8 and cOmplete protease inhibitors) and centrifuged again. Finally, chromatin was resuspended in Buffer 3 (1 mM EDTA, 0,5 mM EGTA and 10 mM Tris pH 8 and cOmplete protease inhibitors). Chromatin was fragmented using a Bioruptor sonicator (Diagenode) with 25 high intensity sonication 30’’ on/off pulses. RNA was isolated with Trizol (Ambion)
RNA-seq experiments consisted of biological triplicates, but the total RNA samples were pooled and sequenced together. Before RNA-sequencing, and in order to obtain adequate sequencing coverage for RNAs over such a broad size range, the RNA preparations were fractionated using AMPure XP paramagnetic beads (Agilent technologies) at a concentration of 0,6X to select RNAs larger than 500 nt and 1,6X to select caRNAs smaller than 500 nt. The 0-500 nt caRNAs were directly submitted to ribosomal depletion and library preparation, whereas caRNAs >500 nt were first fragmented by sonication. The NEBNext rRNA Depletion kit was used for ribosomal RNA depletion. Single-end strand-specific libraries were prepared using NEBNext Ultra RNA library Prep Kit for Illumina (NEB) according to the manufacturer's instructions. Samples were sequenced in a Illumina NextSeq 500 sequencer aiming for a depth of 15 million reads in average per sample with a length of 80 nucleotides per read

treatment_protocol: The MegaScript RNAi kit was used to produce dsRNA for RNAi experiments. Primer sequences are listed in Suppl. Table S1. Cells were incubated with dsRNAs complementary to GFP (control), Rrp6, Dis3, or both (double knockdown condition) for 48 hours at 28°C. The treatment was repeated once more at 48 hours and cells were harvested 96 hours after the initial transfection. All experiments were carried out in biological triplicates.

value: dsGFP knockdown (control)


title: old_ctrl_48h_hippocampus_4

description:
Library name: FACS80_HP
FACS80_HP

value: hippocampus

value: 20-22 months


title: dsRrp6_chromatin_associated_(0-500bp_fraction) S22_B2S

description:
dsRrp6_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Rrp6-kd S2 cells. Replicate 2. This sample together with S14_B2L, correspond to B2_merged_chromatin_fractions column in each processed data file

value: dsRrp6 knockdown


title: rtgill.dmso.4.E10

description:
Library name: rtgill.dmso.4.E10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.E10.expression.values

source_name: RTgill-W1 ctrl rep 20


title: old_ctrl_48h_hemisphere_4

description:
Library name: FACS80_HM
FACS80_HM

value: brain


title: dsDouble-kd_chromatin_associated_(>500bp_fraction) S20_C4L

description:
dsDouble-kd_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Double-kd S2 cells. Replicate 3. This sample together with S29_C4S, correspond to C4_merged_chromatin_fractions column in each processed data file

value: dsDouble knockdown (Rrp6+Dis3)


title: Sample_UIC3_336_241

description:
PA_UC_3_0
nup107_mo_tpm_polyA.tsv.gz

value: 3 hpf


title: Sample_UIC3_5_312_265

description:
PA_UC_3_5
nup107_mo_tpm_polyA.tsv.gz

value: 3.5 hpf


title: rtgill.dmso.4.D10

description:
Library name: rtgill.dmso.4.D10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.D10.expression.values

source_name: RTgill-W1 ctrl rep 19

value: ctrl

value: Rainbow trout gill


title: dsDis3_chromatin_associated_(>500bp_fraction) S19_C3L

description:
dsDis3_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Dis3-kd S2 cells. Replicate 3. This sample together with S28_C3S, correspond to C3_merged_chromatin_fractions column in each processed data file

value: dsDis3 knockdown


title: rtgill.dmso.4.C10

description:
Library name: rtgill.dmso.4.C10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.C10.expression.values

source_name: RTgill-W1 ctrl rep 18


title: Sample_UIC2_5_360_217

description:
PA_UC_2_5
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 2.5 hpf

value: UC


title: dsDis3_chromatin_associated_(0-500bp_fraction) S23_B3S

description:
dsDis3_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Dis3-kd S2 cells. Replicate 2. This sample together with S15_B3L, correspond to B3_merged_chromatin_fractions column in each processed data file


title: dsRrp6_chromatin_associated_(>500bp_fraction) S18_C2L

description:
dsRrp6_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Rrp6-kd S2 cells. Replicate 3. This sample together with S26_C2S, correspond to C2_merged_chromatin_fractions column in each processed data file


title: old_surgery_48h_hippocampus_4

description:
Library name: FACS77_HP
FACS77_HP

value: microglia

value: WT

value: surgery

value: 48 hours


title: Sample_UIC2_384_193

description:
PA_UC_2_0
nup107_mo_tpm_polyA.tsv.gz

value: 2 hpf

value: PolyA+ RNA


title: Sample_UIC4_383_194

description:
PA_UC_4_0
nup107_mo_tpm_polyA.tsv.gz

value: 4 hpf


title: dsGFP_chromatin_associated_(>500bp_fraction) S17_C1L

description:
dsGFP_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in GFP-Control S2 cells. Replicate 3. This sample together with S25_C1S, correspond to C1_merged_chromatin_fractions column in each processed data file

value: dsGFP knockdown (control)


title: Sample_UIC12_379_198

description:
PA_UC_12_0
nup107_mo_tpm_polyA.tsv.gz

value: 12 hpf


title: old_surgery_48h_hemisphere_4

description:
Library name: FACS77_HM
FACS77_HM

value: brain

value: hemisphere

value: 20-22 months


title: dsDouble-kd_chromatin_associated_(>500bp_fraction) S16_B4L

description:
dsDouble-kd_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Double-kd S2 cells. Replicate 2. This sample together with S24_B4S, correspond to B4_merged_chromatin_fractions column in each processed data file

value: dsDouble knockdown (Rrp6+Dis3)


title: old_ctrl_48h_hippocampus_3

description:
Library name: FACS76_HP
FACS76_HP

value: hippocampus

value: control


title: rtgill.dmso.3.E03

description:
Library name: rtgill.dmso.3.E03
Cell lysate
dmso.counts2.txt
dmso.lib22_S1.E03.expression.values

source_name: RTgill-W1 ctrl rep 15

value: ctrl

value: Rainbow trout gill


title: rtgill.dmso.3.D03

description:
Library name: rtgill.dmso.3.D03
Cell lysate
dmso.counts2.txt
dmso.lib22_S1.D03.expression.values

source_name: RTgill-W1 ctrl rep 14


title: dsDis3_chromatin_associated_(>500bp_fraction) S15_B3L

description:
dsDis3_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Dis3-kd S2 cells. Replicate 2. This sample together with S23_B3S, correspond to B3_merged_chromatin_fractions column in each processed data file

value: dsDis3 knockdown


title: Sample_UIC11_332_245

description:
PA_UC_11_0
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 11 hpf

value: UC


title: young_ctrl_48h_hippocampus_1

description:
Library name: FACS78_HP
FACS78_HP

value: microglia

value: WT

value: 3-5 months

value: 48 hours


title: Sample_UIC10_5_356_221

description:
PA_UC_10_5
nup107_mo_tpm_polyA.tsv.gz

value: PolyA+ RNA


title: young_surgery_48h_hippocampus_1

description:
Library name: FACS75_HP
FACS75_HP

value: brain

value: surgery


title: rtgill.dmso.3.C03

description:
Library name: rtgill.dmso.3.C03
Cell lysate
dmso.counts2.txt
dmso.lib22_S1.C03.expression.values

source_name: RTgill-W1 ctrl rep 13


title: Sample_UIC10_380_197

description:
PA_UC_10_0
nup107_mo_tpm_polyA.tsv.gz

value: 10 hpf


title: dsGFP_chromatin_associated_(>500bp_fraction) S13_B1L

description:
dsGFP_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in GFP-Control S2 cells. Replicate 2. This sample together with S21_B1S, correspond to B1_merged_chromatin_fractions column in each processed data file

value: dsGFP knockdown (control)


title: rtgill.dmso.3.B03

description:
Library name: rtgill.dmso.3.B03
Cell lysate
dmso.counts2.txt
dmso.lib22_S1.B03.expression.values

source_name: RTgill-W1 ctrl rep 12


title: young_surgery_48h_hemisphere_1

description:
Library name: FACS75_HM
FACS75_HM

value: hemisphere


title: young_ctrl_48h_hemisphere_1

description:
Library name: FACS78_HM
FACS78_HM

value: control


title: dsDouble-kd_chromatin_associated_(0-500bp_fraction) S12_A4S

description:
dsDouble-kd_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Double-kd S2 cells. Replicate 1. This sample together with S8_A4L, correspond to A4_merged_chromatin_fractions column in each processed data file

value: dsDouble knockdown (Rrp6+Dis3)


title: rtgill.dmso.4.B10

description:
Library name: rtgill.dmso.4.B10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.B10.expression.values

source_name: RTgill-W1 ctrl rep 17

value: ctrl

value: Rainbow trout gill


title: old_ctrl_6h_hippocampus_8

description:
Library name: FACS72_HP
FACS72_HP

value: hippocampus

value: 20-22 months

value: 6 hours


title: rtgill.dmso.3.A03

description:
Library name: rtgill.dmso.3.A03
Cell lysate
dmso.counts2.txt
dmso.lib22_S1.A03.expression.values

source_name: RTgill-W1 ctrl rep 11


title: Sample_MO9_5_297_280

description:
PA_MO_9_5
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 9.5 hpf

value: MO


title: rtgill.dmso.4.A10

description:
Library name: rtgill.dmso.4.A10
Cell lysate
dmso.counts.txt
dmso.13_DMSO_col10_S1.A10.expression.values

source_name: RTgill-W1 ctrl rep 16


title: dsDis3_chromatin_associated_(0-500bp_fraction) S11_A3S

description:
dsDis3_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Dis3-kd S2 cells. Replicate 1. This sample together with S7_A3L, correspond to A3_merged_chromatin_fractions column in each processed data file

value: dsDis3 knockdown


title: old_ctrl_6h_hemisphere_8

description:
Library name: FACS72_HM
FACS72_HM

value: microglia

value: WT


title: Sample_MO9_321_256

description:
PA_MO_9_0
nup107_mo_tpm_polyA.tsv.gz

source_name: Whole Embryo

value: 9 hpf

value: PolyA+ RNA


title: dsRrp6_chromatin_associated_(0-500bp_fraction) S10_A2S

description:
dsRrp6_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Rrp6-kd S2 cells. Replicate 1. This sample together with S6_A2L, correspond to A2_merged_chromatin_fractions column in each processed data file

value: dsRrp6 knockdown


title: Sample_UIC11_5_308_269

description:
PA_UC_11_5
nup107_mo_tpm_polyA.tsv.gz

value: UC


title: rtgill.dmso.2.E01

description:
Library name: rtgill.dmso.2.E01
Cell lysate
dmso.counts2.txt
dmso.lib18_S1.E01.expression.values

source_name: RTgill-W1 ctrl rep 10


title: Sample_MO8_5_345_232

description:
PA_MO_8_5
nup107_mo_tpm_polyA.tsv.gz

value: 8.5 hpf


title: old_surgery_6h_hippocampus_7

description:
Library name: FACS71_HP
FACS71_HP

source_name: brain

value: brain

value: surgery


title: Sample_MO8_369_208

description:
PA_MO_8_0
nup107_mo_tpm_polyA.tsv.gz

value: 8 hpf


title: dsRrp6_chromatin_associated_(>500bp_fraction) S14_B2L

description:
dsRrp6_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Rrp6-kd S2 cells. Replicate 2. This sample together with S22_B2S, correspond to B2_merged_chromatin_fractions column in each processed data file


title: old_ctrl_48h_hemisphere_3

description:
Library name: FACS76_HM
FACS76_HM

value: hemisphere

value: control

value: 48 hours


title: Sample_MO7_5_298_279

description:
PA_MO_7_5
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 7.5 hpf


title: old_surgery_6h_hemisphere_7

description:
Library name: FACS71_HM
FACS71_HM

value: 20-22 months

value: 6 hours


title: dsDouble-kd_chromatin_associated_(>500bp_fraction) S8_A4L

description:
dsDouble-kd_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Double-kd S2 cells. Replicate 1. This sample together with S12_A4S, correspond to A4_merged_chromatin_fractions column in each processed data file

value: dsDouble knockdown (Rrp6+Dis3)


title: rtgill.dmso.2.D01

description:
Library name: rtgill.dmso.2.D01
Cell lysate
dmso.counts2.txt
dmso.lib18_S1.D01.expression.values

source_name: RTgill-W1 ctrl rep 9

value: ctrl

value: Rainbow trout gill


title: old_ctrl_6h_hippocampus_7

description:
Library name: FACS64_HP
FACS64_HP

value: hippocampus

value: microglia

value: WT


title: Sample_MO7_322_255

description:
PA_MO_7_0
nup107_mo_tpm_polyA.tsv.gz

value: 7 hpf

value: MO

value: PolyA+ RNA


title: rtgill.dmso.2.B01

description:
Library name: rtgill.dmso.2.B01
Cell lysate
dmso.counts2.txt
dmso.lib18_S1.B01.expression.values

source_name: RTgill-W1 ctrl rep 7


title: rtgill.dmso.2.A01

description:
Library name: rtgill.dmso.2.A01
Cell lysate
dmso.counts2.txt
dmso.lib18_S1.A01.expression.values

source_name: RTgill-W1 ctrl rep 6


title: dsGFP_chromatin_associated_(0-500bp_fraction) S9_A1S

description:
dsGFP_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in GFP-Control S2 cells. Replicate 1. This sample together with S5_A1L, correspond to A1_merged_chromatin_fractions column in each processed data file

source_name: S2 cell line

value: dsGFP knockdown (control)


title: old_ctrl_6h_hemisphere_7

description:
Library name: FACS64_HM
FACS64_HM

value: brain

value: hemisphere


title: dsDis3_chromatin_associated_(>500bp_fraction) S7_A3L

description:
dsDis3_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Dis3-kd S2 cells. Replicate 1. This sample together with S11_A3S, correspond to A3_merged_chromatin_fractions column in each processed data file

value: dsDis3 knockdown


title: Sample_MO6_5_346_231

description:
PA_MO_6_5
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 6.5 hpf


title: dsRrp6_chromatin_associated_(>500bp_fraction) S6_A2L

description:
dsRrp6_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in Rrp6-kd S2 cells. Replicate 1. This sample together with S10_A2S, correspond to A2_merged_chromatin_fractions column in each processed data file

value: dsRrp6 knockdown


title: rtgill.dmso.1.D02

description:
Library name: rtgill.dmso.1.D02
Cell lysate
dmso.counts2.txt
dmso.lib14_S1.D02.expression.values

source_name: RTgill-W1 ctrl rep 4


title: dsGFP_chromatin_associated_(>500bp_fraction) S5_A1L

description:
dsGFP_chromatin_associated_(>500bp_fraction)
chromatin-associated RNA (>500bp fraction)
RNA extracted from the > 500bp chromatin fraction in GFP-Control S2 cells. Replicate 1. This sample together with S9_A1S, correspond to A1_merged_chromatin_fractions column in each processed data file


title: dsDouble-kd_total_RNA S4_T4

description:
dsDouble-kd_total_RNA
total RNA
Total RNA extracted from Double-kd S2 cells


title: Sample_MO6_370_207

description:
PA_MO_6_0
nup107_mo_tpm_polyA.tsv.gz

value: 6 hpf


title: old_surgery_6h_hemisphere_6

description:
Library name: FACS63_HM
FACS63_HM

value: 20-22 months

value: surgery

value: 6 hours


title: Sample_MO5_5_299_278

description:
PA_MO_5_5
nup107_mo_tpm_polyA.tsv.gz

value: 5.5 hpf


title: rtgill.dmso.1.C02

description:
Library name: rtgill.dmso.1.C02
Cell lysate
dmso.counts2.txt
dmso.lib14_S1.C02.expression.values

source_name: RTgill-W1 ctrl rep 3

value: ctrl

value: Rainbow trout gill


title: rtgill.dmso.1.E02

description:
Library name: rtgill.dmso.1.E02
Cell lysate
dmso.counts2.txt
dmso.lib14_S1.E02.expression.values

source_name: RTgill-W1 ctrl rep 5


title: old_surgery_6h_hippocampus_6

description:
Library name: FACS63_HP
FACS63_HP

value: hippocampus

value: microglia

value: WT


title: Sample_MO5_323_254

description:
PA_MO_5_0
nup107_mo_tpm_polyA.tsv.gz

value: 5 hpf

value: MO

value: PolyA+ RNA


title: rtgill.dmso.2.C01

description:
Library name: rtgill.dmso.2.C01
Cell lysate
dmso.counts2.txt
dmso.lib18_S1.C01.expression.values

source_name: RTgill-W1 ctrl rep 8


title: dsDis3_total_RNA S3_T3

description:
dsDis3_total_RNA
total RNA
Total RNA extracted from Dis3-kd S2 cells

value: dsDis3 knockdown


title: rtgill.dmso.1.B02

description:
Library name: rtgill.dmso.1.B02
Cell lysate
dmso.counts2.txt
dmso.lib14_S1.B02.expression.values

source_name: RTgill-W1 ctrl rep 2


title: old_ctrl_6h_hippocampus_6

description:
Library name: FACS60_HP
FACS60_HP

value: brain

value: control


title: old_ctrl_6h_hemisphere_6

description:
Library name: FACS60_HM
FACS60_HM

value: hemisphere


title: rtgill.dmso.1.A02

description:
Library name: rtgill.dmso.1.A02
Cell lysate
dmso.counts2.txt
dmso.lib14_S1.A02.expression.values

source_name: RTgill-W1 ctrl rep 1


title: dsRrp6_total_RNA S2_T2

description:
dsRrp6_total_RNA
total RNA
Total RNA extracted from Rrp6-kd S2 cells

value: dsRrp6 knockdown


title: dsGFP_total_RNA S1_T1

description:
dsGFP_total_RNA
total RNA
Total RNA extracted from GFP-Control S2 cells

value: dsGFP knockdown (control)


title: Sample_MO4_371_206

description:
PA_MO_4_0
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 4 hpf


title: Sample_MO4_5_347_230

description:
PA_MO_4_5
nup107_mo_tpm_polyA.tsv.gz

value: 4.5 hpf


title: old_surgery_6h_hemisphere_5

description:
Library name: FACS59_HM
FACS59_HM

value: 20-22 months

value: surgery

value: 6 hours


title: old_surgery_6h_hippocampus_5

description:
Library name: FACS59_HP
FACS59_HP

value: hippocampus

value: microglia


title: rtgill.mbz.3.H12

description:
Library name: rtgill.mbz.3.H12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.H12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 1

value: Rainbow trout gill


title: rtgill.mbz.3.F12

description:
Library name: rtgill.mbz.3.F12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.F12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 3


title: old_surgery_6h_hippocampus_4

description:
Library name: FACS55_HP
FACS55_HP

value: WT


title: rtgill.mbz.3.E12

description:
Library name: rtgill.mbz.3.E12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.E12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 4


title: Sample_MO2_5_348_229

description:
PA_MO_2_5
nup107_mo_tpm_polyA.tsv.gz

value: 2.5 hpf

value: MO

value: PolyA+ RNA


title: old_ctrl_6h_hippocampus_5

description:
Library name: FACS56_HP
FACS56_HP

value: brain

value: control


title: Sample_MO3_324_253

description:
PA_MO_3_0
nup107_mo_tpm_polyA.tsv.gz

value: 3 hpf


title: Sample_MO2_372_205

description:
PA_MO_2_0
nup107_mo_tpm_polyA.tsv.gz

value: 2 hpf


title: old_ctrl_6h_hemisphere_5

description:
Library name: FACS56_HM
FACS56_HM

value: hemisphere


title: old_surgery_6h_hemisphere_4

description:
Library name: FACS55_HM
FACS55_HM


title: rtgill.mbz.3.D12

description:
Library name: rtgill.mbz.3.D12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.D12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 5


title: young_ctrl_6h_hemisphere_4

description:
Library name: FACS54_HM
FACS54_HM

value: 3-5 months


title: Sample_MO3_5_300_277

description:
PA_MO_3_5
nup107_mo_tpm_polyA.tsv.gz

source_name: Whole Embryo

value: Whole Embryo

value: 3.5 hpf


title: Sample_MO12_367_210

description:
PA_MO_12_0
nup107_mo_tpm_polyA.tsv.gz

value: 12 hpf


title: young_ctrl_6h_hippocampus_4

description:
Library name: FACS54_HP
FACS54_HP

value: 6 hours


title: Sample_MO11_5_296_281

description:
PA_MO_11_5
nup107_mo_tpm_polyA.tsv.gz


title: rtgill.mbz.2.H12

description:
Library name: rtgill.mbz.2.H12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.H12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 1


title: young_surgery_6h_hemisphere_4

description:
Library name: FACS53_HM
FACS53_HM

source_name: brain

value: surgery


title: rtgill.mbz.3.B12

description:
Library name: rtgill.mbz.3.B12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.B12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 7


title: sham group 4

type: RNA

city: Haerbin

first: Yongliang

last: Hua

state: Heilongjiang

address: Department of Pediatric Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Harbin, Heilongjiang, China

country: China

institute: 哈医大一院

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: liver

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

tag: sample group

value: sham group

value: liver

tag: molecule subtype

value: lncRNA and mRNA


title: Sample_MO11_320_257

description:
PA_MO_11_0
nup107_mo_tpm_polyA.tsv.gz

value: 11 hpf


title: sham group 5


title: rtgill.mbz.3.A12

description:
Library name: rtgill.mbz.3.A12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.A12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 8

value: Rainbow trout gill


title: rtgill.mbz.3.G12

description:
Library name: rtgill.mbz.3.G12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.G12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 2


title: sham group 2


title: rtgill.mbz.3.C12

description:
Library name: rtgill.mbz.3.C12
Cell lysate
mbz.counts.txt
mbz.lib25_S1.C12.expression.values

source_name: RTgill-W1 mbz rep 3 conc 6


title: old_ctrl_6h_hemisphere_4

description:
Library name: FACS52_HM
FACS52_HM

value: microglia

value: WT

value: 20-22 months


title: Sample_MO10_5_344_233

description:
PA_MO_10_5
nup107_mo_tpm_polyA.tsv.gz

value: MO

value: PolyA+ RNA


title: young_surgery_6h_hippocampus_4

description:
Library name: FACS53_HP
FACS53_HP

value: brain

value: hippocampus


title: Ischaemic preconditioning was applied to the ischaemia-reperfusion group 5


title: Ischaemic preconditioning was applied to the ischaemia-reperfusion group 3


title: sham group 3


title: rtgill.mbz.2.G12

description:
Library name: rtgill.mbz.2.G12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.G12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 2


title: Ischaemic preconditioning was applied to the ischaemia-reperfusion group 4


title: Ischaemic preconditioning was applied to the ischaemia-reperfusion group 2


title: rtgill.mbz.2.E12

description:
Library name: rtgill.mbz.2.E12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.E12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 4


title: 44 right end

city: Leuven

first: Johan

last: Van Weyenbergh

address: Herestraat 49

department: DMIT

country: Belgium

institute: KU Leuven

data_processing: Data were normalized for background (negative control probes), internal positive control probes and housekeeping genes using nSolver software version 4.0 (NanoString Technologies, US). Differentially expressed genes and predefined biological pathway scores were determined using nSolver, with correction for multiple testing by the Benjamini-Hochberg method at a 5%  false discovery rate for multiple comparisons cut-off. Comparison of baseline RNA levels for lung side, mechanical ventilation time, donation type and cold ischemia time was done according to the negative binomial distribution with generalized linear models.

organism: Homo sapiens

source_name: lung biopsy

label_protocol: We did nCounter (NanoString Technologies, US) digital gene expression analysis with the Immunology V2 panel targeting 579 immune system-associated genes. The workflow was carried out as established before in critical COVID-191, fatal COVID-19 nursing home outbreaks2, and respiratory infections at the emergency department3. In short, transcripts -including 15 housekeeping genes - were quantified by hybridization with specific fluorescent barcodes linked to a 50 bp reporter probe and an adjacent 50 bp capture probe.

extract_protocol: Lung tissue biopsy pieces preserved at -80°C were homogenized in Total RNA Lysis Solution (Bio-Rad, Cat#7326820, US) with a 3mm tungsten carbide bead (Qiagen, Cat#69997, Netherlands) using the TissueLyser II (Qiagen, Netherlands). The homogenate underwent RNA extraction with TRIzol (Invitrogen, Cat#15596026, US) and RNA purification with the Aurum Total RNA mini Kit (Bio-Rad, Cat#7326820, US). RNA quality was verified using the NanoPhotometer NP80 Touch (Implen, Germany).

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 44 Right

tag: donor age (y)

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

value: yes

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: old_surgery_6h_hippocampus_3

description:
Library name: FACS51_HP
FACS51_HP

tag: tissue

tag: region

tag: cell type

tag: genotype

tag: age

tag: treatment

value: surgery

value: 6 hours


title: sham group 1

tag: strain

tag: sample group

value: sham group

value: liver

tag: molecule subtype

value: lncRNA and mRNA


title: old_surgery_6h_hemisphere_3

description:
Library name: FACS51_HM
FACS51_HM

value: hemisphere

value: microglia

value: WT

value: 20-22 months

tag: timepoint


title: old_ctrl_6h_hippocampus_4

description:
Library name: FACS52_HP
FACS52_HP

value: brain

value: hippocampus

value: control


title: rtgill.mbz.2.D12

description:
Library name: rtgill.mbz.2.D12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.D12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 5

tag: cell line

value: Rainbow trout gill


title: 43 right end

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 43 Right

tag: donor age (y)

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

tag: donor mechanical ventilation (hours)


title: 44 left end

tag: tissue

value: left lung

value: 44 Left

value: yes

value: intracranial bleeding

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: rtgill.mbz.2.C12

description:
Library name: rtgill.mbz.2.C12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.C12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 6

tag: cell type

tag: treatment


title: young_ctrl_6h_hippocampus_3

description:
Library name: FACS50_HP
FACS50_HP

tag: region

value: microglia

tag: genotype

tag: age

value: 3-5 months

tag: timepoint

value: 6 hours


title: rtgill.mbz.2.F12

description:
Library name: rtgill.mbz.2.F12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.F12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 3

tag: cell line


title: Sample_MO10_368_209

description:
PA_MO_10_0
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

tag: time

value: 10 hpf

value: MO

tag: fraction

value: PolyA+ RNA


title: rtgill.mbz.2.B12

description:
Library name: rtgill.mbz.2.B12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.B12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 7

value: Rainbow trout gill


title: young_ctrl_6h_hemisphere_3

description:
Library name: FACS50_HM
FACS50_HM

value: brain

value: hemisphere

value: WT

value: control


title: 38 right end

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 38 Right

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

tag: donor smoking history

tag: donor cause of death


title: rtgill.mbz.2.A12

description:
Library name: rtgill.mbz.2.A12
Cell lysate
mbz.counts.txt
mbz.lib21_S1.A12.expression.values

source_name: RTgill-W1 mbz rep 2 conc 8


title: mTELSCs-derived TOs at day 8, H3K27me3, CUT&Tag

city: Beijing

first: Chunhui

last: Wang

state: Beijing

address: 5 Summer Palace Road, Haidian District, Beijing

department: School of Life Sciences

institute: Peking University

library_source: genomic

data_processing:
ATAC-seq data were firstly trimmed by Trimmomatic software. Bowtie2 was used to align the clean reads to mm10 reference genome “-X 1000 –mm -local”. Picard was used to remove duplicates and we only remained the high-quality reads. Then, after calling the peaks by MACS2, we used the merge and multicov commands in bedtools to extract the count of the peaks in all the samples and bdgdiff function in MACS2 was used to normalize the count matrix and calculate the differential peaks with parameters “-g 100 -l 50 -C 2”.
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the mouse genome (mm10, UCSC). Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate counts per million (CPM).
ATAC-seq data were firstly trimmed by Trimmomatic software (version 0.39). Bowtie2 (version 2.4.4) was used to align the clean reads to mm10 reference genome “-X 1000 –mm -local”. Picard was used to remove duplicates and we only remained the high-quality reads. Then, after calling the peaks by MACS2, we used the merge and multicov commands in bedtools to extract the count of the peaks in all the samples and bdgdiff function in MACS2 was used to normalize the count matrix and calculate the differential peaks with parameters “-g 100 -l 50 -C 2”.
ChIP-seq data were firstly trimmed by Trimmomatic software. Bowtie2 (version 2.4.4) was used to align the clean reads to mm10 reference genome with parameters “--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”. We used MACS2 (version 2.1.4) to call peaks and differential peaks were detected by macs2 bdgdiff command.
WGBS reads were trimmed by Trimmomatic software with default parameters. The cleaned data were aligned to the mm10 reference with Bismark. Duplicate reads were removed by deduplicate_bismark command and the methylation calls were extracted from unique alignment using bismark_methylation_extractor with ‘‘–bedGraph’’ parameter. Bismark2 summary command was used to calculate the genome CpG methylation level.
Single-cell transcriptome data were first applied to Cell Ranger (version 3.6.0) against mm10 genome reference to generate count matrix, which of the column was cell name and the row was gene. The downstream analysis was performed in Seurat (version 3.1.0) R package.
Assembly: mm10
Supplementary files format and content: Big wig files for ATAC-seq and CUT&Tag samples, comma-separated value files include CPM values for RNA-seq samples, bedGraph files for Bisulfite-seq samples
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
DNA and RNA were extracted from mESCs, mTBLCs, mTELCs, mTELSCs, mTSCs and TOs for highthrough sequencing, including ATAC-seq, CHIP-seq, WGBS and scRNA-seq. TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions. 100 ng genomic DNA was used as input and was bisulfite-converted using the EpiArt DNA Methylation Bisulfite Kit (Vazyme). A total of 50, 000 viable cells were extracted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) for ATAC-seq.  A total of 50, 000 viable cells were extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme).
RNA-seq libraries were conducted using VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) .To assess chromatin accessibility of TELCs and TELSCs, ATAC-seq were conducted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s instructions. Bisulfite-converted DNA was used to construct the library with the EpiArtTM DNA Methylation Library Kit V3 (Vazyme) according to the manufacturer’s instructions. A total of 50, 000 viable cells were used for CUT&Tag experiments with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s instructions.

value: mTELSCs-derived TOs at day 8

tag: antibody


title: young_surgery_6h_hippocampus_3

description:
Library name: FACS49_HP
FACS49_HP

tag: tissue

value: hippocampus

value: microglia

value: surgery


title: 38 left end

value: left lung

value: 38 Left

value: yes

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: rtgill.mbz.1.H12

description:
Library name: rtgill.mbz.1.H12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.H12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 1

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: ischaemia-reperfusion group 2 (subjected to partial (70%) liver ischaemia-reperfusion)

tag: strain

tag: sample group

value: ischaemia-reperfusion group

value: liver

tag: molecule subtype

value: lncRNA and mRNA


title: ischaemia-reperfusion group 3(subjected to partial (70%) liver ischaemia-reperfusion)


title: mTELSCs-derived TOs at day 4, H3K27me3, CUT&Tag

value: mTELSCs-derived TOs at day 4


title: ischaemia-reperfusion group 1(subjected to partial (70%) liver ischaemia-reperfusion)


title: young_surgery_6h_hemisphere_3

description:
Library name: FACS49_HM
FACS49_HM

value: brain

tag: region

value: hemisphere

tag: genotype

value: WT

tag: age

value: 3-5 months

tag: timepoint

value: 6 hours


title: rtgill.mbz.1.G12

description:
Library name: rtgill.mbz.1.G12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.G12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 2


title: old_ctrl_6h_hippocampus_3

description:
Library name: FACS48_HP
FACS48_HP

tag: tissue

value: hippocampus

value: microglia

value: 20-22 months

value: control


title: 37 left end

value: left lung

value: end donor lung implantation

tag: biopsy set

value: 37 Left

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

tag: donor mechanical ventilation (hours)


title: rtgill.mbz.1.F12

description:
Library name: rtgill.mbz.1.F12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.F12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 3

tag: cell line

tag: cell type

value: Rainbow trout gill


title: old_ctrl_6h_hemisphere_3

description:
Library name: FACS48_HM
FACS48_HM

source_name: brain

tag: treatment


title: mTELSCs, H3K27me3, CUT&Tag

value: mTELSC cultured in TX medium

tag: antibody


title: old_surgery_6h_hippocampus_2

description:
Library name: FACS47_HP
FACS47_HP

value: surgery


title: 43 left end

value: 43 Left

value: male

value: intracranial bleeding

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: rtgill.mbz.1.E12

description:
Library name: rtgill.mbz.1.E12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.E12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 4


title: 36 right end

tag: tissue

value: right lung

tag: timepoint

value: 36 Right


title: 37 right end

tag: biopsy set

value: 37 Right

tag: donor age (y)


title: rtgill.mbz.1.D12

description:
Library name: rtgill.mbz.1.D12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.D12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 5


title: 36 left end

value: 36 Left

tag: donor sex

tag: donor bmi


title: 34 right end

value: 34 Right

tag: donor smoking history

tag: donor cause of death

value: head trauma


title: old_surgery_6h_hemisphere_2

description:
Library name: FACS47_HM
FACS47_HM

value: brain

tag: region

value: hemisphere

value: microglia

tag: genotype

value: WT

tag: age

value: 20-22 months

value: 6 hours


title: FACS-purified mTELCs using CD40, H3K27me3, CUT&Tag

tag: cell line

tag: cell type

value: mTELCs induced from mTBLCs

tag: antibody


title: rtgill.mbz.1.C12

description:
Library name: rtgill.mbz.1.C12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.C12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 6

value: Rainbow trout gill

tag: treatment


title: mTELSCs-derived TOs at day 8, H3K4me3, CUT&Tag

value: mTELSCs-derived TOs at day 8

value: H3K4me3 (Abcam, #ab6002)


title: young_ctrl_6h_hippocampus_2

description:
Library name: FACS46_HP
FACS46_HP

value: hippocampus

value: 3-5 months

value: control


title: young_ctrl_6h_hemisphere_2

description:
Library name: FACS46_HM
FACS46_HM


title: mTELSCs-derived TOs at day 4, H3K4me3, CUT&Tag

value: mTELSCs-derived TOs at day 4


title: ischaemia-reperfusion group 4(subjected to partial (70%) liver ischaemia-reperfusion)

source_name: liver

tag: strain

tag: sample group

value: ischaemia-reperfusion group

value: liver

tag: molecule subtype

value: lncRNA and mRNA


title: mTSCs, H3K27me3, CUT&Tag

source_name: ICR

value: ICR

value: mTSCs cultured in TX medium


title: rtgill.mbz.1.B12

description:
Library name: rtgill.mbz.1.B12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.B12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 7


title: 33 right end

tag: tissue

value: right lung

tag: timepoint

value: end donor lung implantation

value: 33 Right

value: male

value: no

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: mTSCs, H3K4me3, CUT&Tag

value: H3K4me3 (Abcam, #ab6002)


title: 33 left end

value: left lung

tag: biopsy set

value: 33 Left

tag: donor age (y)

tag: donor sex

tag: donor bmi

tag: donor smoking history

tag: donor cause of death


title: rtgill.mbz.1.A12

description:
Library name: rtgill.mbz.1.A12
Cell lysate
mbz.counts.txt
mbz.lib17_S1.A12.expression.values

source_name: RTgill-W1 mbz rep 1 conc 8

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: young_surgery_6h_hippocampus_2

description:
Library name: FACS45_HP
FACS45_HP

tag: tissue

value: brain

tag: region

value: hippocampus

value: microglia

tag: genotype

value: WT

tag: age

value: 3-5 months

value: surgery

value: 6 hours


title: rtgill.dip.3.H11

description:
Library name: rtgill.dip.3.H11
Cell lysate
dip.counts.txt
dip.lib25_S1.H11.expression.values

source_name: RTgill-W1 dip rep 3 conc 1


title: mTELSCs, H3K4me3, CUT&Tag

value: mTELSC cultured in TX medium

tag: antibody


title: young_surgery_6h_hemisphere_2

description:
Library name: FACS45_HM
FACS45_HM

value: hemisphere

tag: timepoint


title: 31 right end

source_name: lung biopsy

value: right lung

value: end donor lung implantation

value: 31 RIght

value: female

value: yes

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: FACS-purified mTELCs using CD40, H3K4me3, CUT&Tag

value: mTELCs induced from mTBLCs

value: H3K4me3 (Abcam, #ab6002)


title: 31 left end

value: left lung

tag: biopsy set

value: 31 Left

tag: donor age (y)

tag: donor sex

tag: donor bmi

tag: cold ischemia (min)


title: rtgill.dip.3.G11

description:
Library name: rtgill.dip.3.G11
Cell lysate
dip.counts.txt
dip.lib25_S1.G11.expression.values

source_name: RTgill-W1 dip rep 3 conc 2

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: old_ctrl_6h_hippocampus_2

description:
Library name: FACS44_HP
FACS44_HP

tag: tissue

value: brain

tag: region

value: hippocampus

value: microglia

tag: genotype

value: WT

value: 20-22 months

value: control


title: M16DKw3_ter119_R2

first: Hsiang-Ying

last: Lee

address: No.5 Yiheyuan Road

data_processing:
After checking data quality using FastQC (version 0.11.7), the paired-end reads were mapped to the GRCm39 human reference genome by Hisat2 (version 2.1.0).
Read counts were estimated with HTSeq (version 0.12.4).
The reads counts were normalized to TPM (transcription per million).
The DESeq2 package was used to identify differentially expressed genes.
Motif enrichment was performed using Homer software54 with “-start -400 -end 100” parameters.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
RNA was  harvested using TRIzol. For RNA-seq, the quality was evaluated using an Agilent 2100 Bioanalyzer. 1 μg of total RNA was used to prepare RNA-seq libraries.
RNA libraries for RNA-seq were prepared using Illumina mRNA-seq Library Prep Kit following manufacturer’s protocols

value: bone marrow

tag: time

value: 3 weeks

value: Ter119+ cell

value: Med16 KO

tag: developmental stage

value: erythroid stage


title: 30 right end

value: right lung

tag: timepoint

value: end donor lung implantation

value: 30 Right

value: female

tag: donor smoking history

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DCD


title: rtgill.dip.3.F11

description:
Library name: rtgill.dip.3.F11
Cell lysate
dip.counts.txt
dip.lib25_S1.F11.expression.values

source_name: RTgill-W1 dip rep 3 conc 3

value: Rainbow trout gill


title: old_ctrl_6h_hemisphere_2

description:
Library name: FACS44_HM
FACS44_HM

value: brain

value: hemisphere

value: microglia

tag: age

value: 6 hours


title: 30 left end

value: left lung

tag: biopsy set

value: 30 Left

tag: donor age (y)

tag: donor sex

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: M16DKw3_ter119_R1

tag: tissue

value: bone marrow

value: 3 weeks

tag: cell type

value: Ter119+ cell


title: rtgill.dip.3.E11

description:
Library name: rtgill.dip.3.E11
Cell lysate
dip.counts.txt
dip.lib25_S1.E11.expression.values

source_name: RTgill-W1 dip rep 3 conc 4

tag: cell line

tag: treatment


title: old_surgery_6h_hippocampus_1

description:
Library name: FACS43_HP
FACS43_HP

tag: region

value: hippocampus

tag: genotype

value: WT

value: 20-22 months

value: surgery


title: M16flflw3_ter119_R2

tag: time

value: Med16 fl/fl

tag: developmental stage

value: erythroid stage


title: ischaemia-reperfusion group 5(subjected to partial (70%) liver ischaemia-reperfusion)

tag: strain

tag: sample group

value: ischaemia-reperfusion group

value: liver

tag: molecule subtype

value: lncRNA and mRNA


title: old_surgery_6h_hemisphere_1

description:
Library name: FACS43_HM
FACS43_HM

value: brain

value: hemisphere

tag: age

tag: timepoint


title: 29 right end

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 29 RIght

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DBD

tag: cold ischemia (min)


title: rtgill.dip.3.D11

description:
Library name: rtgill.dip.3.D11
Cell lysate
dip.counts.txt
dip.lib25_S1.D11.expression.values

source_name: RTgill-W1 dip rep 3 conc 5

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: M16flflw3_ter119_R1

tag: tissue

value: bone marrow

tag: time

value: 3 weeks

value: Ter119+ cell

tag: genotype

tag: developmental stage


title: young_ctrl_6h_hippocampus_1

description:
Library name: FACS42_HP
FACS42_HP

tag: region

value: hippocampus

value: microglia

value: WT

tag: age

value: 3-5 months

value: control

tag: timepoint

value: 6 hours


title: rtgill.dip.3.C11

description:
Library name: rtgill.dip.3.C11
Cell lysate
dip.counts.txt
dip.lib25_S1.C11.expression.values

source_name: RTgill-W1 dip rep 3 conc 6


title: MED16_M16flfl

description: CUT&Tag

data_processing:
Raw ChIP-seq data were trimmed using trim_galore (version 0.4.4_dev) and the cleaned reads were mapped to the GRCm39 mouse genome using Bowtie2 (version 2.3.4.1).
Duplicated reads and low-quality reads (MAPQ < 30) were removed using the Picard tool (http:
The bigwig files were generated using bamCoverage and normalized using RPKM (Reads Per Kilobase per Million) in 10 bp bins.
The results were visualized using IGV software. MACS2 was used for peak calling with default parameters for all samples.
Peaks were annotated using the R package ChIPseeker, and co-localization analysis was performed using deeptools.
Assembly: GRCm39
Supplementary files format and content: bigWig

extract_protocol:
106 cells were collected for the assay. 27 µL 37% formaldehyde was added to each sample in a centrifuge tube, followed by incubation at 10 min at room temperature (RT). 110 µL 10X Glycine solution was added, followed by incubation for 5 min at RT and centrifugation at 4000 rpm for 5 min. The supernatant was removed and the cells were washed with 1 mL PBS. The cells were centrifuged at 4°C at 4000 rpm for 5 min and the supernatant was discarded. The cell pellet was resuspended with 100 µL 1X MDB (50 mM Tris‐HCl, pH 8.0, 2 mM CaCl2, 0.2 % Triton X‐100) and 1.5 µL 1X MNase, followed by incubation at 37°C for 5 min, after which 10 µL of 10X Stop buffer (110 mM Tris‐HCl pH 8.0, 55 mM EDTA) was added to stop the reaction. 110 µL 2X RIPA was added to the sample, and the sample was left on ice for 2 min. The sample was subjected to sonic shearing (20w for 2 min). The samples were spun for 15 mins in a microfuge at top speed at 4°C. The supernatant containing chromatin was moved to a fresh pre‐cooled tube (1.5 mL low bind), which was stored at -80°C. Protein A and Protein G beads (Sigma) were mixed (1:1), pre-washed and re-suspended with an equal volume of 1X RIPA. 100 µL of chromatin was pre-cleaned with 15 µL pre-washed beads for 1 h at 4°C, after which 1-2 µg antibody was added to each IP sample. The samples were incubated at 4°C overnight, 15 µL protein A+G beads were added per IP, and the samples were incubated 2‐3 h with rotation at 4°C. RIPA and LiCl wash buffers were prepared and supplemented with protease inhibitors (1:1000). All subsequent washes were performed with rotation at 4°C for 5 mins. The washes were performed as follows: 5 washes with 150 µL RIPA buffer + 1 wash with 150 µL LiCl wash buffer + 1 wash with 150 µL cold TE. The Elution/Digestion buffer for each sample contained 45 µL TE, 5 µL 5M NaCl, and 2.5 µL Proteinase K. Each bead pellet was resuspended in 50 µL Elution/Digestion buffer and incubated with shaking (1200 rpm) at 65°C for 4-6 h. Each sample was separated, the protein A+G beads were discarded, and DNA was recovered with 1.2X NGS beads (Vazyme).
A subsequent PCR step was used to add an additional index to the fragments. Two biological replicates per sample were sequenced using a HiSeq X-Ten (PE150, Illumina) by Novogene (Beijing).

tag: chip antibody

value: Med16 fl/fl

value: erythroid stage


title: 29 left end

value: left lung

value: end donor lung implantation

tag: biopsy set

value: 29 Left

tag: donor age (y)

tag: donor sex

tag: donor bmi

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: 28 right end

value: right lung

value: 28 Right

value: female

tag: donor smoking history

value: no

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: cold ischemia (min)


title: young_ctrl_6h_hemisphere_1

description:
Library name: FACS42_HM
FACS42_HM

tag: tissue

value: brain

value: hemisphere

tag: cell type

tag: genotype

tag: treatment


title: MED16_M16DK

description: CUT&Tag

value: bone marrow

tag: chip antibody

value: Ter119+ cell

value: Med16 KO

tag: developmental stage


title: 28 left end

tag: timepoint

tag: biopsy set

value: 28 Left

tag: donor age (y)

value: DBD


title: rtgill.dip.3.B11

description:
Library name: rtgill.dip.3.B11
Cell lysate
dip.counts.txt
dip.lib25_S1.B11.expression.values

source_name: RTgill-W1 dip rep 3 conc 7

tag: cell line

value: Rainbow trout gill


title: young_surgery_6h_hippocampus_1

description:
Library name: FACS41_HP
FACS41_HP

source_name: brain

tag: region

value: hippocampus

value: microglia

value: WT

tag: age

value: 3-5 months

value: surgery

value: 6 hours


title: rtgill.dip.2.H11

description:
Library name: rtgill.dip.2.H11
Cell lysate
dip.counts.txt
dip.lib21_S1.H11.expression.values

source_name: RTgill-W1 dip rep 2 conc 1


title: 27 right end

value: right lung

value: end donor lung implantation

value: 27 right

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

value: head trauma

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: SPT16_M16DK

description: CUT&Tag

tag: tissue

value: bone marrow

value: SPT16 (BioLegend, Cat.#607002)

tag: cell type

value: erythroid stage


title: SPT16_M16flfl

description: CUT&Tag

value: Ter119+ cell

tag: genotype

value: Med16 fl/fl


title: old_ctrl_6h_hippocampus_1

description:
Library name: FACS40_HP
FACS40_HP

value: brain

value: 20-22 months

tag: treatment

value: control


title: young_surgery_6h_hemisphere_1

description:
Library name: FACS41_HM
FACS41_HM

value: hemisphere

value: microglia

value: WT


title: 27 left end

value: left lung

value: 27 left

value: no

tag: donor cause of death

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DBD

tag: cold ischemia (min)


title: rtgill.dip.2.F11

description:
Library name: rtgill.dip.2.F11
Cell lysate
dip.counts.txt
dip.lib21_S1.F11.expression.values

source_name: RTgill-W1 dip rep 2 conc 3

tag: cell line

value: Rainbow trout gill


title: RUNX1_M16flfl

description: CUT&Tag

tag: chip antibody

value: RUNX1 (Abcam, Cat.#23980)

tag: developmental stage


title: old_ctrl_6h_hemisphere_1

description:
Library name: FACS40_HM
FACS40_HM

tag: region

tag: age

tag: timepoint

value: 6 hours


title: RUNX1_M16DK

description: CUT&Tag

value: bone marrow

value: Med16 KO


title: 26 right end

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 26 right

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

tag: donor smoking history

value: yes

value: intracranial bleeding

tag: donation type


title: rtgill.dip.2.G11

description:
Library name: rtgill.dip.2.G11
Cell lysate
dip.counts.txt
dip.lib21_S1.G11.expression.values

source_name: RTgill-W1 dip rep 2 conc 2

tag: cell type

tag: treatment


title: rtgill.dip.2.E11

description:
Library name: rtgill.dip.2.E11
Cell lysate
dip.counts.txt
dip.lib21_S1.E11.expression.values

source_name: RTgill-W1 dip rep 2 conc 4


title: rtgill.dip.3.A11

description:
Library name: rtgill.dip.3.A11
Cell lysate
dip.counts.txt
dip.lib25_S1.A11.expression.values

source_name: RTgill-W1 dip rep 3 conc 8


title: rtgill.dip.2.D11

description:
Library name: rtgill.dip.2.D11
Cell lysate
dip.counts.txt
dip.lib21_S1.D11.expression.values

source_name: RTgill-W1 dip rep 2 conc 5


title: old_surgery_48h_hemisphere_3

description:
Library name: FACS109_HM
FACS109_HM

tag: tissue

value: brain

value: hemisphere

value: microglia

tag: genotype

value: 20-22 months

value: surgery

value: 48 hours


title: old_surgery_48h_hippocampus_3

description:
Library name: FACS109_HP
FACS109_HP

value: hippocampus

value: WT


title: M16flfld3_ter119_R2

data_processing:
The adaptors were removed from the raw ATAC-seq paired data for Ter119+ cell  using trim_galore software with default parameters.
Trimmed cleaned reads were aligned to mouse reference genome GRCm39 using Bowtie2 (version 2.3.4.1) with default parameters and converted to bam files using samtools.
ATAC-seq peaks were identified using MACS2 with the following parameters: “-q 0.05 --nomodel --shift -100 --extsize 200”.
The signal enrichment plot around the TSS of all protein coding genes was generated using deeptools.
The example tracks were visualized using IGV software. The motifs of ATAC-seq peaks were enriched using Homer.
Assembly: GRCm39
Supplementary files format and content: bigWig

source_name: Ter119+ cell

extract_protocol:
~105 Ter119+ cell were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 8 mM MgCl2 and NP-40) on ice for 5 min to extract nuclei. The cells were centrifuged at 500 g for 5 min to remove the supernatant. The nuclei were incubated with the Tn5 transposome and corresponding buffer at 37°C for 30 min (Vazyme, Cat. # 11 TD501). The stop buffer was added to the reaction to terminate the tagmentation.  DNA Clean Beads were used to purify DNA.
A subsequent PCR step was used to add an additional index to the fragments. Two biological replicates per sample were sequenced using a HiSeq X-Ten (PE150, Illumina) by Novogene (Beijing).

value: Ter119+ cell

value: Med16 fl/fl

tag: time

value: Day 3


title: 25 right end

value: right lung

value: 25 right

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: M16DKd3_ter119_R2

tag: cell line

value: Med16 KO


title: rtgill.dip.2.C11

description:
Library name: rtgill.dip.2.C11
Cell lysate
dip.counts.txt
dip.lib21_S1.C11.expression.values

source_name: RTgill-W1 dip rep 2 conc 6

value: Rainbow trout gill


title: M16flfld3_ter119_R1


title: old_surgery_48h_hemisphere_2

description:
Library name: FACS107_HM
FACS107_HM

value: brain

tag: region

tag: age

tag: timepoint


title: rtgill.dip.2.B11

description:
Library name: rtgill.dip.2.B11
Cell lysate
dip.counts.txt
dip.lib21_S1.B11.expression.values

source_name: RTgill-W1 dip rep 2 conc 7


title: old_surgery_48h_hippocampus_2

description:
Library name: FACS107_HP
FACS107_HP


title: 25 left end

source_name: lung biopsy

value: left lung

value: end donor lung implantation

tag: biopsy set

value: 25 left

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

tag: donor smoking history

value: yes


title: rtgill.dip.2.A11

description:
Library name: rtgill.dip.2.A11
Cell lysate
dip.counts.txt
dip.lib21_S1.A11.expression.values

source_name: RTgill-W1 dip rep 2 conc 8

tag: cell type

tag: treatment


title: 22 right end

tag: tissue

value: 22 right

value: male

value: no

tag: donor cause of death

value: ischemic stroke

tag: donation type

value: DBD


title: M16DKd3_ter119_R1

value: Ter119+ cell

tag: genotype

tag: time

value: Day 3


title: old_ctrl_48h_hippocampus_2

description:
Library name: FACS106_HP
FACS106_HP

value: hippocampus

value: microglia

value: WT

value: 20-22 months

value: control

value: 48 hours


title: 22 left end

value: left lung

value: end donor lung implantation

value: 22 left

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: Colon, MPZH36

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

data_processing:
Data were filtered using the following specifications fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it if the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window, remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed, if the truncated read length is less than 50 bp, the entire read is removedRemove unmatched reads
Q30，Q20 explanation：
Q30 indicates that the sequencing error rate of the base is 0.1%.
Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: mm10
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

source_name: Model +PZH group, 91 days treated with PZH and AOM/DSS

extract_protocol:
The abdominal aorta were dissected and  stored in RNA later.Total RNA was extracted with  TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

treatment_protocol: Mice in Control and Model groups were  intragastrically with double distilled water, while mice in PZH and Model + PZH groups were intragastrically with 250 mg/kg/d of PZH for 91 days.  Then the colon tissues were used to identify differentially expressed genes among different groups.

tag: group

value: Model + PZH

value: colon

tag: disease state

value: AOM/DSS induced colitis-associated cancer (CAC) mouse model

tag: disease induction

value: AOM (12.5 mg/kg) was intraperitoneally injected into the mice at the first day of modeling. After 7 days, 2% DSS was given in free drinking water for 5 days and then changed to normal drinking water for 2 weeks. The modeling was completed after a total of four cycles.

value: PZH


title: 26 left end

tag: timepoint

tag: biopsy set

value: 26 left

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

value: yes

value: intracranial bleeding

value: DBD


title: rtgill.dip.1.H11

description:
Library name: rtgill.dip.1.H11
Cell lysate
dip.counts.txt
dip.lib17_S1.H11.expression.values

source_name: RTgill-W1 dip rep 1 conc 1

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: Colon, MPZH35

tag: tissue


title: 21 right end

value: right lung

value: 21 right

value: male

tag: donor smoking history

value: no

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donation type

value: DCD


title: 20 right end

value: end donor lung implantation

value: 20 right

tag: donor pao2/fio2 ratio

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: old_surgery_48h_hippocampus_1

description:
Library name: FACS105_HP
FACS105_HP

value: brain

tag: region

value: hippocampus

value: microglia

tag: genotype

value: WT

tag: age

value: 20-22 months

value: surgery

tag: timepoint

value: 48 hours


title: 23 left end

value: left lung

tag: biopsy set

value: 23 left

tag: donor age (y)

tag: donor sex

tag: donor bmi

value: yes

value: intracranial bleeding

value: DBD


title: old_surgery_48h_hemisphere_1

description:
Library name: FACS105_HM
FACS105_HM

tag: tissue

value: hemisphere

tag: cell type

tag: treatment


title: Colon, MPZH15

tag: group

value: Model + PZH

value: colon

tag: disease state

value: AOM/DSS induced colitis-associated cancer (CAC) mouse model

tag: disease induction

value: AOM (12.5 mg/kg) was intraperitoneally injected into the mice at the first day of modeling. After 7 days, 2% DSS was given in free drinking water for 5 days and then changed to normal drinking water for 2 weeks. The modeling was completed after a total of four cycles.

value: PZH


title: Colon, MPZH13


title: rtgill.dip.1.E11

description:
Library name: rtgill.dip.1.E11
Cell lysate
dip.counts.txt
dip.lib17_S1.E11.expression.values

source_name: RTgill-W1 dip rep 1 conc 4

tag: cell line

value: Rainbow trout gill


title: rtgill.dip.1.F11

description:
Library name: rtgill.dip.1.F11
Cell lysate
dip.counts.txt
dip.lib17_S1.F11.expression.values

source_name: RTgill-W1 dip rep 1 conc 3


title: old_ctrl_48h_hippocampus_1

description:
Library name: FACS102_HP
FACS102_HP

value: brain

value: hippocampus

value: microglia

value: control


title: 20 left end

value: end donor lung implantation

value: 20 left

value: male

tag: donor smoking history

value: no

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: Colon, MPZH2


title: 16 right end

value: right lung

tag: timepoint

tag: biopsy set

value: 16 right

tag: donor age (y)

value: female

value: yes

value: intracranial bleeding

tag: cold ischemia (min)


title: Colon, model52

source_name: Model group, 91 days treated with double distilled water and AOM/DSS

value: Model

tag: tissue

value: colon

value: AOM/DSS induced colitis-associated cancer (CAC) mouse model

value: AOM (12.5 mg/kg) was intraperitoneally injected into the mice at the first day of modeling. After 7 days, 2% DSS was given in free drinking water for 5 days and then changed to normal drinking water for 2 weeks. The modeling was completed after a total of four cycles.

value: double distilled water


title: old_ctrl_48h_hemisphere_1

description:
Library name: FACS102_HM
FACS102_HM

source_name: brain

value: brain

tag: region

value: hemisphere

tag: cell type

value: microglia

tag: genotype

value: WT

tag: age

value: 20-22 months

tag: treatment

value: control

value: 48 hours


title: rtgill.dip.1.D11

description:
Library name: rtgill.dip.1.D11
Cell lysate
dip.counts.txt
dip.lib17_S1.D11.expression.values

source_name: RTgill-W1 dip rep 1 conc 5

tag: cell line

value: Rainbow trout gill


title: 16 left end

value: left lung

value: end donor lung implantation

value: 16 left

tag: donor sex

tag: donor bmi

tag: donor smoking history

tag: donor cause of death

value: DCD


title: Saline Adherent neural stem cells, cell line 29, culture differentitation 7days

city: London

first: Sandra

middle: Maria

last: Martin-Guerrero

address: Charterhouse Square Campus

department: Cancer Genomics and Computational Biology

institute: Barts Cancer Institute, Queen Mary University of London

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "29D"

data_processing:
miARma-Seq pipeline (DOI: 10.1038/srep25749) (DOI: 10.1016/j.ymeth.2018.09.002)
raw data were evaluated using FastQC software to analyze the quality of the reads.
the number of reads per sample were homogenized using Seqtk software (https://github.com/lh3/seqtk)
miARma-Seq alignment using STAR (DOI: 10.1093/bioinformatics/bts635)
featureCounts software was used to assign sequence reads to genes by using reference gene annotation that was obtained from Gencode from the same assembly and genome build (DOI: 10.1093/bioinformatics/btt656). Expression analysis was carried out by edgeR package (DOI: 10.1007/978-1-4939-0512-6_3)
Low expressed genes were removed, and remaining genes were normalized by the trimmed mean of M-values (TMM) method. The normalized gene expression (TMM) was log2 scaled. (DOI: 10.1186/gb-2010-11-3-r25)
Assembly: Mus musculus Gencode version M31 genome-build: mmGRCm39
Supplementary files format and content: tab-delimited text file (.txt) containing Log2TMM for each sample

source_name: fetus dorsal forebrain

growth_protocol: Neural Stem cells (NSCs) were plated in 100 mm culture dishes and washed with ice-cold PBS. Cellular pellets from either non-differentiated NSCs or cells differentiated for 7 days were collected and processed for transcriptomics.

extract_protocol:
Both, library preparation and Illumina sequencing were carried out at the IPBLN Genomics Facility (CSIC, Granada, Spain). Total RNA integrity was verified by Bioanalyzer RNA 6000 Nano chip electrophoresis (Agilent Technologies).  Every RNA sample showed a RIN value above 8.5.
RNA-seq libraries were prepared using Illumina stranded mRNA Prep Ligation kit (Illumina®) from 200 ng of input total RNA. Quality and size distribution of PCR-enriched libraries were validated through Bioanalyzer High Sensitivity DNA assay and concentration was measured on the Qubit® fluorometer (Thermo). Final libraries were pooled, in an equimolecular manner, and then diluted and denatured as recommended by Illumina NextSeq® 500 library preparation guide.

value: fetus dorsal forebrain

tag: developmental stage

value: Differentiated neuron/glial cells

value: Adherent neural stem cell

value: Differentiated glial/neuron cells

value: Culture differentiation, 7 days


title: Colon, model44

tag: group

value: Model

value: colon

tag: disease state

value: AOM/DSS induced colitis-associated cancer (CAC) mouse model

tag: disease induction

value: AOM (12.5 mg/kg) was intraperitoneally injected into the mice at the first day of modeling. After 7 days, 2% DSS was given in free drinking water for 5 days and then changed to normal drinking water for 2 weeks. The modeling was completed after a total of four cycles.

value: double distilled water


title: 15 right end

value: right lung

tag: timepoint

tag: biopsy set

value: 15 right

tag: donor age (y)

value: male

value: no

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: old_ctrl_48h_hemisphere_2

description:
Library name: FACS106_HM
FACS106_HM

tag: tissue

value: brain

tag: region

value: hemisphere

tag: cell type

value: microglia

tag: genotype

value: WT

tag: age

value: 20-22 months

tag: treatment

value: control

value: 48 hours


title: rtgill.dip.1.B11

description:
Library name: rtgill.dip.1.B11
Cell lysate
dip.counts.txt
dip.lib17_S1.B11.expression.values

source_name: RTgill-W1 dip rep 1 conc 7

tag: cell line

value: Rainbow trout gill


title: rtgill.dip.1.G11

description:
Library name: rtgill.dip.1.G11
Cell lysate
dip.counts.txt
dip.lib17_S1.G11.expression.values

source_name: RTgill-W1 dip rep 1 conc 2


title: Colon, model33

tag: group

value: Model

value: colon

tag: disease state

value: AOM/DSS induced colitis-associated cancer (CAC) mouse model


title: Saline Adherent neural stem cells, cell line 20, culture differentitation 7days

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "20D"

value: fetus dorsal forebrain

tag: developmental stage

value: Differentiated neuron/glial cells

value: Adherent neural stem cell

value: Differentiated glial/neuron cells

value: Culture differentiation, 7 days


title: 15 left end

value: left lung

tag: timepoint

value: end donor lung implantation

tag: biopsy set

value: 15 left

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

value: intracranial bleeding

value: DBD

tag: cold ischemia (min)


title: 14 right end

tag: tissue

value: right lung

value: 14 right

tag: donor age (y)

value: female

value: yes

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: Colon, model30

tag: group

value: Model

value: colon

value: AOM/DSS induced colitis-associated cancer (CAC) mouse model

tag: disease induction

value: AOM (12.5 mg/kg) was intraperitoneally injected into the mice at the first day of modeling. After 7 days, 2% DSS was given in free drinking water for 5 days and then changed to normal drinking water for 2 weeks. The modeling was completed after a total of four cycles.

tag: treatment

value: double distilled water


title: Poly I:C Adherent neural stem cells, cell line 12, culture differentitation 7days

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "12D"

value: fetus dorsal forebrain

tag: developmental stage

value: Differentiated neuron/glial cells

tag: cell line

value: Adherent neural stem cell

tag: cell type

value: Differentiated glial/neuron cells

value: Culture differentiation, 7 days


title: rtgill.dic.3.H10

description:
Library name: rtgill.dic.3.H10
Cell lysate
dic.counts.txt
dic.lib25_S1.H10.expression.values

source_name: RTgill-W1 dic rep 3 conc 1

value: Rainbow trout gill


title: 14 left end

value: left lung

tag: timepoint

value: end donor lung implantation

tag: biopsy set

value: 14 left

tag: donor sex

tag: donor bmi

value: DBD


title: Poly I:C Adherent neural stem cells, cell line 10, culture differentitation 7days

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "10D"

tag: tissue


title: Colon, model23

tag: disease state


title: rtgill.dic.3.F10

description:
Library name: rtgill.dic.3.F10
Cell lysate
dic.counts.txt
dic.lib25_S1.F10.expression.values

source_name: RTgill-W1 dic rep 3 conc 3


title: 12 right end

value: right lung

value: 12 right

tag: donor age (y)

value: female

tag: donor smoking history

value: no

tag: donor cause of death

tag: donor mechanical ventilation (hours)

tag: cold ischemia (min)


title: Ischaemic preconditioning was applied to the ischaemia-reperfusion group 1

source_name: liver

tag: strain

tag: sample group

value: liver

tag: molecule subtype

value: lncRNA and mRNA


title: rtgill.dic.3.G10

description:
Library name: rtgill.dic.3.G10
Cell lysate
dic.counts.txt
dic.lib25_S1.G10.expression.values

source_name: RTgill-W1 dic rep 3 conc 2

tag: treatment


title: Saline Adherent neural stem cells, cell line 7, culture differentitation 7days

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "7D"

tag: developmental stage

tag: cell line


title: 12 left end

tag: timepoint

value: 12 left

value: hypoxic-ischemic encefalopathy

tag: donor pao2/fio2 ratio

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: rtgill.dic.3.E10

description:
Library name: rtgill.dic.3.E10
Cell lysate
dic.counts.txt
dic.lib25_S1.E10.expression.values

source_name: RTgill-W1 dic rep 3 conc 4

tag: cell type


title: Colon, PZH27

source_name: PZH group, 91 days treated with PZH

tag: group

value: PZH

tag: tissue

value: colon

tag: disease state

value: control

tag: disease induction

value: double distilled water


title: Saline Adherent neural stem cells, cell line 29

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "29"

value: fetus dorsal forebrain

value: Stem cell

value: Adherent neural stem cell

value: Neural Stem Cells

value: Undifferentiated


title: 11 right end

source_name: lung biopsy

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 11 right

tag: donor age (y)

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

tag: donor cause of death

tag: donor mechanical ventilation (hours)

value: DCD

tag: cold ischemia (min)


title: rtgill.dip.1.A11

description:
Library name: rtgill.dip.1.A11
Cell lysate
dip.counts.txt
dip.lib17_S1.A11.expression.values

source_name: RTgill-W1 dip rep 1 conc 8

tag: cell line

value: Rainbow trout gill

tag: treatment


title: rtgill.dip.1.C11

description:
Library name: rtgill.dip.1.C11
Cell lysate
dip.counts.txt
dip.lib17_S1.C11.expression.values

source_name: RTgill-W1 dip rep 1 conc 6


title: Colon, PZH46


title: Poly I:C Adherent neural stem cells, cell line 28

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "28"

tag: developmental stage


title: Poly I:C Adherent neural stem cells, cell line 28, culture differentitation 7days

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "28D"

value: Differentiated neuron/glial cells

value: Differentiated glial/neuron cells

value: Culture differentiation, 7 days


title: 11 left end

value: left lung

tag: timepoint

value: 11 left

value: no

value: hypoxic-ischemic encefalopathy

tag: donor pao2/fio2 ratio

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: Colon, PZH14

tag: group

value: PZH

tag: tissue

value: colon

tag: disease state

value: control

tag: disease induction

value: double distilled water


title: rtgill.dic.3.C10

description:
Library name: rtgill.dic.3.C10
Cell lysate
dic.counts.txt
dic.lib25_S1.C10.expression.values

source_name: RTgill-W1 dic rep 3 conc 6

tag: cell type


title: Saline Adherent neural stem cells, cell line 20

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "20"

value: fetus dorsal forebrain

value: Stem cell

value: Adherent neural stem cell

value: Neural Stem Cells

value: Undifferentiated


title: 10 right end

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 10 right

tag: donor age (y)

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

value: DCD


title: Colon, PZH8

tag: treatment


title: rtgill.dic.3.B10

description:
Library name: rtgill.dic.3.B10
Cell lysate
dic.counts.txt
dic.lib25_S1.B10.expression.values

source_name: RTgill-W1 dic rep 3 conc 7

tag: cell line

value: Rainbow trout gill


title: Colon, PZH53


title: Colon, con50

source_name: Control group, 91 days treated with double distilled water

value: Control


title: 10 left end

value: left lung

tag: timepoint

value: 10 left

value: no

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: cold ischemia (min)


title: Poly I:C Adherent neural stem cells, cell line 12

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "12"

tag: developmental stage


title: rtgill.dic.3.A10

description:
Library name: rtgill.dic.3.A10
Cell lysate
dic.counts.txt
dic.lib25_S1.A10.expression.values

source_name: RTgill-W1 dic rep 3 conc 8


title: 9 right end

value: 9 right

value: female

value: head trauma

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: Saline Adherent neural stem cells,  cell line 7

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "7"

tag: tissue

value: fetus dorsal forebrain

value: Stem cell

value: Adherent neural stem cell

tag: cell type

value: Neural Stem Cells


title: rtgill.dic.2.H10

description:
Library name: rtgill.dic.2.H10
Cell lysate
dic.counts.txt
dic.lib21_S1.H10.expression.values

source_name: RTgill-W1 dic rep 2 conc 1


title: Colon, con41

tag: group

value: colon

tag: disease state

value: control

tag: disease induction

value: double distilled water


title: 9 left end

value: end donor lung implantation

tag: biopsy set

value: 9 left

tag: donor age (y)

tag: donor sex

tag: donor bmi

tag: donor smoking history


title: rtgill.dic.2.G10

description:
Library name: rtgill.dic.2.G10
Cell lysate
dic.counts.txt
dic.lib21_S1.G10.expression.values

source_name: RTgill-W1 dic rep 2 conc 2

tag: cell line

value: Rainbow trout gill

tag: treatment


title: rtgill.dic.3.D10

description:
Library name: rtgill.dic.3.D10
Cell lysate
dic.counts.txt
dic.lib25_S1.D10.expression.values

source_name: RTgill-W1 dic rep 3 conc 5


title: 8 right end

value: right lung

tag: timepoint

value: 8 right

value: male

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: cold ischemia (min)


title: Colon, con37

value: Control


title: YS1 ATAC

city: Kumamoto

first: Naofumi

last: Takahashi

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSCmm10 using Bowtie2
PCR duplicates were removed using MarkDuplicates (Picard)
The bigwig files were created using bamCoverage (deepTools)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Macrophage

extract_protocol:
DNA samples were extracted from 80000 cells using ATAC-Seq Kit (Active Motif).
Library constraction was performed using ATAC-Seq Kit (Active Motif).

tag: origin

value: Yolk sac

value: Macrophage


title: Colon, con17

tag: tissue


title: FL2 ATAC

value: Fetal liver

tag: cell type


title: 8 left end

value: left lung

value: 8 left

value: no

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: rtgill.dic.2.E10

description:
Library name: rtgill.dic.2.E10
Cell lysate
dic.counts.txt
dic.lib21_S1.E10.expression.values

source_name: RTgill-W1 dic rep 2 conc 4


title: 7 right end

tag: biopsy set

value: 7 right

tag: donor age (y)


title: rtgill.dic.2.F10

description:
Library name: rtgill.dic.2.F10
Cell lysate
dic.counts.txt
dic.lib21_S1.F10.expression.values

source_name: RTgill-W1 dic rep 2 conc 3


title: FL1 ATAC


title: ern0160-deleted Aus0004 mutant with recombinant pAT29Wern0160 plasmid - sample 2 [p160-2]

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

country: France

institute: CHU de Rennes

data_processing:
The reads were mapped against the genomic sequence of E. faecium Aus0004 (Genbank accession no. CP003351) and counted using the CLC Genomics Workbench software v10.0.1 (Qiagen).
The expression of genes in different RNA-seq samples was compared using the DESeq2 R package.
Assembly: E. faecium Aus0004 (Genbank accession no. CP003351)
Supplementary files format and content: Tab-delimited text files with number of mapped reads (generated using the CLC Genomics Workbench software v10.0.1, Qiagen)

organism: Enterococcus faecium Aus0004

source_name: late-exponential culture

growth_protocol: Bacterial cells of E. faecium Aus0004 were cultured at 37°C to the late-exponential-growth phase in BHI broth

extract_protocol:
Total RNA was extracted from using the phenol/chloroform method. Residual chromosomal DNA was removed by treating samples with the TURBO DNA-free kit (Life Technologies).
The strand-specific library preparation was performed using the Ovation Universal Prokaryotic RNA-Seq kit (Nugen) with custom depletion (Anydeplete rRNA design Enterococcus faecium) and the samples were sequenced using the Illumina NextSeq500 instrument (multiplex protocol, single-end 75-bp reads).

tag: strain

value: late-exponential culture


title: 7 left end

value: end donor lung implantation

value: 7 left

tag: donor sex

tag: donor bmi

tag: donor smoking history


title: rtgill.dic.2.D10

description:
Library name: rtgill.dic.2.D10
Cell lysate
dic.counts.txt
dic.lib21_S1.D10.expression.values

source_name: RTgill-W1 dic rep 2 conc 5

tag: cell line

value: Rainbow trout gill

tag: treatment


title: rtgill.dic.2.C10

description:
Library name: rtgill.dic.2.C10
Cell lysate
dic.counts.txt
dic.lib21_S1.C10.expression.values

source_name: RTgill-W1 dic rep 2 conc 6


title: Poly I:C Adherent neural stem cells, cell line 10

description: In JFLopez_log2_TMM.txt file, this sample correspond to column named "10"

source_name: fetus dorsal forebrain

value: fetus dorsal forebrain

tag: developmental stage

value: Stem cell

value: Adherent neural stem cell

value: Neural Stem Cells

value: Undifferentiated


title: BM2 ATAC

value: Bone marrow


title: ern0160-deleted Aus0004 mutant with empty pAT29 plasmid - sample 2 [160pv2]


title: Colon, con48

tag: group

value: Control

value: colon

tag: disease state

value: control

tag: disease induction

value: double distilled water


title: 6 right end

source_name: lung biopsy

tag: tissue

value: right lung

tag: timepoint

value: 6 right

value: male

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: cold ischemia (min)


title: ern0160-deleted Aus0004 mutant with empty pAT29 plasmid - sample 1 [160-pv1]

value: late-exponential culture


title: rtgill.dic.2.A10

description:
Library name: rtgill.dic.2.A10
Cell lysate
dic.counts.txt
dic.lib21_S1.A10.expression.values

source_name: RTgill-W1 dic rep 2 conc 8

tag: cell type

value: Rainbow trout gill


title: YS2 ATAC

tag: origin

value: Yolk sac

value: Macrophage


title: 5 left end

value: left lung

value: end donor lung implantation

tag: biopsy set

value: 5 left

tag: donor age (y)

value: head trauma

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: ern0160-deleted Aus0004 mutant - sample 2 [d0160-2]

tag: strain


title: 4 right end

value: 4 right

tag: donor sex

value: female

tag: donor bmi

tag: donor smoking history

value: hypoxic-ischemic encefalopathy

value: DCD


title: 4 left end

tag: tissue

value: 4 left


title: BM2 RNA

data_processing:
Making FASTQ were performed using Local Run Manager v2.4.0 for NextSeq 500 output
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSCmm10 using STAR v2.7.9a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: UCSCmm10
Supplementary files format and content: TPM values for each sample are included in a matrix file

extract_protocol: Total RNA was isolated using ISOGEN II (Nippon Genen). 1ng of total RNA was used for the construction of sequencing libraries. Agilent 2100 Bioanalyzer was used for QC. RNA libraries were prepared using Next Poly(A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: Bone marrow


title: rtgill.dic.1.H10

description:
Library name: rtgill.dic.1.H10
Cell lysate
dic.counts.txt
dic.lib17_S1.H10.expression.values

source_name: RTgill-W1 dic rep 1 conc 1

tag: cell line

tag: treatment


title: ern0160-deleted Aus0004 mutant - sample 1 [d0160-1]


title: rtgill.dic.1.G10

description:
Library name: rtgill.dic.1.G10
Cell lysate
dic.counts.txt
dic.lib17_S1.G10.expression.values

source_name: RTgill-W1 dic rep 1 conc 2


title: Aus0004 wild-type strain - sample 2 [WT6]


title: BM1 RNA


title: ern0160-deleted Aus0004 mutant with recombinant pAT29Wern0160 plasmid - sample 1 [p160-1]


title: FL3 RNA

value: Fetal liver


title: Aus0004 wild-type strain - sample 1 [WT1]


title: rtgill.dic.1.F10

description:
Library name: rtgill.dic.1.F10
Cell lysate
dic.counts.txt
dic.lib17_S1.F10.expression.values

source_name: RTgill-W1 dic rep 1 conc 3


title: 3 left end

tag: timepoint

value: 3 left

value: male

value: no

tag: donor cause of death

tag: donor mechanical ventilation (hours)


title: rtgill.dic.2.B10

description:
Library name: rtgill.dic.2.B10
Cell lysate
dic.counts.txt
dic.lib21_S1.B10.expression.values

source_name: RTgill-W1 dic rep 2 conc 7

tag: cell type

value: Rainbow trout gill


title: FPE RNA -R-case 129, miRNA

city: Donostia-San Sebastián

first: María

last: Armesto

state: NorthEurope

address: Paseo Dr. Begiristain s/n

department: Molecular Oncology

institute: IIS Biogipuzkoa

description: miRNA expression data from RNA from ccRCC cases

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA processed in affymetrix TAC (v.4.0.3)

label: biotin

source_name: FFPE

label_protocol: standard Affymetrix protocol

growth_protocol: ccRCC were classified as responders and non responders to sunitinib treatment, RNA was extracted from FFPE biopsy material from ccRCC cases

extract_protocol: RNA was extracted from ccRCC cases using the RecoverAll kit according to manufacturers

tag: case

value: case 129

tag: phenotype

value: sunitinib responder

value: ccRCC


title: FL2 RNA

tag: origin

value: Macrophage


title: 2 right end

value: right lung

value: end donor lung implantation

tag: biopsy set

value: 2 right

tag: donor age (y)

value: intracranial bleeding

tag: donor pao2/fio2 ratio

tag: donation type

tag: cold ischemia (min)


title: FL1 RNA


title: BM1 ATAC


title: FPE RNA -NR-case 110, miRNA

value: case 110

value: sunitinib non-responder


title: FPE RNA -R-case 103, miRNA

value: case 103


title: YS3 RNA

value: Yolk sac


title: 1 left end

value: left lung

value: 1 left

tag: donor sex

tag: donor bmi

value: yes

value: hypoxic-ischemic encefalopathy

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: rtgill.dic.1.C10

description:
Library name: rtgill.dic.1.C10
Cell lysate
dic.counts.txt
dic.lib17_S1.C10.expression.values

source_name: RTgill-W1 dic rep 1 conc 6

tag: cell line

value: Rainbow trout gill

tag: treatment


title: BM3 RNA

value: Bone marrow


title: 44 right start

tag: tissue

tag: timepoint

value: start donor lung implantation

value: 44 Right

value: male

tag: donor smoking history

tag: donor cause of death

value: DCD


title: rtgill.dic.1.B10

description:
Library name: rtgill.dic.1.B10
Cell lysate
dic.counts.txt
dic.lib17_S1.B10.expression.values

source_name: RTgill-W1 dic rep 1 conc 7

tag: cell type


title: 44 left start

value: 44 Left

tag: donor mechanical ventilation (hours)


title: FPE RNA -NR-case 99, miRNA

tag: case

value: case 99

tag: phenotype

value: ccRCC


title: rtgill.dic.1.A10

description:
Library name: rtgill.dic.1.A10
Cell lysate
dic.counts.txt
dic.lib17_S1.A10.expression.values

source_name: RTgill-W1 dic rep 1 conc 8


title: YS1 RNA

source_name: Macrophage

tag: origin

value: Macrophage


title: rtgill.ampa.3.H09

description:
Library name: rtgill.ampa.3.H09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.H09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 1


title: YS2 RNA


title: 43 right start

value: right lung

tag: biopsy set

value: 43 Right

tag: donor age (y)

value: no

value: intracranial bleeding

tag: donor pao2/fio2 ratio

tag: donation type


title: FPE RNA -NR-case 72, miRNA

value: case 72

value: sunitinib non-responder


title: rtgill.dic.1.D10

description:
Library name: rtgill.dic.1.D10
Cell lysate
dic.counts.txt
dic.lib17_S1.D10.expression.values

source_name: RTgill-W1 dic rep 1 conc 5


title: AAV9-DdCBE_2X_rep1 (mouse #26)

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.3.5) using the parameters:  --species Mmus --cluster-id 0.97 --threads 10 --min-cov 0.0005 --max-mismatches 0.1 --deconv-cov-ratio 0.4 -- max-multi 6 --remap --remap-mismatches 0.075 --crosstalks.
Assembly: mm39
Supplementary files format and content: csv; mim-tRNAseq generated tRNA transcript resad counts
Library strategy: mim-tRNAseq

source_name: mouse heart tissue

extract_protocol:
Total RNA from either two cell passages of four different cell lines or eight representative hearts from the m.5024T mouse model was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta-elimination (Behrens and Nedialkova, 2022).
tRNA-seq libraries were prepared using the mim-tRNAseq workflow (Behrens and Nedialkova, 2022) and sequenced on an Illumina NextSeq 500 platform.

value: mouse heart tissue