title: OCU-CH102

description:
SAMPLE 15
microRNA in blood exosome of CHC patients

value: CHC patient 1


title: Mouse_Vehicle_09h_4

status: Public on Jun 20 2023

type: RNA

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

country: United Kingdom

institute: University of Liverpool

description: Gene expression data from liver of mice treated with vehicle at 9h after administration

hyb_protocol: Following fragmentation, 30 µg of cRNA were hybridized for 16h at 45°C on Affymetrix GeneChip™ Mouse Genome 430 2.0 Array or GeneChip™ Rat Genome 230 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Quality control and low level analysis of raw fluorescence intensities was performed using the affy package (v1.64.0) in R v3.6.1. Raw data were processed using RMA normalization and a custom chip-definition file (CDF version 24 for mouse and version 19 for rat) from the BrainArray (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated microarray probes to 18,180 and 13,877 genes for mouse and rat, respectively. Differential expression analyses were carried out using the limma package (v3.42.2) in R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

extract_protocol: Frozen liver samples were homogenised in Qiazol Lysis Reagent (Qiagen), and total RNA was purified following the manufacturer’s instructions.

tag: tissue

value: liver

tag: strain

tag: Sex

value: male

tag: treatment

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)

tag: hours after treatment


title: OCU-CH105

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

description:
SAMPLE 16
microRNA in blood exosome of CHC patients

hyb_protocol: Labeled RNA was hybridized on microarray for 20hours at 55℃ by using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to the manufacturer’s protocol (protocol for use with Agilent microRNA microarrays Version 1.0).

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505B (Agilent Technologies) and the scanned images were analyzed using Agilent feature extraction software (v9.5.3.1).

data_processing:
Data were analyzed using the GeneSpring GX10.0.2 (Agilent). Quality control (QC) was applied according to the manufacturer’s instructions, and all data were approved by GeneSpring.
We used raw data (gProcessedSignal) and normalized each expression so as to have zero mean and unit sample variance.

organism: Homo sapiens

source_name: CHC patient

label_protocol: To detect serum miRNA, 60 ng of RNA was labeled using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to the manufacturer’s protocol (protocol for use with Agilent microRNA microarrays Version 1.0).

extract_protocol: Total RNA from 200 ul of serum was prepared using miRNeasy mini kit (Qiagen, Hilden Germany) according to the manufacturer’s instruction. Exosome rich fractionated RNA was prepared using Exoquick (System Biosciences, CA, USA). Briefly, 900 ul of serum was mixed with 250 ul of Exoquick and incubated for 12 hr at 4℃. The tubes were centrifuged at 1500 g for 30 min at room temperature and then supernatant was discarded. The pellet was dissolved with 200 ul of PBS with vigorous vortex. RNA was extracted using miRNeasy mini kit (Qiagen).

treatment_protocol: Peripheral blood was collected from all subjects directly into serum tubes before anti-viral treatment. The tubes were centrifuged at 1,500 g for 10 min at 4℃, sera were aliquoted and additionally centrifuged at 2,000 g to completely remove any remaining cells. Sera were stored at -80℃ until use.

tag: subject status/id

value: CHC patient 2

tag: age

tag: gender

value: female

tag: hbsag

tag: anti-hcv

tag: afp

value: NT

tag: dcp

tag: cea

value: peripheral blood

tag: molecule subtype

value: microRNA


title: 7d_SS2_14681.30e [SLX-19435.i723_i506]

type: SRA

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19435_scB5Tom_7d_ss2_fcounts.txt

library_source: transcriptomic single cell

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

source_name: bone marrow

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.

treatment_protocol: Mice were treated with tamoxifen to induce a persistent fluorescent label, cells were harvested at indicated time intervals

value: bone marrow

tag: cell type

value: Lin-negative, (cKit OR Sca1)-positive

tag: genotype

value: WT


title: 7d_SS2_14681.30e [SLX-19435.i723_i505]


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i522]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt


title: OCU-CCC13

description:
SAMPLE 13
microRNA in blood exosome of ICC patients

source_name: ICC patient

value: ICC patient 13


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i522]


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i522]


title: OCU-CCC14

description:
SAMPLE 14
microRNA in blood exosome of ICC patients

value: ICC patient 14


title: 7d_SS2_14681.30e [SLX-19435.i723_i502]


title: 7d_SS2_14681.30e [SLX-19435.i723_i503]


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i521]


title: 7d_SS2_14681.32c [SLX-19435.i722_i511]


title: OCU-CCC12

description:
SAMPLE 12
microRNA in blood exosome of ICC patients

value: ICC patient 12


title: Mouse_Vehicle_06h_5

description: Gene expression data from liver of mice treated with vehicle at 6h after administration


title: OCU-CCC11

description:
SAMPLE 11
microRNA in blood exosome of ICC patients

value: ICC patient 11


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i522]


title: 7d_SS2_14681.32c [SLX-19435.i722_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i522]


title: Mouse_Vehicle_09h_2


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i521]


title: Mouse_Vehicle_09h_1


title: OCU-CCC10

description:
SAMPLE 10
microRNA in blood exosome of ICC patients

value: ICC patient 10


title: 7d_SS2_14681.32c [SLX-19435.i722_i508]


title: Mouse_Vehicle_06h_4


title: OCU-CCC9

description:
SAMPLE 9
microRNA in blood exosome of ICC patients

value: ICC patient 9


title: Mouse_Vehicle_06h_3

value: liver


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i521]


title: 7d_SS2_14681.32c [SLX-19435.i722_i507]


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i521]


title: 7d_SS2_14681.32c [SLX-19435.i722_i506]


title: Mouse_Vehicle_06h_2

value: male


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i521]


title: OCU-CCC7

description:
SAMPLE 7
microRNA in blood exosome of ICC patients

value: ICC patient 7


title: Mouse_Vehicle_06h_1

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)


title: OCU-CCC8

description:
SAMPLE 8
microRNA in blood exosome of ICC patients

value: ICC patient 8


title: 7d_SS2_14681.32c [SLX-19435.i722_i505]


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i521]


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i521]


title: 7d_SS2_14681.32c [SLX-19435.i722_i503]


title: Mouse_Vehicle_03h_4

description: Gene expression data from liver of mice treated with vehicle at 3h after administration


title: 7d_SS2_14681.32c [SLX-19435.i722_i502]


title: OCU-CCC5

description:
SAMPLE 5
microRNA in blood exosome of ICC patients

value: ICC patient 5


title: Mouse_Vehicle_03h_5


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i521]


title: 7d_SS2_14681.30e [SLX-19435.i721_i511]


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i521]


title: Mouse_Vehicle_03h_2


title: OCU-CCC4

description:
SAMPLE 4
microRNA in blood exosome of ICC patients

value: ICC patient 4

value: peripheral blood


title: Mouse_Vehicle_03h_3


title: OCU-CCC6

description:
SAMPLE 6
microRNA in blood exosome of ICC patients

value: ICC patient 6

value: female

value: NT

value: microRNA


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i521]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: 7d_SS2_14681.30e [SLX-19435.i721_i510]


title: OCU-CCC3

description:
SAMPLE 3
microRNA in blood exosome of ICC patients

value: ICC patient 3


title: Mouse_Vehicle_03h_1


title: Mouse_Baseline_0h_4

description: Gene expression data from liver of untreated mice (baseline 0h controls)

value: Untreated


title: Mouse_Baseline_0h_5

value: liver


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i521]


title: HCC10

description:
SAMPLE 32
microRNA in blood exosome of HCC patients

source_name: HCC patient

value: HCC patient 14

value: male


title: 7d_SS2_14681.30e [SLX-19435.i721_i508]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19435_scB5Tom_7d_ss2_fcounts.txt


title: Mouse_Baseline_0h_3


title: NL109

description: SAMPLE 76

source_name: patient with normal liver

growth_protocol: none listed

tag: subject id

value: blood exosome

tag: extraction date

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs

tag: tg


title: OCU-CCC1

description:
SAMPLE 1
microRNA in blood exosome of ICC patients

tag: subject status/id

value: ICC patient 1

tag: age

tag: gender

tag: hbsag

tag: anti-hcv

tag: afp

tag: dcp

tag: cea

tag: tissue

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i721_i507]

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i521]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt


title: 7d_SS2_14681.30e [SLX-19435.i721_i506]


title: genomic DNA of sample F073_WB

type: genomic

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS/NIH

description: Non-smoker WB genomic DNA

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and MethylationEPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw IDAT files of 450K and EPIC methylation arrays were read into R with the minfi package separately; the combineArrays function in minfi was utilized to combine the two arrays’ data together based on their common CpG sites. Then, the data was preprocessed with background and dye bias correction using the preprocess Noob method. The ChAMP package was used to do BMIQ normalization. The combat function in sva package was used to do batch (“Sample_Plate”) correction on methylation array data. Prior to normalization, DNA methylation data were filtered based on these criteria: any samples having more than 5% probes that failed array QC standards, all CpG probes on the X and Y chromosomes, probes containing SNPs with a minor allele frequency ≥ 1% (in EUR or AFR populations of the 1000 Genomes Project) within 5 nucleotides to the CpG site, and probes failing QC standards. We also removed 43,254 probes reported to hybridize to one or more non-target sites in the genome.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Nucleated DNA from cells was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.

value: NS


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i520]


title: Mouse_Baseline_0h_2

tag: strain

tag: Sex

tag: hours after treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i520]


title: genomic DNA of sample F072_WB

description: Smoker WB genomic DNA

value: SM


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i520]


title: 7d_SS2_14681.30e [SLX-19435.i721_i505]


title: OCU-CCC2

description:
SAMPLE 2
microRNA in blood exosome of ICC patients

value: ICC patient 2

value: peripheral blood


title: genomic DNA of sample F069_WB

description: Smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i520]


title: NL108

description: SAMPLE 75

tag: subject id

tag: extraction date

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs

tag: tg


title: 7d_SS2_14681.30e [SLX-19435.i721_i502]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: genomic DNA of sample F068_WB

description: Smoker WB genomic DNA


title: NL107

description: SAMPLE 74

tag: subject id

tag: extraction date

tag: gender

value: female

tag: age (yrs)

tag: height (cm)

tag: hbsag

tag: anti-hcv

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i520]


title: 7d_SS2_14681.32c [SLX-19435.i720_i510]


title: NL104

description: SAMPLE 71

tag: weight (kg)

tag: bmi

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp


title: NL106

description: SAMPLE 73

tag: tissue

tag: hb

tag: alb

tag: bs

tag: tg


title: 7d_SS2_14681.32c [SLX-19435.i720_i511]

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i520]


title: genomic DNA of sample F065_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i520]


title: 7d_SS2_14681.32c [SLX-19435.i720_i508]


title: genomic DNA of sample F056_WB

description: Smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i721_i503]


title: NL103

description: SAMPLE 70

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: hbsag

tag: anti-hcv

tag: molecule subtype


title: genomic DNA of sample F064_WB

description: Smoker WB genomic DNA


title: genomic DNA of sample F055_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i520]


title: Mouse_Baseline_0h_1

tag: strain

tag: Sex

tag: hours after treatment


title: 7d_SS2_14681.32c [SLX-19435.i720_i506]

tag: tissue


title: genomic DNA of sample F108_WB

description: Non-smoker WB genomic DNA


title: NL101

description: SAMPLE 68

tag: weight (kg)

tag: bmi

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs


title: NL105

description: SAMPLE 72

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: hbsag

tag: anti-hcv

tag: tg


title: 7d_SS2_14681.32c [SLX-19435.i720_i505]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i520]


title: genomic DNA of sample F104_WB

description: Smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i520]


title: CT27, Stem, input, rep2

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

library_source: genomic

data_processing:
PhiX  reads were removed using HTStream's (Version 1.3.2) hts_SeqScreener with default parameters.
Duplicates were removed using HTStream's (Version 1.3.2) hts_SuperDeduper (-e 250000).
Adapter sequences were trimmer using HTStream's (Version 1.3.2) hts_AdapterTrimmer (-p 4).
N's were removed using HTStream's (Version 1.3.2) hts_Ntrimmer.
Base quality trimming was performed using HTStream's (Version 1.3.2) hts_QWindowTrim (-w10 -q 20).
Reads shorted than 50bp were remvoed using HTStream's (Version 1.3.2) hts_LengthFilter (-n -m 50).
Reads were aligned to the human genome (GRCh38) using BWA mem (0.7.17-r1188).
Alignments in the ENCODE blacklisted regions were removed using Bedtools (Version 2.30.0).
Peaks were called using MACS3 callpeak (Version 3.0.0a6) with the following parameters: -B -q 0.01.
Assembly: GRCh38.86
Supplementary files format and content: tab-separated narrowPeak files containing coordinates and scores for discovered peaks by MACS3

source_name: human trophoblast stem cell

extract_protocol:
ChIP was performed on CT27 human TS cells in three replicates using the SimpleChiP Enzymatic Chromatin IP kit (Cell Signaling Technology. Anti-rabbit AP-2 gamma antibody (1:50, 2320, Cell Signaling) was used in the analysis.
In total of 100 ng of fragmented DNA in 25 µL of water was used as input in library preparation. A KAPA HyperPrep Kit (07962347001, Roche) was used for library preparation, following the protocol associated with the kit with the following modifications. During end repair and a-tailing, 35 µL of water was added to the master mix containing 7 µL of end-repair and a-tailing buffer and 3 µL of end-repair and a-tailing enzyme. Forty-five µL of the end-repair and a-tailing master mix was added to each sample and was mixed thoroughly by pipetting. During the adapter ligation step, Illumina TruSeq DNA LT adapters, supplied at 15 µM, were diluted 1:100 in water and 5 µL of diluted adapters were added to the sample. A master mix of 30 µL of ligation buffer and 10 µL of DNA ligase was made and 40 µL of ligation master mix was added to each sample. After adapter ligation, a 0.8x bead clean-up was performed using AMPure XP Beads (A63881, Beckman Coulter) with a 10 min incubation at room temperature to allow the DNA to bind to the beads and a 7 min incubation after two 80% ethanol washes to allow the beads to dry. Once the beads were dry, the beads were resuspended in 25 µL of water and incubated at room temperature for 2 min. Twenty µL of post-ligation sample was then transferred to a new tube to be used in library amplification. The PCR library amplification master mix consisted of 25 µL of 2x KAPA HiFi HotStart ReadyMix, 1.5 µL of 10x PCR primer cocktail, and 3.5 µL of water. Thirty µL of the PCR master mix was added to each post-ligation sample and 13 cycles of PCR were performed. After library amplification, the library underwent a 0.6/0.8x double-sized size selection with 10 min incubations to allow the library to bind to the beads. Two 80% ethanol washes were performed, and the beads were allowed to dry at room temperature for 2 min. Thirty-six µL of water was added to the dried beads and was incubated at room temperature for 2 min to elute the DNA.

tag: cell line

tag: cell state

value: stem state trophoblast cell

tag: chip antibody


title: CT27, Stem, input, rep1


title: CT27, Stem, input, rep3


title: 7d_SS2_14681.32c [SLX-19435.i720_i503]


title: CT27, Stem, AP2C, rep3

value: Anti-rabbit AP-2 gamma antibody (1:50, #2320, Cell Signaling)


title: genomic DNA of sample F103_WB

description: Non-smoker WB genomic DNA


title: NL102

description: SAMPLE 69

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: molecule subtype

value: microRNA


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i520]

tag: tissue

value: bone marrow

tag: cell type

value: Lin-negative, (cKit OR Sca1)-positive


title: genomic DNA of sample F102_WB

description: Non-smoker WB genomic DNA


title: CT27, Stem, AP2C, rep2


title: 7d_SS2_14681.32c [SLX-19435.i720_i507]

tag: genotype

value: WT

tag: treatment


title: genomic DNA of sample F098_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i719_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i520]


title: 7d_SS2_14681.30e [SLX-19435.i719_i511]


title: genomic DNA of sample F096_WB

description: Smoker WB genomic DNA


title: CT27, Stem, AP2C, rep1

tag: cell line

tag: cell state


title: 7d_SS2_14681.30e [SLX-19435.i719_i508]


title: 7d_SS2_14681.30e [SLX-19435.i719_i507]


title: genomic DNA of sample F054_WB

description: Smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i518]


title: genomic DNA of sample F084_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F083_WB

description: Smoker WB genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i720_i502]


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i518]


title: 7d_SS2_14681.30e [SLX-19435.i719_i506]


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i518]


title: genomic DNA of sample F081_WB

description: Non-smoker WB genomic DNA


title: HCT15, 5-FU resistant, H3K27ac, replicate2, CUT&Tag

city: Shanghai

first: Xuelong

address: No. 100 Banxia Road

country: China

institute: Chinese Academy of Sciences

data_processing:
All ATAC-Seq data sets were trimmed and aligned to human genome build hg19 using Bowtie2.
Duplicate reads of all RNA-seq and CUT&Tag data were removed with SAMtools.
MACS2 was used to identify regions of CUT&Tag peaks.
The CUT&Tag peaks were used for known motif enrichment analysis of each sample, which were performed using HOMER (v4.10).
Assembly: hg19
Supplementary files format and content: BigWig (bw) files were generated using deepTools.

extract_protocol:
50,000 fresh cells were colected for each sample.
CUT&Tag assay was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (TD903, Vazyme Biotech, China) according to the manufacturer’s protocol.For each capture experiment, ~ 50,000 fresh cells were incubated with 10 μl pre-washed Concanavalin A-coated beads in single low-bind PCR tubes. 50 μl of antibody buffer with 1 μg antibody was added. Samples were further cultured overnight at 2-8°C, and then beads were washed twice with 200 μl of Dig-wash buffer, then 50 μl of Dig-wash buffer containing 1 μg secondary antibody was added and cultured for 30 - 60 min at room temperature. After washing three times with Dig-wash buffer, 100 μl of pA/G-Tnp was added to resuspend the beads. Samples were incubated with continuous rotation for 1 h at room temperature and washed twice with 200 μl Dig-wash buffer. Then, 50 μl of prepared Tagmentation mix was added and samples were incubated for 1 h at 37°C. A constant amount of spike-in control DNA was added to each library according to the manufacturer's protocol. Then the DNA was extracted and purified with Proteinase K and DNA Extract Beads (TD903, Vazyme Biotech, China) for 30min at 55°C. The purified DNA fragments were resuspended in 20 μl of ddH2O and can be stored at -20℃ for long periods. For library amplification, a total volume of 50μl of the sample was placed in a Thermocycler for PCR. VAHTS DNA Clean Beads (N411, Vazyme Biotech, China) were used to purify the PCR products.

value: colon cancer

value: treated with 20μg/mL 5-FU


title: HCT15, parental, H3K27ac, replicate1, CUT&Tag

value: treated with DMSO


title: HCT15, 5-FU resistant, H3K27ac, replicate1, CUT&Tag


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i518]


title: HCT15, 5-FU resistant, H3K23su, replicate2,CUT&Tag


title: 7d_SS2_14681.30e [SLX-19435.i719_i505]


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i518]


title: HCT15, 5-FU resistant, H3K23su, replicate1, CUT&Tag


title: 7d_SS2_14681.30e [SLX-19435.i719_i503]


title: genomic DNA of sample F079_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F078_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i719_i502]


title: 7d_SS2_14681.32c [SLX-19435.i718_i511]


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i518]


title: HCT15, parental, H3K27ac, replicate2, CUT&Tag


title: HCT15, parental, H3K23su, replicate2, CUT&Tag


title: 7d_SS2_14681.32c [SLX-19435.i718_i510]


title: genomic DNA of sample F076_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F074_WB

description: Non-smoker WB genomic DNA


title: 48_D0

city: Edinburgh

first: Jennifer

last: Rynne

email: jrynne@ed.ac.uk, jenrynne@gmail.com

address: QMRI, Edinburgh BioQuarter, Little France Crescent

institute: University of Edinburgh

library_source: transcriptomic

data_processing:
CGC cloud platform for QC (multiQC), trimming (trimmomatic) and alignment (Salmon index & quant)
Assembly: gencode.v38
Supplementary files format and content: quant file - output from salmon

source_name: whole blood

extract_protocol:
Qiagen PAXgene blood RNA tube extraction by Qiacube
NEB Ultra II directional library prep kit with polyA selection and unique dual indexes

value: whole blood

tag: timepoint

value: Placebo


title: genomic DNA of sample F199_WB

description: Non-smoker WB genomic DNA


title: 47_D0

value: ORBCEL-C


title: 7d_SS2_14681.32c [SLX-19435.i718_i508]


title: 7d_SS2_14681.32c [SLX-19435.i718_i507]


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i518]


title: 46_D7


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i517]


title: genomic DNA of sample F199_CD56

description: Non-smoker CD56 genomic DNA

value: NS


title: genomic DNA of sample F199_CD15

description: Non-smoker CD15 genomic DNA


title: 46_D4


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i517]


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i517]


title: genomic DNA of sample F199_CD19

description: Non-smoker CD19 genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i718_i505]


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i517]


title: 45_D0


title: 7d_SS2_14681.32c [SLX-19435.i718_i502]


title: 44_D7


title: 7d_SS2_14681.32c [SLX-19435.i718_i503]


title: genomic DNA of sample F199_CD14

description: Non-smoker CD14 genomic DNA


title: HCT15, parental, H3K23su, replicate1, CUT&Tag


title: 44_D4


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i517]


title: genomic DNA of sample F158_WB

description: Smoker WB genomic DNA

value: SM


title: 44_D0


title: 45_D7


title: genomic DNA of sample F155_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i718_i506]


title: genomic DNA of sample F209_WB

description: Smoker WB genomic DNA


title: genomic DNA of sample F209_CD56

description: Smoker CD56 genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i517]


title: 43_D7


title: 43_D4


title: 7d_SS2_14681.30e [SLX-19435.i716_i508]


title: 7d_SS2_14681.30e [SLX-19435.i716_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i517]


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i517]


title: 7d_SS2_14681.30e [SLX-19435.i716_i507]


title: genomic DNA of sample F199_CD8

description: Non-smoker CD8 genomic DNA


title: genomic DNA of sample F209_CD15

description: Smoker CD15 genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i716_i505]


title: 43_D0


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i517]


title: 7d_SS2_14681.30e [SLX-19435.i716_i511]


title: 42_D4


title: 7d_SS2_14681.30e [SLX-19435.i716_i503]


title: 7d_SS2_14681.30e [SLX-19435.i716_i506]


title: 41_D7


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i517]


title: genomic DNA of sample F209_CD14

description: Smoker CD14 genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i517]


title: 7d_SS2_14681.30e [SLX-19435.i716_i502]


title: 40_D7


title: genomic DNA of sample F209_CD8

description: Smoker CD8 genomic DNA


title: genomic DNA of sample F199_CD4

description: Non-smoker CD4 genomic DNA


title: genomic DNA of sample F198_WB

description: Smoker WB genomic DNA


title: genomic DNA of sample F209_CD19

description: Smoker CD19 genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i516]


title: 7d_SS2_14681.30e [SLX-19435.i715_i511]


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i516]


title: 40_D4


title: 39_D4


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i517]


title: 7d_SS2_14681.30e [SLX-19435.i715_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i516]


title: 7d_SS2_14681.30e [SLX-19435.i715_i508]


title: genomic DNA of sample F198_CD56

description: Smoker CD56 genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i516]


title: genomic DNA of sample F198_CD19

description: Smoker CD19 genomic DNA


title: genomic DNA of sample F198_CD15

description: Smoker CD15 genomic DNA


title: 39_D0


title: 38_D7


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i516]


title: genomic DNA of sample F198_CD14

description: Smoker CD14 genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i715_i503]


title: 38_D4


title: 7d_SS2_14681.30e [SLX-19435.i715_i507]


title: 7d_SS2_14681.30e [SLX-19435.i715_i505]


title: 7d_SS2_14681.30e [SLX-19435.i715_i506]


title: 40_D0


title: genomic DNA of sample F198_CD8

description: Smoker CD8 genomic DNA


title: 38_D0


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i516]


title: genomic DNA of sample F151_WB

description: Smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i516]


title: 37_D0


title: 7d_SS2_14681.32c [SLX-19435.i714_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i516]


title: 36_D0


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i516]


title: 7d_SS2_14681.32c [SLX-19435.i714_i508]


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i516]


title: 7d_SS2_14681.30e [SLX-19435.i715_i502]


title: genomic DNA of sample F148_WB

description: Smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i516]


title: 7d_SS2_14681.32c [SLX-19435.i714_i507]


title: 36_D4


title: 35_D4


title: genomic DNA of sample F147_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i516]


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i515]


title: 7d_SS2_14681.32c [SLX-19435.i714_i505]


title: genomic DNA of sample F144_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i515]


title: 7d_SS2_14681.32c [SLX-19435.i714_i511]


title: 35_D0


title: 34_D4


title: 7d_SS2_14681.32c [SLX-19435.i714_i506]


title: genomic DNA of sample F130_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F093_WB

description: Non-smoker WB genomic DNA


title: 34_D0


title: 7d_SS2_14681.32c [SLX-19435.i714_i502]


title: 35_D7


title: genomic DNA of sample F149_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F092_WB

description: Smoker WB genomic DNA


title: 33_D0


title: genomic DNA of sample F091_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i712_i511]


title: genomic DNA of sample F090_WB

description: Smoker WB genomic DNA


title: 31_D7


title: 32_D0


title: genomic DNA of sample F154_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i712_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i515]


title: 7d_SS2_14681.30e [SLX-19435.i712_i508]


title: 31_D0


title: genomic DNA of sample F089_WB

description: Smoker WB genomic DNA


title: genomic DNA of sample F087_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i714_i503]


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i515]


title: 30_D7


title: 7d_SS2_14681.30e [SLX-19435.i712_i506]


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i515]


title: 30_D0


title: genomic DNA of sample F085_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i712_i507]


title: 7d_SS2_14681.30e [SLX-19435.i712_i505]


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i515]


title: 29_D7


title: 7d_SS2_14681.30e [SLX-19435.i712_i503]


title: genomic DNA of sample F086_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i515]


title: 29_D4


title: genomic DNA of sample F124_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i515]


title: 7d_SS2_14681.30e [SLX-19435.i712_i502]


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i513]


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i513]


title: genomic DNA of sample F120_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i711_i511]


title: 28_D7


title: 7d_SS2_14681.32c [SLX-19435.i711_i510]


title: 29_D0


title: 28_D4


title: genomic DNA of sample F119_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i513]


title: 28_D0


title: 7d_SS2_14681.32c [SLX-19435.i711_i507]


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i513]


title: genomic DNA of sample F118_WB

description: Non-smoker WB genomic DNA


title: 26_D7


title: genomic DNA of sample F115_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F117_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i513]


title: genomic DNA of sample F129_WB

description: Smoker WB genomic DNA


title: 26_D4


title: 7d_SS2_14681.32c [SLX-19435.i711_i505]


title: genomic DNA of sample F192_CD4

description: Non-smoker CD4 genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i711_i506]


title: 26_D0


title: 7d_SS2_14681.32c [SLX-19435.i711_i503]


title: 7d_SS2_14681.32c [SLX-19435.i711_i508]


title: genomic DNA of sample F111_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i513]


title: 7d_SS2_14681.32c [SLX-19435.i711_i502]


title: 25_D7


title: genomic DNA of sample F209_CD4

description: Smoker CD4 genomic DNA


title: 24_D0


title: genomic DNA of sample F198_CD4

description: Smoker CD4 genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i704_i513]


title: 7d_SS2_14681.30e [SLX-19435.i710_i511]


title: 2w4w_SS2_146818.66b [SLX-20544.i703_i513]


title: 7d_SS2_14681.30e [SLX-19435.i710_i510]


title: 27_D0


title: genomic DNA of sample F192_WB

description: Non-smoker WB genomic DNA


title: 23_D0


title: 2w4w_SS2_146818.66b [SLX-20544.i702_i513]


title: 7d_SS2_14681.30e [SLX-19435.i710_i508]


title: genomic DNA of sample F192_CD56

description: Non-smoker CD56 genomic DNA


title: 22_D4


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i513]


title: 22_D0


title: genomic DNA of sample F192_CD19

description: Non-smoker CD19 genomic DNA


title: 2w4w_SS2_146818.66b [SLX-20544.i701_i513]


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i511]


title: 7d_SS2_14681.30e [SLX-19435.i710_i506]


title: genomic DNA of sample F192_CD15

description: Non-smoker CD15 genomic DNA


title: 21_D7


title: 7d_SS2_14681.30e [SLX-19435.i710_i507]


title: 7d_SS2_14681.30e [SLX-19435.i710_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i511]


title: genomic DNA of sample F192_CD14

description: Non-smoker CD14 genomic DNA


title: 21_D4


title: 21_D0


title: 7d_SS2_14681.30e [SLX-19435.i710_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i511]


title: 7d_SS2_14681.30e [SLX-19435.i710_i502]


title: genomic DNA of sample F223_WB

description: Smoker WB genomic DNA


title: 20_D7


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i511]


title: 7d_SS2_14681.32c [SLX-19435.i707_i511]


title: 20_D0


title: 7d_SS2_14681.32c [SLX-19435.i707_i510]


title: genomic DNA of sample F204_WB

description: Non-smoker WB genomic DNA


title: genomic DNA of sample F200_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i707_i506]


title: 19_D4


title: 19_D0


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i511]


title: 7d_SS2_14681.32c [SLX-19435.i707_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i511]


title: genomic DNA of sample F097_WB

description: Smoker WB genomic DNA


title: 7d_SS2_14681.32c [SLX-19435.i707_i507]


title: 7d_SS2_14681.32c [SLX-19435.i707_i503]


title: genomic DNA of sample F213_WB

description: Smoker WB genomic DNA


title: 20_D4


title: 7d_SS2_14681.32c [SLX-19435.i707_i502]


title: genomic DNA of sample F214_WB

description: Smoker WB genomic DNA


title: 18_D0


title: genomic DNA of sample F207_WB

description: Non-smoker WB genomic DNA


title: 18_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i511]


title: genomic DNA of sample F105_WB

description: Non-smoker WB genomic DNA


title: 19_D7


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i511]


title: genomic DNA of sample F192_CD8

description: Non-smoker CD8 genomic DNA


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i511]


title: 18_D7


title: genomic DNA of sample F067_WB

description: Smoker WB genomic DNA


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i510]


title: genomic DNA of sample F082_WB

description: Non-smoker WB genomic DNA


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i510]


title: 7d_SS2_14681.30e [SLX-19435.i706_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i510]


title: 17_D0


title: genomic DNA of sample F062_WB

description: Smoker WB genomic DNA


title: 17_D4


title: genomic DNA of sample F077_WB

description: Non-smoker WB genomic DNA


title: 7d_SS2_14681.30e [SLX-19435.i706_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i510]


title: 7d_SS2_14681.30e [SLX-19435.i706_i507]


title: 17_D7


title: E13.5, scRNAseq TotalSeq2 [MP]

city: oxford

first: Sam

last: Palmer

address: mathematics institute, radcliffe observatory quarter

institute: university of Oxford

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Thymus cells

extract_protocol:
Cells from each condition were resuspended in 90μl FACS buffer (PBS without Ca2+ or Mg2+ with 10% FCS), stained with barcode tagged antibodies against MHCII (B0117), CD40 (B0903), CD80 (B0849), with biotinylated UEA1 bound to SAV-PE-B0952) and with a-EPCAM-magnetic beads (Miltenyi) (see Supplementary Table 3), and washed.  Each condition was then hashed with 100ullipid anchoredCell Multiplexing Oligosfor sample multiplexing (CMOs, 10x Genomics).
Cells eluted from the column were spun down and resuspended in 50µlFACS buffer, of which 10µlwas taken for cell counting.Approximately a total of 15000-30000 cells pooled from each condition were then filtered and loaded on a Chip G (10X Genomics). Cell-bead encapsulation was performed running the chip in a Chromium X instrument (10X Genomics). Upon encapsulation, gene expression and multiplexing libraries were prepared following the manufacturer’s instructions using the Chromium Next GEM single cell reagent kit 3’ V3.1 (dual index) with Feature Barcoding technology for Cell Multiplexing (CG000388, 10x Genomics). Libraries were quantified using a Bioanalyzer DNA High-sensitivity Kit (Agilent Technologies), pooled at a molar ratio of 6:1 between gene expression and multiplexing libraries, and sequenced on an Illumina NextSeq 2000 P3 flow cell (100 cycles configuration) to obtain approximately 1.4B paired-end reads.

value: Thymus cells

value: TEC

value: WT, Rosa26CreERt2;iFoxn1 (iFoxn1; called enforced Foxn1) and Rosa26CreERt2 (called Cre-only)


title: 16_D4


title: E13.5, scRNAseq TotalSeq2 [GEX]


title: 16_D0


title: 7d_SS2_14681.30e [SLX-19435.i706_i506]


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i510]


title: 7d_SS2_14681.30e [SLX-19435.i706_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i510]


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i511]


title: 7d_SS2_14681.30e [SLX-19435.i706_i503]


title: 14_D7


title: 7d_SS2_14681.32c [SLX-19435.i705_i511]


title: 7d_SS2_14681.30e [SLX-19435.i706_i502]


title: 13_D7


title: E12.5, scRNAseq TotalSeq2 [CITE]


title: E12.5, scRNAseq TotalSeq2 [GEX]


title: 7d_SS2_14681.32c [SLX-19435.i707_i508]


title: 7d_SS2_14681.32c [SLX-19435.i705_i510]


title: 7d_SS2_14681.32c [SLX-19435.i705_i507]


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i510]


title: 15_D0


title: Overnight, scRNAseq TotalSeq2 [MP]


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i510]


title: 7d_SS2_14681.32c [SLX-19435.i705_i508]


title: 14_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i510]


title: 12_D7


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i510]


title: 7d_SS2_14681.30e [SLX-19435.i706_i510]


title: E12.5, scRNAseq TotalSeq2 [MP]


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i508]


title: 15_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i510]


title: 13_D0


title: Overnight, scRNAseq TotalSeq2 [GEX]


title: Overnight, scRNAseq TotalSeq2 [CITE]


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i510]


title: 7d_SS2_14681.32c [SLX-19435.i705_i506]


title: 12_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i508]


title: 12_D0


title: 7d_SS2_14681.32c [SLX-19435.i705_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i508]


title: 7d_SS2_14681.30e [SLX-19435.i704_i511]


title: E13.5, scRNAseq TotalSeq2 [CITE]


title: 7d_SS2_14681.32c [SLX-19435.i705_i503]


title: 11_D7


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i508]


title: 11_D0


title: 10_D7


title: 2w4w_SS2_146818.66b [SLX-20544.i705_i513]


title: 7d_SS2_14681.32c [SLX-19435.i705_i502]


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i508]


title: BM-T48-Rep4

city: TOULOUSE cedex 3

first: Léon

last: Kautz

address: CHU Purpan - Place du Dr Baylac - CS 60 039

department: IRSD U1220

country: France

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 10 out of 12 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 36314 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33665 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Bone Marrow

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Total RNA from mouse bone marrow from Erfe-/- mice at t= 0, 24 and 48h hours after phlebotomy was extracted using Trizol (MRC) / Chloroform (Sigma). RNA quality was assessed on RNA 6000 Nano chips using a 2100 Bioanalyzer (Agilent Technologies).

value: Bone Marrow

value: phlebotomy

tag: time

tag: gender

value: Male

value: Erfe-/-


title: BM-T0-Rep4

value: control


title: BM-T48-Rep3


title: 7d_SS2_14681.30e [SLX-19435.i704_i507]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: BM-T24-Rep3


title: BM-T0-Rep3


title: 7d_SS2_14681.30e [SLX-19435.i704_i510]


title: BM-T24-Rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i508]


title: 7d_SS2_14681.30e [SLX-19435.i704_i508]


title: 10_D0


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i508]


title: BM-T24-Rep4


title: 9_D7


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i508]


title: 9_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i508]


title: 9_D0


title: BM-T48-Rep2


title: 7d_SS2_14681.30e [SLX-19435.i704_i505]


title: BM-T0-Rep2


title: BM-T48-Rep1


title: 8_D0


title: BM-T24-Rep1


title: 7_D7


title: 7d_SS2_14681.30e [SLX-19435.i704_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i507]


title: 7_D4


title: 7d_SS2_14681.30e [SLX-19435.i704_i506]


title: 7d_SS2_14681.30e [SLX-19435.i704_i502]


title: 7_D0


title: Molm13-Rescue-mut_rep2

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

institute: Wuhan University

data_processing:
All raw sequencing data were preprocessed using Trim_galore.
Kallisto was used to quantify the read counts for each transcripts (GRCh38, cDNA sequences).
The reads count for genes were assessed by R packages tximport.
Used HOMER (getDiffExpression.pl) to analysis differential genes.
Assembly: GRCh38
Supplementary files format and content: IGF2BP2_Res.vs.Resmut.vs.KD.vs.CON_expr.txt: Tab-delimited text file includes normalized reads for each Sample.

molecule: polyA RNA

growth_protocol: The human acute leukemia cell lines were maintained in Roswell Park Memorial Institute 1640 medium (RPMI-1640) with 10% FBS, 100 IU/mL penicillin and 100 mg/mL streptomycin.

extract_protocol:
Total RNA were extracted with Trizol, and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer, cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends, add A-tail, and connection connector. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Target cells were infected with the virus and 8 µg/mL polybrene with centrifugation at 2200 rpm. Media were changed at 12 hours after infection, and antibiotics (1-2 µg/mL puromycin) were added at 48 hours after infection if selection was needed.

value: AML leukemia cells

value: IGF2PB2-mut rescue


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i507]


title: 7d_SS2_14681.32c [SLX-19435.i703_i510]


title: 7d_SS2_14681.32c [SLX-19435.i703_i508]


title: 7d_SS2_14681.32c [SLX-19435.i703_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i507]


title: Molm13-Rescue-mut_rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i507]


title: Molm13-Rescue_rep2

value: IGF2BP2 rescue


title: 7d_SS2_14681.32c [SLX-19435.i703_i507]


title: 6_D0

value: whole blood

value: ORBCEL-C


title: Molm13-shIGF2PB2_rep2

value: IGF2BP2 knockdown


title: Molm13-Rescue_rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i507]


title: 6_D7


title: BM-T0-Rep1


title: 7d_SS2_14681.32c [SLX-19435.i703_i506]


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i507]


title: 5_D7


title: 5_D4


title: Molm13-con_rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i507]


title: Molm13-con_rep1


title: 4_D7


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i507]


title: 7d_SS2_14681.30e [SLX-19435.i702_i511]


title: 7d_SS2_14681.32c [SLX-19435.i703_i503]


title: 3_D7

value: Placebo


title: 7d_SS2_14681.30e [SLX-19435.i702_i510]


title: SS5-AS-SMInput-rep1

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Sequenced reads were trimmed for adaptor sequence using Fastp, and then mapped to hg38. p13. whole genome using HiSat2 version 2.1.0 with defalt parameters.
Transcripts Per Million (TPM) were calculated.
Assembly: hg38. p13.
Supplementary files format and content: TPMs of G3BP1 KD and SG.csv

growth_protocol: SH-SY5Y cells were grown with 5% CO2 at 37°C in culture medium prepared from Advanced DMEM/F-12 supplemented with 10% FBS, 1×GlutaMAX I, and 1×Penicillin-Streptomycin.

extract_protocol:
For KD RNA-seq and SG RNA-seq, total RNAs were isolated using ISOGEN II following the manufacturer’s instructions. For eCLIP-seq, G3BP1- and G3BP2-bound RNAs were isolated using their antibodies as .
For KD and SG RNA-seq, RNA libraries were prepared for sequencing using standard DNBSEQ protocols. For eCLIP-seq, RNA libraries were prepared according to the eCLIP-seq protocol in König et al., 2010.
KD and SG RNA-seq were polyA RNA-Seq, whereas eCLIP-seq was manurally constructed according to the eCLIP-seq protocol in König et al., 2010.

treatment_protocol: SH-SY5Y cells were treated with 50 mM Sodium arsenite for 1 hr.


title: 7d_SS2_14681.32c [SLX-19435.i703_i502]


title: 7d_SS2_14681.30e [SLX-19435.i702_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i507]


title: 3_D0


title: Molm13-shIGF2PB2_rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i507]


title: 7d_SS2_14681.32c [SLX-19435.i703_i505]


title: 5_D0


title: SS5-AS-G3BP2-eCLIP-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i507]


title: SS5-AS-SMInput-rep2


title: 1_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i506]


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i507]


title: 2_D0


title: 7d_SS2_14681.30e [SLX-19435.i702_i507]


title: 7d_SS2_14681.30e [SLX-19435.i702_i506]


title: 11_D4


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i506]


title: 7d_SS2_14681.30e [SLX-19435.i702_i505]


title: SS5-AS-G3BP1-eCLIP-rep1


title: SS5-Ctrl-SMInput-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i506]


title: Normal

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

data_processing:
Count matrices were generated using cellranger
Seurat objects were created using count matrices and the counts were normalized for library size
Seurat objects of normalized counts for all samples were integrated into one combined object
Assembly: hg38
Supplementary files format and content: Tab-delimited text files of raw counts for each sample generated using cellranger

source_name: PBMC

extract_protocol:
Blood samples were diluted 1:1 with phosphate-buffered saline (PBS, Gibco) and layered onto the Ficoll Paque Plus (GE-healthcare) and centrifuged at 400g for 30 min, the buffy layer containing the peripheral blood mononuclear cells (PBMCs) were collected in 1.5mL centrifuge tubes. Cells were first isolated then washed twice in PBS by centrifugation at 10,000g for 4 min. Cell viability was determined using Trypan Blue and found to be greater than 9
Single-cell suspension samples were loaded on the Chromium platform (10X Genomics) for cell barcoding and library preparation was done using the Chromium Single Cell 5’ Reagent kit (10X Genomics) using the manufacturer’s instructions. Briefly, single-cell gel beads in emulsion (GEMs) generated from the Chromium controller were reverse transcribed to produce 10X barcoded cDNA. cDNA was then amplified, and the library generated.
Sequencing was performed on the Illumina NovaSeq6000 platform according to Illumina standard conditions with 10X Genomics recommended read parameters.

value: PBMC

tag: est. conc. of cells

tag: mean reads per cells

tag: fraction reads in cells (%)

tag: fraction of reads mapped to transcriptome (%)


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i506]


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i506]


title: PRO-seq_DKO-rep2

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

data_processing:
library strategy: PRO-seq
Raw PRO-seq reads were trimmed by Trim Galore v0.6.6 with the reads longer than 15 bp were remained. Then ribosomal RNA reads were removed using Bowtie v2.4.4 with “--un-conc-gz”. The remaining reads were aligned to human hg19 and mouse mm10 genome assemblies using Bowtie v2.4.4 with parameters ‘--local --very-sensitive-local --no-unal --no-mixed --no-discordant’.
All unmapped reads, low mapping quality reads (MAPQ < 30), and PCR duplicates were removed using SAMtools v1.12 and MarkDuplicates function of Picard Tools v2.25.5. The scale factor for normalizing was calculated as 1 over the number of reads mapping to spike-in genome (mm10) per million.
Single-base-pair resolution, normalized, stranded read coverage tracks were generated by bamCoverage function of deepTools v3.5.1 with the parameters ‘--Offset 1 --samFlagInclude 82’ and ‘--Offset 1 --samFlagInclude 98’ for the forward and reverse strand, respectively.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: The human DLD-1 cells were grown in McCoy's 5A medium (BasalMedia) supplemented with 10% fetal bovine serum (FBS, Yeasen), 1XPenicillin-Streptomycin (Gibco).

extract_protocol:
Nascent RNA was extracted using TRIzol LS (Ambion) followed by ethanol precipitation.
Reverse transcription was carried out using the 200 U superscript III enzyme (Invitrogen). The reverse transcription products were immediately proceeded to PreCR, test amplification, and full-scale library amplification by using the Q5 DNA polymerase (NEB). The libraries were then sequenced with NovaSeq 6000 platform.

value: Human colorectal cancer cell

value: DKO


title: SS5-Ctrl-SMInput-rep1


title: SS5-AS-G3BP2-eCLIP-rep1


title: SS5-Ctrl-G3BP2-eCLIP-rep1


title: 7d_SS2_14681.30e [SLX-19435.i702_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i506]


title: 7d_SS2_14681.32c [SLX-19435.i701_i510]


title: 7d_SS2_14681.30e [SLX-19435.i702_i502]


title: PRO-seq_DKO-rep1


title: SS5-Ctrl-G3BP2-eCLIP-rep2


title: 1_D0


title: 7d_SS2_14681.32c [SLX-19435.i701_i511]


title: 7d_SS2_14681.32c [SLX-19435.i701_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i506]


title: SS5-Ctrl-G3BP1-eCLIP-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i506]


title: On immunosuppressants with stable graft function at 12 months


title: SS5-AS-G3BP1-eCLIP-rep2


title: KAS-seq_DKO-rep2

data_processing:
library strategy: KAS-seq
Raw reads of KAS-seq were trimmed by Trim Galore v0.6.6. Trimmed reads were aligned to human hg19 and mouse mm10 genomes using Bowtie v2.4.4 with option ‘-X 1000’.
All unmapped reads, low mapping quality reads (MAPQ < 30), and PCR duplicates were removed using SAMtools v1.12 and MarkDuplicates function of Picard Tools v2.25.5. Peaks were called using MACS2 v2.2.7.1 with option ‘nomodel’ and peak annotation was performed with R package ChIPseeker v1.28.3.
The scale factor for normalizing ssDNA signals was calculated as 1 over the number of reads mapping to spike-in genome (mm10) per million as previously described.
Normalized bigwig was generated with bamCoverage function from deepTools v3.5.1 and reads mapped to the ENCODE blacklist regions were removed using bedTools v2.30.0.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
One million of DLD-1 cells were labeled with 2.5 mM N3-kethoxal for 10 minutes at 37 °C. The gDNA was isolated by PureLink genomic DNA mini kit (ThermoFisher Scientific). The extracted gDNA was biotinylated with 1mM DBCO-PEG4-biotin (Sigma-Aldrich) through click cycloaddition reaction. After sonication, the biotinylated gDNA was fragmented into sizes of ~300 bp. Mix the fragments with 10 μl of Dynabeads Myone Streptavidin C1 beads (ThermoFisher Scientific). After incubation and brief washes, resuspend the beads in nuclease-free water at 95 °C for 15 min to facilitate the dissolution of N3-kethoxal-modified gDNA fragments. Next, the DNA fragments were repaired with the phi29 DNA polymerase (NEB) and purified by the VAHTS DNA Clean Beads.
Library preparation was done by using the VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazymes). The library was then sequenced on the NovaSeq 6000 platform.


title: PRO-seq_CTR-rep2

value: CTR


title: 7d_SS2_14681.32c [SLX-19435.i701_i507]


title: PRO-seq_CTR-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i506]


title: SS5-Ctrl-G3BP1-eCLIP-rep1


title: KAS-seq_DKO-rep1


title: 7d_SS2_14681.32c [SLX-19435.i701_i506]


title: 7d_SS2_14681.32c [SLX-19435.i701_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i506]


title: KAS-seq_CTR-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i506]


title: iWAT, mormal, rep2

city: Chengdu

first: mailin

last: gan

state: Sichuan

address: No. 211, Huimin Road, Wenjiang District, Chengdu, Sichuan, China

institute: Sichuan Agricultural University

data_processing:
Raw sequencing data generated form Illumina NextSeq 500 that pass the Illumina chastity filter are used to the following analysis.
Trimmed reads (trimmed 5', 3'-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software
The abundance of tRF & tiRNA is evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). For each tRF & tiRNA, estimated the expression level using the mapped reads number and given an ID. Then the tRF & tiRNA are filtered if CPM less than 20 in all samples.
The CPM value of tRF & tiRNA can be calculated with the formula:CPM =10^6Count/N
Assembly: tRNA sequences of cytoplasmic were downloaded from GtRNAdb. tRNA sequences of mitochondrial were predicted with tRNAscan-SE software.
Supplementary files format and content: An excel file contains the COUNT and CPM values of tsRNAs for each sample.

source_name: iWAT

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (TaKaRa, Japan) according to the manufacturer's instructions.Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.The libraries were denatured and diluted to a loading volume of 1.3ml and loading concentration of 1.8pM.

value: iWAT


title: 7d_SS2_14681.32c [SLX-19435.i701_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i506]


title: iWAT, mormal, rep1


title: KAS-seq_CTR-rep1


title: ChIP-SSB1_WT-rep2

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6 in paired-end mode.
Trimmed reads were aligned to human hg19 and mouse mm10 genome assemblies using Bowtie v2.4.4 with default parameters.
All unmapped reads, low mapping quality reads (MAPQ < 30), and PCR duplicates were removed using SAMtools v1.12 and MarkDuplicates function of Picard Tools v2.25.5.
Peaks were called using MACS2 v2.2.7.1 with option ‘nomodel’ and peak annotation was performed with R package ChIPseeker v1.28.3.
Normalized bigwig was generated with bamCoverage function from deepTools v3.5.1 using scale factors calculated according to the method in manuscript. Reads mapped to the ENCODE blacklist regions were removed using bedTools v2.30.0
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were crosslinked with 1% formaldehyde at room temperature for 10 min. After quenching and cell lysis, chromatin was sonicated (Qsonica) to appropriate fragment (200-700bp). After sonication, the lysate was centrifuged at maximal speed for 15 min to collect the supernatant and mixed with 20% of lysate from mouse embryonic fibroblast (MEF) cells processed identically as spike-in for normalization.
The DNA samples were purified using Phenol/Chloroform DNA extraction method. Library preparation using the VAHTS Universal Plus DNA Library Prep Kit for Illumina.

tag: chip antibody


title: 7d_SS2_14681.32c [SLX-19435.i701_i502]


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i505]


title: eWAT, mormal, rep3

source_name: eWAT

value: eWAT


title: eWAT, mormal, rep2


title: ChIP-SSB1_WT-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i505]


title: graft of mature rat recipients, rep2

city: Chongqing

first: Chengjun

last: Yu

address: No.136, Zhongshan 2nd Road, Yuzhong District, Chongqing City, China

institute: Children’s Hospital of Chongqing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

tag: group

value: mature

value: kidney

value: WT (common)

value: kidney transplantation


title: eWAT, mormal, rep1


title: graft of immature rat recipients, rep3

value: immature


title: BAT, mormal, rep3

source_name: BAT

value: BAT


title: ChIP-SSB1_RNaseH1-DMSO


title: graft of mature rat recipients, rep1


title: graft of mature rat recipients, rep3


title: ChIP-SSB1_RNaseH1-DOX


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i505]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: ChIP-SSB1_DKO-rep2


title: iWAT, mormal, rep3


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i505]


title: graft of immature rat recipients, rep2


title: ChIP-SSB1_DKO-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i505]


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i505]


title: ChIP-SSB1_CTR-rep2


title: BAT, mormal, rep2


title: BAT, mormal, rep1


title: Lung of Donor 2, after 10h EVLP

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

description: 10x Genomics

data_processing:
The reads were aligned with Cell Ranger v3.1.0 on the human genome using the GRCh38 assembly and the GTF file downloaded from Ensembl release 101. The 6 samples (3 times points, 2 donors) were pre-processed and normalized together using Seurat v4.0.0. Cells expressing less than 1000 genes were removed. Dead or lysed cells were excluded by removing cells with a percentage of mitochondrial genes above a threshold calculated using the Scater package (median percentage of mitochondrial genes across all individual cells + 3 median absolute deviations)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung biopsies

extract_protocol:
Lung tissue from biopsies kept in HypoThermosol was minced finely with scissors, placed in Multi Tissue Dissociation Kit 1 solution as recommended by the manufacturer (Miltenyi Biotec, Bergisch Gladbach, Germany), and incubated at 37°C for 45 min in gentle agitation. The minced preparation was crushed on nylon mesh (1 mm) and filtered through successive nylon filters (500 µm, 100 µm, 40 µm). The cell suspension was washed in PBS (470 g, 15 min), processed to erythrocyte lysis, resuspended in RPMI + 2 % FCS, filtered twice on 40 µm and counted by 3 independent measurements with a counting Malassez chamber slide. Trypan blue staining indicated that over 90% cells were viable.
Fresh single-cell suspensions (2 x 104 cells) were loaded onto the 10x Chromium to produce sequencing libraries, which were processed according to methods provided by 10x Genomics (v3 Chemistry). Cell cDNA was sequenced using the Truseq Illumina Stranded protocol and the Illumina NextSeq 550 sequencing machine.

treatment_protocol: Donor lung retrieval was carried out according to current clinical practice using Perfadex (Vitrolife, Göteborg, Sweden) flush preservation. After transportation at 4°C, lungs were processed to EVLP that was conducted according to the Toronto protocol for 10 h at the Foch Hospital (Suresnes, France). The circuit was filled with 1.5 L of Steen solution supplemented with 1 mg methylprednisolone, 1.5 mg cefuroxime, and 15000 UI heparin. A flow rate at 40% of the theoretical cardiac output was applied at normothermia. Steen perfusate (200 ml) was replaced with fresh one every 2 h. Lung biopsies (2 g each) were taken from similar lung zones from the upper lobes (wedges)  just before EVLP (0 h), after 4 and 10 h EVLP, cut in 4 pieces, placed in 10 ml HypoThermosol® (STEMCELL Technologies, Vancouver, Canada) and kept on ice for about 24 h. This process was shown to maintain lung tissue stability up to 72 h for scRNA-seq.

value: lung biopsies

value: 10h EVLP

value: Female

tag: age

value: 84 yr

tag: cold ischemia_time


title: ChIP-SSB1_CTR-rep1

value: Human colorectal cancer cell


title: Choroid plexus HFD 5

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

data_processing:
QC quality control and adapter removal was done by Novogene (UK) Company Limited.
Mapping to reference genome (rattus norvegicus Rnor_6.0.104) using STAR (v. 2.7.2a) (--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM)
Abundance quantified by RSEM (v. 1.3.3) (--bam --paired-end --forward-prob 0)
Assembly: Rnor_6.0 (rn6) v.104
Supplementary files format and content: tab-delimited text files for gene abundance for each samples in TPM and FPKM

source_name: Choroid plexus

extract_protocol:
Extraction was performed by Novogene (UK) Company Limited.
Done by Novogene (UK) Company using NEB Next® Ultra™ RNA Library Prep Kit, and sequenced on Illumina NovaSeq 6000, paired-end 150 bp, 12Gb output.

tag: strain

value: Wistar

value: 27 weeks

tag: Sex

tag: tissue

value: Choroid plexus

tag: animals pooled

value: High fat diet


title: ChIP-polII-pSer5_sgCtr-rep2

tag: cell line

tag: cell type

tag: genotype

value: sgCtr

tag: treatment


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i505]

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i505]


title: graft of immature rat recipients, rep1

value: kidney

value: WT (common)


title: Choroid plexus HFD 3


title: ChIP-polII-pSer5_sgCtr-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i505]


title: ChIP-polII-pSer5_INTS2KO-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i505]


title: Choroid plexus HFD 1


title: Lung of Donor 1, after 10h EVLP

description: 10x Genomics

tag: gender

value: Male

value: 56 yr


title: Lung of Donor 1, after 4h EVLP

description: 10x Genomics

value: 4h EVLP


title: Lung of Donor 2, before EVLP

description: 10x Genomics

value: no treatment


title: Choroid plexus HFD 2


title: ChIP-polII-pSer5_INTS2KO-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i505]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: Choroid plexus control 5

value: Female

value: Nutrient source-matched control diet


title: MC38 tumor, scRNAseq

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: barcodes.tsv.gz

data_processing:
The libraries were subjected to high-throughput sequencing on an Illumina Hiseq X Ten PE150 platform, and 150-bp paired-end reads were generated. Library QC and sequencing were performed by SHBIO. Single-cell RNA-seq data were processed with cellranger count (10 × Genomics CellRanger based on the mouse reference genome GRCm38 (mm10). Digital gene expression matrices were analyzed in R, using the Seurat package. Cells were filtered by the number of Features (less than 500 genes) and percentage of mitochondrial genes (“percent.mt” lower than 5%), yielding a total of 9618 cells. Data normalization and scaling and were processed with the default parameters using Seurat functions NormalizeData and ScaleData. Principal component analysis (PCA) and UMAP dimension reduction with the top 20 principal components were performed. A nearest-neighbor graph using the 20 dimensions of the PCA reduction was calculated using FindNeighbors, followed by clustering using FindClusters with a resolution of 0.6. Candidate marker genes for each cell cluster were identified by the FindAllMarkers function. For each cluster of cells, group-specific differentially expressed genes were identified using the Wilcoxon Rank Sum test as implemented in FindAllMarkers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Solid tumors from mice were excised and mechanically dissociated into single cells using Tumor Dissociation Kit (SHBio). Single cells were captured in the 10 × Genomics Chromium Single Cell  Solution
RNA-seq libraries were prepared following the manufacturer’s protocol (10 × Genomics).

value: tumor

value: 6-8 weeks old

value: total RNA


title: ChIP-polII-pSer5_DKO-rep2

value: Human colorectal cancer cell

value: DKO


title: Lung of Donor 1, before EVLP

description: 10x Genomics

value: lung biopsies


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i503]


title: Choroid plexus control 4

value: Wistar

value: 27 weeks

value: Choroid plexus


title: ChIP-polII-pSer5_DKO-rep1


title: Choroid plexus control 3


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i503]


title: ChIP-polII-pSer5_CTR-rep1

value: CTR


title: Choroid plexus control 1


title: Choroid plexus control 2


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i503]


title: ChIP-polII-NTD_sgCtr-rep1

value: sgCtr

value: polII-NTD


title: ChIP-polII-NTD_sgCtr-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i503]

value: bone marrow


title: ChIP-polII-NTD_INTS2KO-rep1


title: LPS tolerant WT macrophages 1

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

description: DEGs Tol

data_processing:
Sequencing reads were mapped against the Mus musculus reference genome GRCm39. Reads were mapped and aligned with HISAT2. Reads were counted by Rsubread. Subsequently, DEGs were compared and analyzed in R version 4.0.3 using the package edgeR. The analyses were conducted from triplicate samples. Genes were considered differentially expressed when the log2 fold change was < -0.75 or > 0.75 (representing down- or upregulation, respectively) and the p-value was < 0.05.
Assembly: GRCm39
Supplementary files format and content: Excel file of the DEGs list for each sample

source_name: Bone marrow-derived macrophages

growth_protocol: BMDMs were harvested from the femurs and tibias of Eedfl/fl; LysM-Cre+/- (Eed KO), Ezh2fl/fl; LysM-Cre+/- (Ezh2 KO), and its littermate control mice by flushing. Bone marrow cells were cultured for 7-10 days in Dulbecco's modified Eagle's medium (DMEM, HyClone,Logan, UT, USA) supplemented with 10% (v/v) fetal bovine serum (Gibco, Grand Island, NY, USA), 1% (w/v) sodium pyruvate, 1% (w/v) HEPES, 100 U/ml pen/strep, 20% L929 cell conditioned media and 5% horse serum.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and reverse transcribed using RevertAid reverse transcriptase (Thermo Fisher Scientific) following the manufacturer's protocol.
cDNA libraries were prepared using a TruSeq stranded mRNA library preparation kit (Illumina, San Diego, CA, USA). The quantity and quality of the libraries were determined using a 2100 Bioanalyzer. Sequencing was carried out on a HiSeq (2 × 150 bp paired end reads) at the Omics Sciences and Bioinformatics Center (Chulalongkorn University, Bangkok, Thailand).

treatment_protocol: BMDMs were primed with Salmonella spp lipopolysaccharide (LPS; Sigma Aldrich, St. Louis, MO, USA) at 100 ng/ml for 24 h. After the priming, the medium was replaced with fresh DMEM complete medium and the cells were rested for 48 h. The resting step was followed by LPS (10 ng/ml) stimulation for the indicated times.

value: Bone marrow-derived macrophages

value: marophages

value: LPS/LPS stimulation


title: LPS tolerant EED KO macrophages 2

description: DEGs Tol

value: EED KO


title: LPS tolerant WT macrophages 4

description: DEGs Tol

value: WT


title: LPS tolerant EED KO macrophages 1

description: DEGs Tol


title: LPS primed EED KO macrophages 3

value: LPS stimulation


title: LPS tolerant WT macrophages 3

description: DEGs Tol


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i503]

first: Bertie

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

source_name: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive


title: ChIP-polII-NTD_INTS2KO-rep2

value: Human colorectal cancer cell


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i503]


title: LPS tolerant EED KO macrophages 3

description: DEGs Tol


title: LPS primed EED KO macrophages 1


title: LPS primed EED KO macrophages 2


title: ChIP-polII-pSer5_CTR-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i503]


title: ChIP-polII-NTD_DKO-rep1

value: DKO


title: LPS primed WT macrophages 4


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i503]


title: LPS primed WT macrophages 3


title: ChIP-polII-NTD_CTR-rep1


title: ChIP-INTS5_WT-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i503]


title: ChIP-polII-NTD_DKO-rep2


title: LPS primed WT macrophages 1


title: 257236329287-6

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

source_name: siControl#2 + TGF_B

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen - miRNeasy

value: Normal lung fibroblasts (NHLF)

tag: amount in (ug)

tag: rin number

tag: transfection

value: siControl#2 + TGF


title: 257236329287-7

source_name: PRRX1 siRNA#1 + TGF_B

value: PRRX1 siRNA#1 + TGF


title: 257236329287-5

source_name: PRRX1 siRNA#2_B

value: PRRX1 siRNA#2


title: 257236329287-8

source_name: PRRX1 siRNA#2 + TGF_B

value: PRRX1 siRNA#2 + TGF


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i503]

last: Gottgens


title: 257236329287-4

source_name: siControl#1 + TGF_B

value: siControl#1 + TGF


title: 257236329287-3

source_name: PRRX1 siRNA#1_B

value: PRRX1 siRNA#1


title: 257236329287-2


title: Unstim EED KO macrophages3

value: Untreated


title: Unstim EED KO macrophages2

value: Bone marrow-derived macrophages


title: ChIP-INTS5_DKO-rep1


title: ChIP-INTS5_DKO-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i727_i502]

value: bone marrow


title: 2w4w_SS2_146818.66h [SLX-20544.i728_i502]


title: ChIP-INTS5_WT-rep1


title: Unstim EED KO macrophages1

value: marophages


title: 2w4w_SS2_146818.66h [SLX-20544.i729_i502]


title: Unstim WT macrophages 4


title: ChIP-INTS5_CTR-rep2

value: CTR


title: ChIP-INTS3_WT-rep2

value: WT


title: 2w4w_SS2_146818.66h [SLX-20544.i724_i502]


title: 257236329286-8

source_name: PRRX1 siRNA#2 + TGF_A


title: 2w4w_SS2_146818.66h [SLX-20544.i726_i502]


title: Unstim WT macrophages 3


title: ChIP-INTS3_WT-rep1


title: Unstim WT macrophages 1


title: 257236329287-1


title: ChIP-INTS5_CTR-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i722_i502]


title: 257236329286-7

source_name: PRRX1 siRNA#1 + TGF_A


title: 257236329286-5

source_name: siControl#1 + TGF_A


title: 257236329286-4

source_name: PRRX1 siRNA#2_A


title: ChIP-INTS3_RNaseH1-DMSO


title: ChIP-INTS3_RNaseH1-DOX


title: 2w4w_SS2_146818.66h [SLX-20544.i721_i502]


title: 257236329286-6

source_name: siControl#2 + TGF_A


title: SST WT cells - Rep 4

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: Somatosensory cortex S1

extract_protocol:
Animals were placed un light sediation and perfused with ice cold ACSF, brains were harvested, S1 cortex was dissected and subjected to light pronase digestion prior to  mechanical dissociation with flame polished pipettes. Samples were filtered and subjected to FACS to isolate SST interneurons from the cortex.
The NYU Genome Technology Center constructed the libraries followed their standard protocol

treatment_protocol: Samples with 'ECS+' were extracted from animals who had been subjected to electroconvulsive shock, permitting in vivo activity-dependent changes within select neurons

value: SST interneuron

value: Swiss Webster+C57BL/6+C57BL/6J-A


title: Qingyu pig Subcutaneous adipose tissue, lean, rep2

organism: Sus scrofa

source_name: Subcutaneous adipose tissue sample

value: Subcutaneous adipose tissue sample


title: ChIP-INTS3_DKO-rep2

value: Human colorectal cancer cell

value: DKO


title: 257236329286-3

source_name: PRRX1 siRNA#1_A

value: Normal lung fibroblasts (NHLF)


title: SST WT cells - Rep3


title: 2w4w_SS2_146818.66h [SLX-20544.i723_i502]

city: Cambridge

value: Lin-negative, (cKit OR Sca1)-positive


title: ChIP-INTS3_DKO-rep1


title: ECS+ SST conditionalKO Rbfox1 - rep4

value: conditionalKO Rbfox1


title: Qingyu pig Subcutaneous adipose tissue, lean, rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i720_i502]


title: ChIP-INTS3_CTR-rep2


title: ECS+ SST conditionalKO Rbfox1 - rep3


title: 2w4w_SS2_146818.66h [SLX-20544.i718_i502]


title: Qingyu pig Subcutaneous adipose tissue, lean, rep3


title: 2w4w_SS2_146818.66h [SLX-20544.i716_i502]


title: 2w4w_SS2_146818.66h [SLX-20544.i719_i502]


title: Qingyu pig omental adipose tissue, lean, rep3

source_name: Omental adipose tissue sample

value: Omental adipose tissue sample


title: SST WT cells - Rep 2


title: 257236329286-1


title: 257236329286-2


title: ECS+ SST conditionalKO Rbfox1 - rep2


title: Lung of Donor 2, after 4h EVLP

description: 10x Genomics

source_name: lung biopsies

value: lung biopsies

value: 4h EVLP

value: Female

value: 84 yr


title: ChIP-Input_sgCtr-rep2

value: sgCtr

value: Input


title: ECS+ SST conditionalKO Rbfox1 - rep1


title: Qingyu pig omental adipose tissue, lean, rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i511]

source_name: bone marrow

value: bone marrow


title: Qingyu pig omental adipose tissue, lean, rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i511]

value: WT


title: Yorkshire pig Subcutaneous adipose tissue, lean, rep3


title: ECS+SST WT cells - Rep 6

value: SST interneuron


title: SST WT cells - Rep 5

value: Swiss Webster+C57BL/6+C57BL/6J-A


title: ChIP-Input_RNaseH1-DOX

value: CTR


title: ChIP-Input_sgCtr-rep1

value: Human colorectal cancer cell


title: ChIP-INTS3_CTR-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i511]


title: ECS+SST WT cells - Rep 5


title: ChIP-Input_RNaseH1-DMSO


title: Yorkshire pig Subcutaneous adipose tissue, lean, rep2

value: Subcutaneous adipose tissue sample


title: ChIP-Input_INTS2KO-rep2


title: ECS+SST WT cells - Rep 4


title: Yorkshire pig Subcutaneous adipose tissue, lean, rep1


title: ChIP-Input_INTS2KO-rep1


title: ECS+SST WT cells - Rep 3


title: Yorkshire pig omental adipose tissue, lean, rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i511]


title: ChIP-Input_DKO-rep2

value: DKO


title: Yorkshire pig omental adipose tissue, lean, rep3


title: ECS+SST WT cells - Rep 2


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i511]

value: Lin-negative, (cKit OR Sca1)-positive