title: SF3B1 K700E WT Replicate 3

city: Boston

first: Claudia

middle: A

last: Mimoso

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

data_processing:
All custom scripts described herein are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts). Dual, 6nt Unique Molecular Identifiers (UMIs) were extracted from read pairs using UMI-tools. Read pairs were trimmed using cutadapt 1.14 to remove adapter sequences (-O 1 --match-read-wildcards -m 26). The UMI length was trimmed off the end of both reads to prevent read-through into the mate’s UMI, which will happen for shorter fragments. An additional nucleotide was removed from the end of read 1 (R1), using seqtk trimfq (https://github.com/lh3/seqtk), to preserve a single mate orientation during alignment.
The paired end reads were then mapped to a combined genome index, including both the spike (dm6) and primary (hg38) genomes, using bowtie2. Properly paired reads were retained. These read pairs were then separated based on the genome (i.e. spike-in vs primary) to which they mapped, and both these spike and primary reads were independently deduplicated, again using UMI-tools.
Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl). We note that this script counts each read once at the exact 3’ end of the nascent RNA. Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution.
BedGraphs were normalized using the normalize_bedGraph script. We observed a consistent increase in reads mapping to dm6 after introducing the SF3B1K700E mutation in hESCs (Average percentage of reads mapping to dm6: WT hESCs = 1.6%, SF3B1K700E hESCs = 2.1%), indicating a global decrease in transcription in SF3B1K700E mutant hESCs. As a result, the PRO-seq libraries were spike-in normalized. To generate the spike-in normalization factors per replicate, the number of reads mapping to dm6 for each sample was divided by the sample with the fewest number of reads mapping to dm6 (WT Replicate #1).
bedgraphs2stdBedgraph was used to generate combined replicate bedGraphs by summing counts per nucleotide across replicates for each condition. BedGraphs were converted to the bigWig format for visualization.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: PRO-seq

source_name: human embryonic stem cells

growth_protocol: hESCs were cultured using the mTeSR1TM1 kit (STEMCELL technology) and 1% penicillin-streptomycin (Sigma) on Matrigel-coated (CORNING) tissue culture plates and incubated at 37°C in humidified 5% (vol/vol) CO2.

extract_protocol:
Cells were permeabilized as in Mimoso and Goldman 2023; run-ons were performed with biotinylated NTPs and then purified.
Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.

value: human embryonic stem cells

value: H9 ES cells (WA09)

value: SF3B1 K700E


title: SF3B1 WT Replicate 3

status: Public on Oct 16 2025

type: SRA

state: MA

country: USA

library_source: transcriptomic

molecule: nuclear RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: SF3B1 WT


title: SF3B1 K700E WT Replicate 2


title: mEER_RT_Xevinapant_2

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

country: United Kingdom

institute: The Institute of Cancer Research

description: Library name: mEER_RT_Xevinapant_2

data_processing:
Salmon quant v1.10.1 was used for transcript-level quantification against the GRCm39 mouse reference (Ensembl release 103). Transcript-level abundance estimates were aggregated to gene-level using tximport v1.34 R package. Differential gene expression analysis was performed using DESeq2 (pseudogenes were excluded and only genes with more than 10 reads in at least 5 samples were kept in the analysis).
Assembly: GRCm39 mouse reference (Ensembl release 103)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: tumour

growth_protocol: All procedures involving animals were approved by the Animal Ethics Committee at The Institute of Cancer Research in accordance with National Home Office Regulations under the Animals (Scientific Procedures) Act 1986. 8- to 14-week-old females C57BL/6 wild-type (Charles River) were inoculated subcutaneously in the right flank with 1 × 10^6 mEER or 4 × 10^6 MOC1 cells suspended in 100 uL PBS under isoflurane anaesthesia.

extract_protocol:
RNA from tumours was extracted and purified from tumours using the RNeasy Plus Mini Kit (Qiagen, 74134) with QIAshredder (Qiagen, 79656) according to manufacturer’s protocol and stored at -80 °C.
Library preparation and sequencing were performed by Genewiz, Germany. Library preparation was strand-specific with polyA selection, with 2×150bp sequencing at 20 million paired-end reads per sample performed on an Illumina NovaSeq.

treatment_protocol: Mouse tumours were harvested 14 days after the last radiation dose, on the last day of vehicle/xevinapant treatment and snap frozen on dry ice. Tumour tissue was homogenised in 1 mL of Buffer RLT Plus (Qiagen, 1053393) with 10 uL beta-mercaptoethanol (Gibco, 21985023) within CK28 hard tissue homogenising 2 mL tubes (Precellys, 10144-494) using the Precellys Evolution Homogeniser. For all studies, mice were randomised prior to therapy for comparable tumour volumes between cohorts. In vivo treatments were commenced when tumour volumes reached approximately 20-50 mm3.  Mice were immobilised for irradiation via a single injection of ketamine 100 mg/kg (Ketavet) and 16 mg/kg xylazine (Rompun) dosed intraperitoneally (i.p.). Mice were irradiated in the prone position under lead shielding with a 15-mm diameter aperture aligned over the tumour. A total of 6 or 8 Gy × 3 fractions was delivered at a dose rate of 1.62 Gy/minute using an AGO 250 kV X-ray machine (AGO, 20090606) with dose measurement performed with a Farmer Chamber and Unidos-E Dosemeter (PTW). Following irradiation, cages were placed on heat mats and mice were monitored until full recovery.  Xevinapant powder for in vivo treatments was provided by the healthcare business of Merck KGaA, Darmstadt, Germany, and dissolved in vehicle formulated with 0.6% Malic Acid (Sigma Aldrich, 240176) (w/v) in 85 mM Sodium Acetate buffer (Calbiochem, 7610), pH 4.5. Xevinapant was administered at 100 mg/kg via oral gavage administered for five consecutive days followed by two days off, repeated twice over the course of 3 weeks.  Cisplatin powder (Sigma Aldrich, P4394) powder was diluted in 0.9% sodium chloride on the day of use and delivered by i.p. injection one hour prior to radiotherapy (if given).

value: tumour

value: mEER

value: WT

tag: treatment

value: Xevinapant/Radiotherapy


title: mEER_RT_Xevinapant_1

description: Library name: mEER_RT_Xevinapant_1


title: mEER_Xevinapant_5

description: Library name: mEER_Xevinapant_5

value: Xevinapant/Vehicle


title: SF3B1 WT Replicate 2


title: mEER_Xevinapant_4

description: Library name: mEER_Xevinapant_4


title: mEER_Xevinapant_1

description: Library name: mEER_Xevinapant_1


title: SF3B1 WT Replicate 1


title: mEER_CRT_5

description: Library name: mEER_CRT_5

value: Chemoradiotherapy


title: SF3B1 K700E WT Replicate 1


title: RT 1

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

institute: University of Oxford

data_processing:
Data processing and sequence alignment were performedbyNovogene UK. The sequencing reads/raw reads were filtered 1) to remove reads with adapter contamination, 2) to remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) and 3) to remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read. Alignments were performed with HISAT2 to the reference.
Gene expression was quantifiedbyNovogene UK. The abundance of transcripts reflects gene expression level directly. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) estimated gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.
Assembly: Paired-end reads were mapped to GRCh38 genome by Novogene UK.
Supplementary files format and content: fpkm

molecule: total RNA

growth_protocol: MDA-MB-231 cells were purchased from ATCC and maintained at 37 °C in a humidified incubator with 5% CO2 in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (F7524, Sigma Aldrich) and 1% antibiotic/antimycotic (15240-062, Gibco). Cells were routinely tested for mycoplasma.

extract_protocol:
RNA samples were extracted from MDA-MB-231 cells 24 hours after being irradiated with 10Gy in a 137Cs irradiator. RNA was extracted using the RNeasy Mini Kit (74104, Qiagen) following the manufacturer’s protocol. RNA concentration was measured by Qubit.
Library construction was performedbyNovogene UK using polyA enrichment library preparation procedure.

treatment_protocol: Cells were exposed to 137Cs sealed source irradiator (GSR D1, Gamma-Service Medical, Leipzig, Germany; dose rate of 1.7 Gy/min) either at 0Gy (control) or 10 Gy.

value: Breast adenocarcinoma

value: 10Gy radiation


title: RT 2


title: mEER_RT_4

description: Library name: mEER_RT_4

value: Radiotherapy


title: mEER_CRT_3

description: Library name: mEER_CRT_3


title: mEER_RT_5

description: Library name: mEER_RT_5


title: control 2

value: control


title: control 3


title: mEER_CRT_2

description: Library name: mEER_CRT_2


title: mEER_RT_2

description: Library name: mEER_RT_2


title: mEER_RT_3

description: Library name: mEER_RT_3


title: mEER_RT_1

description: Library name: mEER_RT_1


title: mEER_Veh_5

description: Library name: mEER_Veh_5

value: Vehicle


title: mEER_Xevinapant_3

description: Library name: mEER_Xevinapant_3


title: mEER_Xevinapant_2

description: Library name: mEER_Xevinapant_2


title: RT 3


title: mEER_CRT_4

description: Library name: mEER_CRT_4


title: mEER_Veh_3

description: Library name: mEER_Veh_3


title: mEER_CRT_1

description: Library name: mEER_CRT_1


title: control 1


title: Primer1_mut-_siISG20L2_rep4

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

description:
Library name: Dataset59
Primer 1

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Zuber et al. 2018 composed of scripts using python (v3), biopython (v1.79) and regex (v2022.9.13) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_3ETS_ITS1)
cf the associated publication
Assembly: Human ribosomal DNA complete repeating unit
Supplementary files format and content: One processed data file per primer is given for total and for nuclear fraction. They include the processed data for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID),  RNA name (Target), the 15N random sequence used for deduplication  (Random), 3' end position (Position), Encoded sequence (Encoded_sequence ), tail sequence (Modification), length of the tail (Modification_size),  a tag (Type) indicating the category of the tail, the barcode, the run number (Run), the genotype (Sample) and the biological replicate (Rep).

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% foetal calf serum and 1x sodium pyruvate at 37°C in the presence of 5% CO2.

extract_protocol:
For total RNA isolation, 10-15 × 106 HeLa cells were collected by centrifugation for 5 min at 300 g and 4°C. After rinsing with 10 ml cold PBS, each pellet was thoroughly mixed with 1 ml TRI reagent and extracted following the manufacturer’s instructions. The upper aqueous phase was further purified by phenol/chloroform/isoamyl alcohol (25:24:1) extractions prior to isopropanol precipitation. Quantifications were performed at 260 nm with an Implen NP80 spectrophotometer.
3'RACE-seq, the protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

treatment_protocol: To knock down expression of the corresponding human protein genes, each siRNA duplex (Eurogentec, Seraing, Belgium; listed in Supplementary Table 1 of the associated paper) was added at a final concentration of 500 nM to 200 µl of cell suspension (50 × 106 cells/ml diluted in Na phosphate buffer, pH 7.25, containing 250 mM sucrose and 1 mM MgCl2). Alternatively, batches of several siRNA duplexes (500 nM each) were added as mentioned in Figure legends. After electroporation at 240 volts, cells were plated and collected 48 hours later. Cells were then electroporated a second time in the same conditions and collected 2 days later. Control cells were electro-transformed with a scramble siRNA (Eurogentec).

value: HeLa cells

value: mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: mEER_Veh_4

description: Library name: mEER_Veh_4


title: mEER_Veh_2

description: Library name: mEER_Veh_2


title: Primer1_mut-_siISG20L2_rep3

description:
Library name: Dataset58
Primer 1


title: Primer1_siURB1_rep2, Primer3__wt+_siISG20L2_rep2

description:
Library name: Dataset56
Primer 1 and 3

value: siURB1, wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: DC-10_ donor 4

type: RNA

city: Nantes

first: Aurelie

last: Moreau

address: 30 bd Jean Monnet

institute: INSERM U1064

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: blood monocytes

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: ATDCs were differentiated following a 6 day-culture of monocytes in AIMV medium supplemented with recombinant human GM-CSF at 100U/ml. MoDC were differentiated following a 6 day-culture of monocytes in IMDM medium supplemented with 10% FBS, 1000U/ml recombinant human GM-CSF and 1000U/ml recombinant human IL-4. DC-10 were obtained following a 7 day-culture of monocytes in RPMI 1640 medium supplemented with 10% FCS with recombinant human IL-4 (10ng/mL), recombinant human GM-CSF (100ng/mL) and recombinant human IL-10 (10ng/ml)

extract_protocol: Total RNA was isolated using RNeasy Plus kits (Qiagen) as previously described (Riquelme, P et al. Mol Ther., 2013).

value: whole blood

value: IL-10 induced dendritic cells (DC-10)

tag: gender

value: male

tag: age


title: MOC1_CRT_Xevinapant_5

description: Library name: MOC1_CRT_Xevinapant_5

value: tumour

value: Xevinapant/Chemoradiotherapy


title: DC-10_ donor 6


title: DC-10_ donor 1


title: MOC1_CRT_Xevinapant_4

description: Library name: MOC1_CRT_Xevinapant_4

value: WT


title: Primer1_siURB1_rep3,Primer3_control_rep2

description:
Library name: Dataset55
Primer 1 and 3


title: mEER_Veh_1

description: Library name: mEER_Veh_1

value: mEER


title: Primer1_wt-_siISG20L2_rep2

description:
Library name: Dataset54
Primer 1

value: wt-ISG20L2-Flag cells (- DOX) + siISG20L2-4, control cells (- DOX)


title: DC-10_ donor 5


title: DC-10_ donor 3


title: Primer1_wt+_siISG20L2_rep4

description:
Library name: Dataset53
Primer 1

value: wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4, control cells (- DOX)


title: Primer1_siRPL3_rep1

description:
Library name: Dataset60
Primer 1


title: MOC1_CRT_Xevinapant_2

description: Library name: MOC1_CRT_Xevinapant_2


title: Primer1_mut+_siISG20L2_rep2,Primer5_mut-_siISG20L2_rep2

description:
Library name: Dataset51
Primer 1 and 5

value: mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4, mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: MOC1_CRT_Xevinapant_1

description: Library name: MOC1_CRT_Xevinapant_1


title: Primer1_siDDX51_rep2,Primer3_control_rep4

description:
Library name: Dataset57
Primer 1 and 3

value: siDDX51, control cells (- DOX)


title: MOC1_RT_Xevinapant_5

description: Library name: MOC1_RT_Xevinapant_5

value: Xevinapant/Radiotherapy


title: Primer1_control_rep_3,Primer5_mut-_siISG20L2_rep1

description:
Library name: Dataset50
Primer 1 and 5

value: control cells (- DOX) + siISG20L2-4,  mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: MOC1_RT_Xevinapant_4

description: Library name: MOC1_RT_Xevinapant_4


title: Primer1_mut+_siISG20L2_rep4,Primer3_wt+_siISG20L2_rep1

description:
Library name: Dataset49
Primer 1 and 3

value: mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4, wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: MOC1_RT_Xevinapant_3

description: Library name: MOC1_RT_Xevinapant_3


title: Primer1_wt-_siISG20L2_rep1,Primer5_wt+_siISG20L2_rep3

description:
Library name: Dataset48
Primer 1 and 5

value: HeLa cells

value: wt-ISG20L2-Flag cells (- DOX) + siISG20L2-4, wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: MOC1_RT_Xevinapant_1

description: Library name: MOC1_RT_Xevinapant_1


title: DC-10_ donor 2


title: MOC1_RT_Xevinapant_2

description: Library name: MOC1_RT_Xevinapant_2


title: MOC1_Xevinapant_5

description: Library name: MOC1_Xevinapant_5

value: Xevinapant/Vehicle


title: MOC1_CRT_Xevinapant_3

description: Library name: MOC1_CRT_Xevinapant_3


title: Primer1_siISG20L2_rep1,Primer5_mut+_siISG20L2_rep3

description:
Library name: Dataset45
Primer 1 and 5

value: control cells (- DOX) + siISG20L2-4, mut-ISG20L2-Flag cells (+ DOX)


title: MOC1_Xevinapant_2

description: Library name: MOC1_Xevinapant_2


title: MOC1_Xevinapant_3

description: Library name: MOC1_Xevinapant_3


title: MOC1_Xevinapant_4

description: Library name: MOC1_Xevinapant_4


title: Primer1_wt+_siISG20L2_rep1, Primer5_wt+_siISG20L2_rep1

description:
Library name: Dataset46
Primer 1 and 5

value: wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: MOC1_Xevinapant_1

description: Library name: MOC1_Xevinapant_1


title: Primer1_mut+_siISG20L2_rep1, Primer5_mut+_siISG20L2_rep2

description:
Library name: Dataset44
Primer 1 and 5

value: mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Primer1_mut-_siISG20L2_rep2,Primer5_mut-_siISG20L2_rep3

description:
Library name: Dataset52
Primer 1 and 5

value: mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: Primer1_wt+_siISG20L2_rep3,Primer5_control_rep3

description:
Library name: Dataset42
Primer 1 and 5


title: Primer1_siDXX51_rep1,Primer5_control_rep2

description:
Library name: Dataset41
Primer 1 and 5


title: Primer1_mut-_siISG20L2_rep1,Primer5_wt+_siISG20L2_rep2

description:
Library name: Dataset47
Primer 1 and 5

value: mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4, wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Primer1_control_rep2,Primer5_control_rep1

description:
Library name: Dataset40
Primer 1 and 5

value: control cells (- DOX)


title: Primer1_control_rep1

description:
Library name: Dataset34
Primer 1


title: Primer1_siRPL26_rep2

description:
Library name: Dataset38
Primer 1


title: MOC1_CRT_1

description: Library name: MOC1_CRT_1

value: tumour

value: WT

value: Chemoradiotherapy


title: Primer1_siRPL3_rep2

description:
Library name: Dataset37
Primer 1


title: MOC1_RT_5

description: Library name: MOC1_RT_5

value: Radiotherapy


title: Primer1_wt+_siISG20L2_rep2

description:
Library name: Dataset36
Primer 1


title: Primer1_siURB1_rep1

description:
Library name: Dataset35
Primer 1


title: Primer1_siRPL26_rep1

description:
Library name: Dataset33
Primer 1


title: MOC1_CRT_2

description: Library name: MOC1_CRT_2


title: MOC1_CRT_3

description: Library name: MOC1_CRT_3


title: MOC1_RT_4

description: Library name: MOC1_RT_4


title: MOC1_Veh_3

description: Library name: MOC1_Veh_3

value: Vehicle


title: Primer1_control_rep4,Primer3_control_rep1

description:
Library name: Dataset32
Primer 1 and 3


title: Primer1_mut+_siISG20L2_rep3,Primer3_mut+_siISG20L2_rep1

description:
Library name: Dataset39
Primer 1 and 3


title: MOC1_CRT_4

description: Library name: MOC1_CRT_4


title: MOC1_Veh_5

description: Library name: MOC1_Veh_5


title: MOC1_Veh_4

description: Library name: MOC1_Veh_4


title: Primer2_wt-_siISG20L2_rep1

description:
Library name: Dataset28
Primer 2

value: wt-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: MOC1_RT_1

description: Library name: MOC1_RT_1


title: Primer2_mut-_siISG20L2_rep1, Primer3_mut+_siISG20L2_rep2

description:
Library name: Dataset29
Primer 2 and 3

value: mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4, mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: MOC1_RT_2

description: Library name: MOC1_RT_2


title: Primer1_control_rep5, Primer5_mut+_siISG20L2_rep1

description:
Library name: Dataset43
Primer 1 and 5

value: control cells (- DOX), mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: MOC1_Veh_2

description: Library name: MOC1_Veh_2


title: Primer2_control_rep3, Primer3_wt+_siISG20L2_rep3

description:
Library name: Dataset30
Primer 2 and 3

value: HeLa cells

value: control cells (- DOX), wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: MOC1_CRT_5

description: Library name: MOC1_CRT_5


title: MOC1_RT_3

description: Library name: MOC1_RT_3


title: Primer2_wt+_siISG20L2_rep2

description:
Library name: Dataset27
Primer 2


title: Primer 2_siDDX51_rep1,Primer3_control_rep3

description:
Library name: Dataset31
Primer 2 and 3

value: siDDX51, control cells (- DOX)


title: Primer2_control_rep5

description:
Library name: Dataset24
Primer 2


title: Primer2_mut+_siISG20L2_rep5

description:
Library name: Dataset25
Primer 2


title: Primer2_control_rep2

description:
Library name: Dataset23
Primer 2


title: Primer2_mut+_siISG20L2_rep1

description:
Library name: Dataset26
Primer 2


title: MOC1_Veh_1

description: Library name: MOC1_Veh_1


title: cut_11_shCoo2

city: Shanghai

first: Wenhao

last: Zhang

address: 270 Dongan Road

country: China

institute: Fudan University of Shanghai Cancer Center

description:
Library name: cut_11
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v9.0.1) and Cell Ranger multi pipeline was used.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: breast

extract_protocol:
Primary tumors from control (shCoo2), FAM114A1-KD#1, and FAM114A1-KD#2 Py8119 cell inoculated mice were collected and processed into formalin-fixed paraffin-embedded (FFPE) tumors. Six control FFPE tumors were combined into one group termed as shCoo2 group. Three FAM114A1-KD#1 FFPE tumors and three FAM114A1-KD#2 FFPE tumors were combined into the FAM114A1-KD group.
shCoo2 and FAM114A1-KD FFPE samples were thawed and divided equally for processing using the standard 10X Flex assays, following the respective recommended protocols. Single-cell RNA sequencing was performed with 10X Chromium Single Cell Gene Expression Flex on the Illumina Novaseq 6000.

value: breast


title: Actr3 KO-1 CB repl.-3

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

description:
Library name: Sample 12
featureCounts

data_processing:
The Galaxy Europe resource was used for processing and analysis of sequencing data (https://usegalaxy.eu).
Sequenced reads were quality and adapter trimmed using fastp v0.23.2.
Reads were mapped to mm10 whole genome using HISAT2 v2.2.1 with default settings for paired-end libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.7 were applied for differential expression analysis
Assembly: Mouse Dec. 2011 (GRCm38/mm10) (mm10)
Supplementary files format and content: tab-delimited text files include normalized counts for all samples

source_name: Actr3 KO-1 CB

growth_protocol: Cells were cultured in DMEM/F12 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #10565018), 10 % FCS (Merck, #S0615), 5 mM HEPES (#15630-056, Thermo Fisher Scientific) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 95% air and 5% CO2. Cell lines were seeded in cell culture dishes,grown to confluence for 48 hours and FCS starved for an additional 24 hours.

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as 10.0 for all samples using an Agilent Fragment Analyzer system.
After polyA selection, RNA libraries were prepared for sequencing using the NEBnext ultra II RNA kit. Libraries were sequenced using an Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

treatment_protocol: 0.5 µM Ciliobrevin D or solvent control was added to the starvation medium.

value: kidney inner medullary collecting duct

value: Actr3 knockout

value: Actr3 KO-1 CB

value: 0.5 µM Ciliobrevin D

value: FCS starved cell culture


title: Actr3-Ift88 dKO repl.-3

description:
Library name: Sample 9
featureCounts

source_name: Actr3-Ift88 dKO

value: Actr3*Ift88 knockout

value: Actr3-Ift88 dKO

value: control


title: Actr3 KO-1 CB repl.-2

description:
Library name: Sample 11
featureCounts


title: Primer2_mut-_siISG20L2_rep3

description:
Library name: Dataset21
Primer 2

value: mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: Primer2_siDDX51_rep2

description:
Library name: Dataset20
Primer 2


title: cut_19_Fam114a1_KD

description:
Library name: cut_19
10x Genomics

value: Fam114a1 KD


title: Actr3 KO-1 CB repl.-1

description:
Library name: Sample 10
featureCounts


title: Actr3-Ift88 dKO repl.-2

description:
Library name: Sample 8
featureCounts

value: Actr3*Ift88  knockout


title: Primer2_siURB1_rep3

description:
Library name: Dataset19
Primer 2


title: Primer2_mut+_siISG20L2_rep3

description:
Library name: Dataset16
Primer 2

value: mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Actr3 KO-1 repl.-1

description:
Library name: Sample 4
featureCounts

source_name: Actr3 KO-1

value: Actr3 KO-1


title: Primer2_wt-_siISG20L2_rep2

description:
Library name: Dataset14
Primer 2

value: HeLa cells

value: wt-ISG20L2-Flag cells (- DOX) + siISG20L2-4


title: Primer2_control_rep4

description:
Library name: Dataset15
Primer 2

value: control cells (- DOX)


title: Primer2_siURB1_rep2

description:
Library name: Dataset18
Primer 2


title: Actr3-Ift88 dKO repl.-1

description:
Library name: Sample 7
featureCounts


title: Actr3 KO-1 repl.-3

description:
Library name: Sample 6
featureCounts


title: Primer2_mut+_siISG20L2_rep4

description:
Library name: Dataset17
Primer 2


title: Actr3 KO-1 repl.-2

description:
Library name: Sample 5
featureCounts


title: Primer2_mut-_siISG20L2_rep4

description:
Library name: Dataset22
Primer 2


title: Actr3 Ctrl.-1 repl.-3

description:
Library name: Sample 3
featureCounts

source_name: Control 1

value: wild type control

value: Control 1


title: KO-2 repl.-2

description:
Library name: Sample 8
featureCounts

data_processing:
The Galaxy Europe resource was used for processing and analysis of sequencing data (https://usegalaxy.eu).
Sequenced reads were quality and adapter trimmed using fastp v0.23.2.
Reads were mapped to mm10 whole genome using HISAT2 v2.2.1 with default settings for paired-end libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.6 were applied for differential expression analysis
Assembly: Mouse Dec. 2011 (GRCm38/mm10) (mm10)
Supplementary files format and content: tab-delimited text files include normalized counts for all samples

source_name: Actr3 KO-2

growth_protocol: Cells were cultured in DMEM/F12 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #10565018), 10 % FCS (Merck, #S0615), 5 mM HEPES (#15630-056, Thermo Fisher Scientific) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 95% air and 5% CO2. Cell lines were seeded in cell culture dishes and grown to confluence for 48 hours.

value: kidney inner medullary collecting duct

value: Actr3 knockout

value: Actr3 KO-2

value: non-starved cell culture


title: Actr3 Ctrl.-1 repl.-2

description:
Library name: Sample 2
featureCounts

value: FCS starved cell culture


title: KO-1 repl.-2

description:
Library name: Sample 6
featureCounts


title: Primer2_mut+_siISG20L2_rep2, Primer4_mut+_siISG20L2_rep2

description:
Library name: Dataset9
Primer 2 and 4


title: KO-2 repl.-1

description:
Library name: Sample 7
featureCounts


title: Primer2_mut-_siISG20L2_rep2,Primer4_mut+_siISG20L2_rep3

description:
Library name: Dataset13
Primer 2 and 4

value: mut-ISG20L2-Flag cells (- DOX) + siISG20L2-4, mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Primer2_control_rep6,Primer4_control_rep4

description:
Library name: Dataset8
Primer 2 and 4


title: Primer2_siISG20L2_rep1,Primer4_wt+_siISG20L2_rep3

description:
Library name: Dataset10
Primer 2 and 4

value: control cells (- DOX) + siISG20L2-4, wt-ISG20L2-Flag cells (+ DOX)


title: KO-1 repl.-1

description:
Library name: Sample 5
featureCounts


title: Primer2_siURB1_rep1,Primer4_control_rep2

description:
Library name: Dataset6
Primer 2 and 4

value: siURB1, control cells (- DOX)


title: Primer2_wt+_siISG20L2_rep1,Primer4_wt+_siISG20L2_rep2

description:
Library name: Dataset7
Primer 2 and 4

value: wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Ctrl.-2 repl.-2

description:
Library name: Sample 4
featureCounts

source_name: Control 2

value: Control 2


title: Ctrl.-1 repl.-2

description:
Library name: Sample 2
featureCounts


title: Actr3 Ctrl.-1 repl.-1

description:
Library name: Sample 1
featureCounts

value: control


title: Primer2_siRPL26_rep2

description:
Library name: Dataset12
Primer 2


title: Ctrl.-2 repl.-1

description:
Library name: Sample 3
featureCounts


title: Primer2_control_rep1,Primer4_wt+_siISG20L2_rep1

description:
Library name: Dataset5
Primer 2 and 4

value: control cells (- DOX), wt-ISG20L2-Flag cells (+ DOX)


title: Primer2_siRPL3_rep1, Primer4_control_rep1

description:
Library name: Dataset3
Primer 2 and 4

value: HeLa cells

value: siRPL3, control cells (- DOX)


title: Melanoma_cell_Calb_4

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Library name: B16_H4

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (Mus musculus.GRCm38.mm10) and read counts obtained for each gene
For the detection of diﬀerentially expressed genes, the following method has been applied: DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281]: a shrinkage estimation has been applied for dispersions and calculation of expression fold changes, to improve stability and interpretability of estimates
Assembly: mm10
Supplementary files format and content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: Skin

growth_protocol: B16-F10 melanoma cells were kept in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin and 0.25 μg/mL amphotericin B (all from Sigma-Aldrich, MO, USA), in a 5% CO2 atmosphere at 37°C.  Candida albicans was grown in Sabouraud Dextrose Agar (SDA; Panreac Química SLU, Castellar del Vallès, Spain) at 37°C overnight. One day prior to the experiment, 10^5 cells/mL were inoculated in Sabouraud Dextrose Broth (SDB; Panreac Química SLU) and incubated at 37°C and 120 rpm overnight. The day of the experiment, yeasts were collected by centrifugation and washed twice with Dulbecco’s Phosphate Buffer Saline (DPBS; Corning, VWR, PA, USA).

extract_protocol:
Total RNA isolation was performed by Total RNA Isolation Kit (NzyTech), following manufacturer’s instructions. Total RNA quantity was measured using the Qubit RNA Assay Kit (Thermo Fisher Scientific) and its quality integrity was measured examined by RNA Nano Chips in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) in the Center for Cooperative Research in Biosciences (CICBiogune) in Derio, Spain.
mRNA stranded libraries were prepared following “TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E)” using the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792)

treatment_protocol: 1 × 106 melanoma cells/well were seeded in 6-well plates (Sarstedt), stimulated with or without MOI 1 of live C. albicans in RPMI/10% FBS medium and incubated in a 5% CO2 atmosphere at 37°C for six hours

value: Skin

value: Adherent

value: Candida albicans MOI 1


title: Ctrl.-1 repl.-1

description:
Library name: Sample 1
featureCounts

value: kidney inner medullary collecting duct

value: wild type control

value: Control 1


title: Primer2_siRPL26_rep1,Primer4_mut+_siISG20L2_rep1

description:
Library name: Dataset4
Primer 2 and 4

value: siRPL26,  mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Primer2_siRPL3_rep2

description:
Library name: Dataset1
Primer 2


title: Primer2_wt+_siISG20L2_rep4,Primer4_control_rep3

description:
Library name: Dataset11
Primer 2 and 4

value: wt-ISG20L2-Flag cells (+ DOX), control cells (- DOX)


title: Melanoma_cell_Calb_6

description: Library name: B16_H6


title: Primer2_wt+_siISG20L2_rep3, Primer3_mut+_siISG20L2_rep3

description:
Library name: Dataset2
Primer 2 and 3

value: wt-ISG20L2-Flag cells (+ DOX) + siISG20L2-4, mut-ISG20L2-Flag cells (+ DOX) + siISG20L2-4


title: Primer2_3_4_ISG20L2-2_rep3_Nuclear

description:
Primers 2, 3 and 4
Processed_table_primer2_nyx.txt
Processed_table_primer3_nyx.txt
Processed_table_primer4_nyx.txt
Dataset23

extract_protocol:
For total RNA isolation, 10-15 × 10^6 HeLa cells were collected by centrifugation for 5 min at 300 g and 4°C. After rinsing with 10 ml cold PBS, each pellet was thoroughly mixed with 1 ml TRI reagent and extracted following the manufacturer’s instructions. The upper aqueous phase was further purified by phenol/chloroform/isoamyl alcohol (25:24:1) extractions prior to isopropanol precipitation. Quantifications were performed at 260 nm with an Implen NP80 spectrophotometer.
3' RACE-seq
3'RACE-seq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.


title: Primer2_3_4_ISG20L2-Six3_rep2_Nuclear

description:
Primers 2, 3 and 4
Processed_table_primer2_nyx.txt
Processed_table_primer3_nyx.txt
Processed_table_primer4_nyx.txt
Dataset22


title: Primer2_3_4_ISG20L2-4_rep1_Nuclear

description:
Primers 2, 3 and 4
Processed_table_primer2_nyx.txt
Processed_table_primer3_nyx.txt
Processed_table_primer4_nyx.txt
Dataset21


title: Melanoma_cell_Control_3

description: Library name: B16_C3

value: Control


title: LPS_109_D5.3

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
Library name: LPS_109_D5.3
Mice challenged with LPS and treated with VT-109 during late phases of injury

data_processing:
Reads were aligned to the mm10 reference using STAR (Dobin et al., 2013). ENSEMBL genes were quantified using FeatureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file

source_name: Lung

extract_protocol:
Total RNA for the bulk RNA-sequencing from the isolated pulmonary endothelial cells were obtained using TRIzol (Invitrogen) according to the manufacturer’s instructions.
The libraries were obtained through reverse transcription of the RNA samples to cDNA using a high-capacity cDNA reverse transcription kit (Thermo Fisher).

treatment_protocol: VT-109 was administered intravenously in two treatment protocols: an early treatment group received VT-109 starting 1-day post-LPS injection, 3 dose in total and one dose per day, and a late treatment group started 3 days post-LPS injection, 2 dose in total and one dose per day.

value: Lung

value: Isolated endothelial cells

value: LPS

tag: condition

tag: time point


title: Primer3_4_ISG20L2_rep5

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset19


title: LPS_109_D5.1

description:
Library name: LPS_109_D5.1
Mice challenged with LPS and treated with VT-109 during late phases of injury


title: LPS_109_D5.2

description:
Library name: LPS_109_D5.2
Mice challenged with LPS and treated with VT-109 during late phases of injury


title: LPS_cont_D5.1

description:
Library name: LPS_cont_D5.1
Mice challenged with LPS

value: Vehicle Control


title: Primer2_3_4_scr_rep1_Nuclear

description:
Primers 2, 3 and 4
Processed_table_primer2_nyx.txt
Processed_table_primer3_nyx.txt
Processed_table_primer4_nyx.txt
Dataset20

value: scramble


title: Primer3_4_ISG20L2_rep2

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset16

value: HeLa cells


title: Primer3_4_ISG20L2_rep4

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset18


title: LPS_cont_D5.3

description:
Library name: LPS_cont_D5.3
Mice challenged with LPS


title: Melanoma_cell_Calb_3

description: Library name: B16_H3


title: Primer3_4_scr_rep5

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset15


title: Melanoma_cell_Control_6

description: Library name: B16_C6


title: LPS_109_D3.3

description:
Library name: LPS_109_D3.3
Mice challenged with LPS and treated with VT-109 during early phase of injury


title: Primer3_4_ISG20L2_rep3

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset17


title: LPS_109_D3.2

description:
Library name: LPS_109_D3.2
Mice challenged with LPS and treated with VT-109 during early phase of injury


title: Primer3_4_scr_rep4

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset14


title: Melanoma_cell_Control_4

description: Library name: B16_C4


title: LPS_109_D3.1

description:
Library name: LPS_109_D3.1
Mice challenged with LPS and treated with VT-109 during early phase of injury


title: Primer3_4_scr_rep3

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset13


title: Primer3_4_scr_rep2

description:
Primers 3 and 4
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset12


title: Primer1_2_ISG20L2_rep4

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset10


title: Primer1_2_ISG20L2_rep5

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset11


title: LPS_cont_D3.2

description:
Library name: LPS_cont_D3.2
Mice challenged with LPS


title: LPS_cont_D3.1

description:
Library name: LPS_cont_D3.1
Mice challenged with LPS


title: Primer1_2_ISG20L2_rep2

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset8


title: UT.3

description:
Library name: UT.3
Naïve mice

value: untreated

value: Negative control


title: LPS_cont_D5.2

description:
Library name: LPS_cont_D5.2
Mice challenged with LPS


title: UT.2

description:
Library name: UT.2
Naïve mice


title: Primer1_2_ISG20L2_rep3

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset9


title: Primer1_2_scr_rep5

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset7


title: UT.1

description:
Library name: UT.1
Naïve mice


title: Primer1_2_scr_rep4

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset6


title: treat_day_15_3

city: Beijing

first: Zhiyu

last: Ning

address: Room C211, Building of Medical Science, Tsinghua University, Haidian District, Beijing, China.

institute: Tsinghua University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
About 48.9M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Then about 48.6M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, CA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Skin


title: treat_day_15_4


title: Primer2_3_4_ISG20L2_rep1_2

description:
Primers 2, 3 and 4
Processed_table_primer2.txt
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset3


title: model_day_15_4


title: treat_day_15_1


title: treat_day_15_2


title: Primer2_3_4_ISG20L2_rep1_1

description:
Primers 2, 3 and 4
Processed_table_primer2.txt
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset2


title: LPS_cont_D3.3

description:
Library name: LPS_cont_D3.3
Mice challenged with LPS


title: rep3-20-lithium

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description: Library name: rep3-20-lithium_S9

data_processing:
Adapter trimming - CutAdapt
Quality control - FastQC
Alignment - HISAT2
Feature counting - HTseq_count
Differential expression - DESeq2
Downstream analysis - RNAlysis
Assembly: WS235/ce11
Supplementary files format and content: Raw count matrices (comma-separated values)

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: N2 worms, fed on E.coli OP-50 bacteria

extract_protocol:
TRIzol®
For worms on ice:Nextera® XT DNA Sequencing kit (Illumina®); For Lithium samples: RNA libraries were prepared using NEBNext® Ultra II directional RNA library prep kit for illumina®.

treatment_protocol: For cold tolerance: worms were cultivated either in 20deg, 15deg overnight, or 15deg overnight followed by 2h at 20deg Celsius . For lithium treatment: worms were placed overnight on plates containing either 15mM LiCl for the experimental group or NGM as control. The worms had been cultivated overnight at one of two temperatures: 15°C, to induce cold tolerance, or 20°C, where the worms remain cold sensitive.

value: Whole worm

tag: cultivation temperature

tag: training group

value: no training

tag: lithium treatment

value: Lithium

tag: cold shock_treatment

value: no cold shock


title: Primer1_2_scr_rep3

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset5


title: model_day_15_2


title: model_day_15_1


title: rep3-20-control

description: Library name: rep3-20-control_S10

value: control


title: model_day_15_3


title: Primer1_2_scr_rep2

description:
Primers 1 and 2
Processed_table_primer1.txt
Processed_table_primer2.txt
Dataset4


title: rep3-15-control

description: Library name: rep3-15-control_S12


title: control_day_15_3


title: rep3-15-lithium

description: Library name: rep3-15-lithium_S11


title: Exercised c

city: East Orange

first: Bruce

middle: A.

last: Citron

state: NJ

address: 385 Tremont Ave.

department: Pharmacology, Physiology, & Neuroscience, Rutgers- NJMS

institute: VA New Jersey Health Care System

description: Library name: 454P

data_processing:
CLC Genomics Workbench v. 25.0
Assembly: Rattus norvegicus (mRatBN7.2)
Supplementary files format and content: Excel file with TPM values for each sample

organism: Rattus norvegicus

source_name: Plasma

extract_protocol:
RNA was isolated with the Total Exosome RNA and Protein Isolation Kit (Invitrogen)
Takara SMARTer Stranded Total RNA-Seq Kit v3- Pico Input Mammalian (Takara Bio USA)

value: Plasma

tag: strain

value: Sprague dawley

value: Exercised


title: Exercised d

description: Library name: 455P


title: Exercised a

description: Library name: 451P


title: rep2-20-control

description: Library name: rep2-20-control_S6


title: Neg_T2_3

city: Zaragoza

first: Inmaculada

last: Martín Burriel

state: Zaragoza

address: Miguel Servet, 177

department: Anatomy, Embriology and Animal Genetics

institute: University of Zaragoza

description:
gene_count.txt
gene_fpkm.txt

data_processing:
Paired-end clean reads were aligned to the reference genome using the software Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie v1.3.3b.
For transcript quantification, the software FeatureCounts v1.5.0-p3 was used and FPKM of each gene was then calculated based on the length of the gene and read count mapped to this gene.
Assembly: oar_rambouillet-v1.0
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

organism: Ovis aries

source_name: Bone marrow

growth_protocol: oBM-MSCs were maintained in DMEM supplemented with 10 % fetal bovine serum (FBS), 1 % L-glutamine and 1 % streptomycin/penicillin in humidified atmosphere with 5% CO2 at 37 ºC

extract_protocol:
RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research). Approximately 2 μg of total RNA per sample were used for RNA sequencing.
The RNA library was formed by polyA capture and reverse transcription of cDNA.

treatment_protocol: For inoculation, basal medium was substituted by inocula diluted 1:10 in DMEM medium (10 % FBS, 1 % L-glutamine and 1 % streptomycin/penicillin). Cells were maintained in this medium for 48 h. Afterwards, the medium was changed twice a week.

value: Bone marrow

value: mesenchymal stem cells

value: ARQ/ARQ

value: Inoculated with negative inoculum

tag: infection time

value: T2 (4 days post-inoculation)


title: control_day_15_2


title: rep2-20-lithium

description: Library name: rep2-20-lithium_S5


title: Exercised b

description: Library name: 452P


title: control_day_15_1


title: rep2-15-lithium

description: Library name: rep2-15-lithium_S7


title: Sedentary d

description: Library name: 453P

value: Sedentary


title: Neg_T2_2

description:
gene_count.txt
gene_fpkm.txt


title: treat_day_10_4


title: Neg_T2_1

description:
gene_count.txt
gene_fpkm.txt


title: rep2-15-control

description: Library name: rep2-15-control_S8


title: Sedentary c

description: Library name: 450P


title: control_day_15_4


title: Pos_T2_3

description:
gene_count.txt
gene_fpkm.txt

value: Inoculated with scrapie-infected inoculum


title: treat_day_10_3


title: rep1-20-lithium

description: Library name: rep1-20-lithium_S1


title: Sedentary b

description: Library name: 449P


title: treat_day_10_2


title: Pos_T2_2

description:
gene_count.txt
gene_fpkm.txt


title: treat_day_10_1


title: Pos_T2_1

description:
gene_count.txt
gene_fpkm.txt


title: rep1-20-control

description: Library name: rep1-20-control_S2


title: Sedentary a

description: Library name: 437P


title: Primer2_3_4_scr_rep1

description:
Primers 2, 3 and 4
Processed_table_primer2.txt
Processed_table_primer3.txt
Processed_table_primer4.txt
Dataset1

value: HeLa cells

value: scramble


title: rep1-15-lithium

description: Library name: rep1-15-lithium_S3

value: Whole worm


title: model_day_10_4

value: Skin


title: Naif_T2_3

description:
gene_count.txt
gene_fpkm.txt

value: Non-inoculated


title: model_day_10_3


title: rep1-15-control

description: Library name: rep1-15-control_S4

value: no training

value: no cold shock


title: Naif_T2_2

description:
gene_count.txt
gene_fpkm.txt


title: 15to20_cond_D

description: Library name: 15to20_cond_D

value: conditioned

value: 2 hours cold shock


title: yH2AX, rep1, OHT, ChIP

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

description: Library name: U2OS_DIvA_yH2AX_OHT_rep1

library_source: genomic

data_processing:
Samples were filtered for low-quality reads and adapter sequences using trim_galore (v0.6.10). All files were aligned to the reference human genome assembly GRCh37 (hg19) using Bowtie2 (v2.5.1). Multiple-matching reads were eliminated using SAMtools (v1.20). Duplicated reads were removed by picard (v3.1.1).
DeepTools (v3.5.5) was used for read depth normalization and visualization. Coverage tracks (bigWig) were generated by the BamCoverage module of deepTools after normalizing counts per million with 200 bp bin size, read extension and length smoothing to 400 bp.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: DIvA, AsiSI-ER-U2OS

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium – DMEM (Invitrogen), supplemented with 1x non-essential amino acids (Thermo Fisher Scientific), 1x Glutamax (Thermo Fisher Scientific), 1mM sodium pyruvate (Thermo Fisher Scientific), 1% penicillin–streptomycin antibiotics (Gibco) and 10% FCS (Westburg) at 37°C and 5% CO2.

extract_protocol:
Approximately 20 x 106 cells were harvested per IP and fixed with 1% methanol-free formaldehyde for 8 min. Crosslinking was quenched by adding glycine to a final concentration of 0.125mM at 4°C for 10 minutes. Cells were washed twice with ice-cold PBS. After washing, cells were harvested by scraping in ice-cold PBS containing proteinase inhibitor cocktail (Roche) and pelleted at 600 × g for 7 min at 4°C. Cells were incubated for 10 min on ice in a buffer containing 10 mM EDTA, 10 mM Tris pH 8, 0.5 mM EGTA and 0.25% Triton X-100. After centrifugation, cells were incubated in 1 mM EDTA, 10 mM Tris pH 8, 0.5 mM EGTA, 200 mM NaCl and passed 3 times through 26-G needles and incubated on ice for 10 minutes. Cells were centrifuged for 600 × g for 7 min at 4°C. Chromatin was extracted in a high-salt buffer containing 50 mM HEPES, pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS and 500 mM NaCl for 2h at 4 °C. Chromatin was sheared using a Bioruptor Pico sonicator (Diagenode). Per IP 50 ul of protein-G Dynabeads (Invitrogen) were washed twice with TE buffer pH 8 for 5 minutes at room temperature. Beads were blocked with 1 mg BSA (Sigma), 100 ng yeast tRNA (Sigma) in TE buffer containing proteinase inhibitor cocktail. 100 µg of chromatin was pre-cleared with 20ul of pre-blocked protein-G magnetic beads for 1 hour at 4°C. Then, 5% of cleared-chromatin was stored at -20 °C as input until de-crosslinked together with the IP-material. For the IP, 1 μg of anti-γH2AX (Sigma) or 7,5 μg anti-GFP (Abcam) was added to cleared chromatin and incubated overnight at 4 °C. The following day, 30 µl blocked protein-G beads was added to the chromatin and incubated for 3h at 4°C. Beads were separated by magnet and washed twice for 8 min with high-salt buffer, once for 8 minutes with 50 mM LiCl, 0.5% NP-40, 0.5% deoxycholate, and twice with TE buffer pH 8, on overhead rotator at 4 °C. Next, chromatin was eluted in 1% SDS and 100 mM NaHCO3 containing 60 µg RNaseA (Roche) and incubated at 37 °C for 30 min. Elution was adjusted to 10mM EDTA, 40mM Tris pH 8.0, and 25µg Proteinase K (Roche) and incubated for 3h at 55°C. Final decrosslinking was done overnight at 65°C. Input-chromatin was de-crosslinked in parallel in TE buffer pH 8 and 60 µg RNaseA was added and incubated at 37°C for 30 min. Chromatin was adjusted to 1% SDS, 100mM NaCl and 60µg Proteinase K and incubated for 3h at 55°C. Final decrosslinking was done overnight at 65°C. Eluted material was cleaned up by phenol-chloroform extraction and DNA was quantified using a Qubit 3.0 fluorometer (Thermo Scientific)
ChIP-seq libraries using the NEBNext Ultra II DNA Library Prep kit for Illumina (E7645) following the standard protocols and using 10 ng of DNA. Samples with different index barcodes were combined at equal molar ratios, with the exception of input DNA (0.7x ratio), and sequenced as pools.

treatment_protocol: Cells were incubated with medium containing either 300nM 4-hydroxytamoxifen (OHT), (Sigma, H6278) or DMSO (mock treatment) for 4h.

tag: chip antibody

value: yH2AX (Sigma, 05636)

value: DIvA, AsiSI-ER-U2OS


title: yH2AX, rep3, OHT, ChIP

description: Library name: U2OS_DIvA_yH2AX_OHT_rep3


title: model_day_10_1


title: model_day_10_2


title: MCPH1-eGFP, rep3, OHT,ChIP

description: Library name: U2OS_DIvA_MCPH1_GFP_OHT_rep3

value: GFP (Abcam, ab290)


title: Naif_T2_1

description:
gene_count.txt
gene_fpkm.txt

value: Bone marrow

value: mesenchymal stem cells

value: ARQ/ARQ


title: 15_naive_G

description: Library name: 15_naive_G

value: naïve


title: Neg_T1_3

description:
gene_count.txt
gene_fpkm.txt

value: Inoculated with negative inoculum

value: T1 (2 days post-inoculation)


title: Neg_T1_2

description:
gene_count.txt
gene_fpkm.txt


title: 20_cond_F

description: Library name: 20_cond_F


title: 15to20_naive_D

description: Library name: 15to20_naive_D


title: MCPH1-eGFP, rep2, OHT,ChIP

description: Library name: U2OS_DIvA_MCPH1_GFP_OHT_rep2


title: Neg_T1_1

description:
gene_count.txt
gene_fpkm.txt


title: 15_naive_B

description: Library name: 15_naive_B


title: MCPH1-eGFP, rep1, OHT,ChIP

description: Library name: U2OS_DIvA_MCPH1_GFP_OHT_rep1


title: control_day_10_2


title: yH2AX, rep2, OHT, ChIP

description: Library name: U2OS_DIvA_yH2AX_OHT_rep2


title: input, OHT

description: Library name: U2OS_DIvA_OHT_input


title: Pos_T1_3

description:
gene_count.txt
gene_fpkm.txt

value: Inoculated with scrapie-infected inoculum


title: yH2AX, DMSO, ChIP

description: Library name: U2OS_DIvA_yH2AX_DMSO_rep1

value: DMSO


title: input, DMSO

description: Library name: U2OS_DIvA_DMSO_input


title: 15to20_naive_H

description: Library name: 15to20_naive_H

value: Whole worm


title: Pos_T1_2

description:
gene_count.txt
gene_fpkm.txt


title: control_day_10_1

value: Skin


title: neo_CMs_shLncBAR_replicate 2

city: wuhan

first: li

last: jun

state: hubei

address: donghu street

department: wuhan

institute: wuhan university

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using STRA software (version 2.5.3a) with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: heart

extract_protocol:
RNA was harvested using TRIzol (Takara). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina) with PE150 model.

value: heart

value: Primary cell

value: cardiomyocytes

value: LncBAR konckdown

value: Infected with shLncBAR lentivirus


title: 15_cond_B

description: Library name: 15_cond_B

value: conditioned

value: 2 hours cold shock


title: Pos_T1_1

description:
gene_count.txt
gene_fpkm.txt

value: Bone marrow


title: MCPH1-eGFP, rep1, DMSO, ChIP

description: Library name: U2OS_DIvA_MCPH1_GFP_DMSO_rep1

value: GFP (Abcam, ab290)

value: DIvA, AsiSI-ER-U2OS


title: neo_CMs_replicate 2

value: WT

value: Infected with shNT lentivirus


title: Naif_T1_3

description:
gene_count.txt
gene_fpkm.txt

value: mesenchymal stem cells

value: ARQ/ARQ

value: Non-inoculated

value: T1 (2 days post-inoculation)


title: Naif_T1_2

description:
gene_count.txt
gene_fpkm.txt


title: MCPH1-eGFP, rep2, DMSO, ChIP

description: Library name: U2OS_DIvA_MCPH1_GFP_DMSO_rep2

value: DMSO


title: 15_naive_H

description: Library name: 15_naive_H

value: Whole worm

value: naïve


title: control_day_10_4

value: Skin


title: 15to20_cond_H

description: Library name: 15to20_cond_H


title: TotalRNA_61_R1.trimmed.fastq.gz

city: Toyama

first: Naoya

last: Kitamura

state: Toyama

address: 2630, Sugitani

department: Thoracic Surgery

country: Japan

institute: University of Toyama

description:
Library name: TotalRNA_61_R1
NovaSeq X Plus used

data_processing:
Raw reads were quality-checked with FastQC (v0.11.7) and trimmed for adapter sequences and low-quality bases using Trimmomatic (v0.38). Cleaned reads were aligned to the Homo sapiens reference genome (hg38) using HISAT2 (v2.1.0). Gene-level counts were obtained with featureCounts (v1.6.3) and normalized to TPM, FPKM, and FPKM-UQ values. Differential expression analysis was performed using DESeq2 (v1.24.0).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data are provided as tab-delimited text files containing lists of differentially expressed genes (DEGs) with associated statistics (gene ID, log2 fold change, p-value, etc.).

growth_protocol: A549 human lung adenocarcinoma epithelial cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere containing 5% CO₂. For 3D cultures, cells were reseeded into decellularized lung scaffolds and maintained under perfusion culture using the same medium.

extract_protocol:
Total RNA was extracted from cultured A549 cells (2D) or lung tissue fragments (3D) using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. RNA quality and concentration were assessed by NanoDrop spectrophotometry.
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) with poly(A) RNA enrichment, following the manufacturer’s instructions.

treatment_protocol: Cells were divided into two groups: one subjected to respiratory motion stimulation and one without. Both groups were cultured for 4 days prior to RNA extraction.

value: Lung

value: Epithelial cell

value: without respiratory motion

tag: batch


title: 15_cond_H

description: Library name: 15_cond_H

tag: tissue

value: conditioned

value: 2 hours cold shock


title: neo_CMs_replicate 1

value: heart

tag: cell line

value: Primary cell

value: cardiomyocytes


title: Naif_T1_1

description:
gene_count.txt
gene_fpkm.txt

value: Bone marrow

tag: cell type


title: IRI_3

city: Nanjing

first: Xinghua

last: Gao

state: Jiangsu

address: #639 Longmian Dadao

institute: China Pharmaceutical University

data_processing:
Firstly, the amounts and integrity of RNA were performed using the Bioanalyzer 2100 system (Agilent Technologies). The sequencing libraries preparations were performed using SMARTer RACE cDNA Amplification Kit (clontech) as per the manufacturer’s recommendations. The cDNA libraries were quantified by Qubit2.0 Fluorometer, then diluted to 1.5 ng/uL. The insert size of the cDNA libraries was detected by Agilent 2100 bioanalyzer.
In order to ensure the quality of the cDNA libraries, qRT-PCR was used to accurately quantify the effective concentration of the cDNA libraries after the insert size of the cDNA libraries meets the expectation. The cDNA libraries were sequenced on the Illumina NovaSeq 6000.
CASAVA base recognition was used to convert the image data measured by the high-throughput sequencer into sequence data (reads). Raw data were performed by fastp software. To obtain the clean data for downstream analyses, reads containing adapter, reads containing N base, and low-quality reads from raw data were removed. We used Hisat2 (v2.0.5) to build the index of the reference genome.
The paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). After using featureCounts (v1.5.0-p3) to count the reads numbers mapped to each gene, the FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 R package (1.20.0) was used to analyze the differential expression between the two groups. The resulting P-values were adjusted using Benjamini and Hochberg’s method. padj <= 0.05 and |log2 (foldchange)| >= 1 were used as thresholds for significant differential expression.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: CT26 subcutaneous tumors

extract_protocol:
CT26 subcutaneous tumors were removed, flash frozen on dry ice, and total RNA was extracted using Trizol (Takara, Japan) and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the CT26 CRC mouse model, BALB/c mice were subcutaneously injected with CT26 tumor cells. Mice were randomized when the volume of tumors reached 100 mm3. Mice received 25 mg/kg CPT-11 by intraperitoneal injection (i.p.) once every four days.

value: CT26 subcutaneous tumors

value: colon cancer cell

tag: genotype

value: WT

value: CPT-11 treatment


title: TotalRNA_60_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_60_R1
NovaSeq X Plus used

tag: treatment

value: with respiratory motion


title: 15_cond_G

description: Library name: 15_cond_G

value: Whole worm


title: control_day_10_3


title: TotalRNA_56_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_56_R1
NovaSeq X Plus used


title: 15to20_naive_C

description: Library name: 15to20_naive_C

value: naïve


title: IRI_2


title: IRI_1


title: 15to20_cond_C

description: Library name: 15to20_cond_C


title: TotalRNA_55_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_55_R1
NovaSeq X Plus used


title: TotalRNA_50_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_50_R1
NovaSeq X Plus used


title: Con_3.

value: Solvent treatment


title: 20_naive_F

description: Library name: 20_naive_F


title: neo_CMs_shLncBAR_replicate 1

value: LncBAR konckdown

value: Infected with shLncBAR lentivirus


title: TotalRNA_49_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_49_R1
NovaSeq X Plus used

value: Lung

value: Epithelial cell


title: TotalRNA_32_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_32_R1
NovaSeq X Plus used

value: without respiratory motion


title: 20_cond_A

description: Library name: 20_cond_A

value: conditioned

value: 2 hours cold shock


title: 20_naive_A

description: Library name: 20_naive_A


title: 20_naive_E

description: Library name: 20_naive_E


title: Con_1.


title: Nsd2 KO3

city: shanghai

first: wenxin

last: feng

address: 1954 Huashan Road, Shanghai

institute: shanghai jiaotong university

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol: mRNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic cancer cell

value: Nsd2 KO


title: TotalRNA_wP_2

description:
Library name: TotalRNA_wP_2
NovaSeq X Plus used

growth_protocol: A549 human lung adenocarcinoma epithelial cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere containing 5% CO₂.


title: TotalRNA_31_R1.trimmed.fastq.gz

description:
Library name: TotalRNA_31_R1
NovaSeq X Plus used


title: miR-17 overexpressing chondrocytes, rep1

city: Nanchang

first: Jinghong

last: Yuan

state: Jiangxi

address: No.1 Minde Road

institute: The Secondly Affiliated Hospital of Nanchang University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: chondrocytes

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

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

value: chondrocytes


title: YHK-Ctrl,rep1,scRNAseq

city: Nantong

first: Xingmin

last: Wang

address: 399 Century Ave.

department: Institute of Genetics and Reproductive Medicine

institute: Nantong Maternity and Child Healthcare Hospital

description: 10k Genomics

data_processing:
The barcode processing,gene counting were made using CellCosmo v1.0  software.
Assembly: Rattus_norvegicus.Rnor_5.0.77
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Small intestine

growth_protocol: IEC-6 cells were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS), 10 μg/mL insulin (Sigma, Shanghai, China), penicillin G (100 units/mL), and streptomycin (100 μg/mL).

extract_protocol:
1. Remove the cryovial from the liquid nitrogen container and place it directly into a 37 ℃ water bath. Shake it from time to time to melt it as quickly as possible. 2. Remove the cryovial from the 37 ° C water bath, open the lid, use a pipette to aspirate the cell suspension, and add it to the centrifuge tube. 3. Centrifuge, 300rcf, 3.5min: 4. Discard the supernatant, add 1ml PBS+0.01% BSA to resuspend the cells, centrifuge at 300rcf for 3.5 minutes. 5. Repeat step 4 twice 6. Count and use as needed.
Sequencing libraries were prepared according to the manufacturer’s instructions of 10K Genomics Library Amp Kit

treatment_protocol: For long-term TNF treatment, IEC-6 cells were repeatedly exposed to 100 ng/mL recombinant rat TNF for 72 hours, resulting in a total of 10 treatment cycles.

value: Small intestine

value: Epithelial cells


title: 20_cond_E

description: Library name: 20_cond_E


title: TotalRNA_wP_1

description:
Library name: TotalRNA_wP_1
NovaSeq X Plus used

value: WT


title: Normal control chondeocytes, rep2

value: NC


title: HDH-TnFa,rep1,scRNAseq

description: 10k Genomics


title: Nsd2 KO1


title: Normal control chondeocytes, rep3


title: TotalRNA_woP_2

description:
Library name: TotalRNA_woP_2
NovaSeq X Plus used


title: 7-C

city: nan chang

first: chuang

last: suan

address: zhan qian road 163

institute: nan chang university

description: hippocampus,control group,day 14

data_processing:
Base Calling,Bcl2fastq (v2.17.1.14).Base Calling was performed on the original image data of sequencing results by using Bcl2fastq (v2.17.1.14) software.
The raw data were preprocessed and the low quality data were filtered to remove contamination and joint sequences.Cutadapt（version 1.9.1）
clean data and reference genome analysis,LncRNA:Hisat2(v2.0.1)，CircRNA:bwa，0.7.12-r1039
Assembly: mm9
Supplementary files format and content: text files include FPKM values for each Sample(CircRNA)
Supplementary files format and content: excel files include FPKM values for each Sample(LncRNA)

source_name: hippocampus tissue

growth_protocol: the 14-month-old healthy male C57BL/6 mice were fed and experimented in the SPF room. These mice were randomly divided into two groups: DHT pretreatment groupand control group.

extract_protocol:
The hippocampus tissue of representative mice was extracted for circRNA sequencing in the testosterone group and the control group.
Gene abundance was calculated and normalized by the SRPBM (spliced reads per billion mapping) method.

treatment_protocol: Mice in the T group were subcutaneously injected with dihydrotestosterone (DHT). And mice in the C group were injected with the same dose of medical corn oil. The entire injection process lasted 14 days and were given once a day in the morning

value: hippocampus tissue

value: C57BL/6 mice

value: injected with  medical corn oil


title: miR-17 overexpressing chondrocytes, rep2


title: miR-17 overexpressing chondrocytes, rep3


title: 2-C

description: hippocampus,control group,day 14


title: TotalRNA_woP_1

description:
Library name: TotalRNA_woP_1
NovaSeq X Plus used


title: Nsd2 WT2

value: Nsd2 WT


title: Nsd2 WT3


title: 10763_S1_S4

city: Cambridge

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

institute: University of Cambridge

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2, relative gene expression was determined using RSEM.
Assembly: hg38
Supplementary files format and content: CSV gene_count_matrix include raw counts per sample
Supplementary files format and content: gene_count_matrix

source_name: skin

growth_protocol: Cells were culture in Endothelial Cell Medium supplemented with 10% FBS.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
Purified RNA (1µg) was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the KAPA Stranded mRNA-seq Kit (KR0960) Illumina platforms sample preparation protocol (v3.15). Briefly, poly(A) RNA was captured with magnetic oligo-dT beads and heat fragmented (94°C) to a size of 200-300bp. Fragmented RNA was used for 1st strand cDNA synthesis, generating cDNA-RNA hybrids which were used for 2nd strand synthesis and marking to obtain dscNDA marked with dUTP. Newly synthesized fragments were end-repaired and A-tailed to add dAMP to the 3’-end of dscDNA fragments. These 3’-dA-tailed library fragments were then ligated with 3’-dTMP adapters. After adapter ligation, libraries were cleaned up using the Agencourt AMPure XP reagent (A63880) according to manufacturer’s recommendations. Purified, adapter-ligated DNA was amplified for 15 cycles. PCR libraries were pooled in equimolar concentrations and sequenced.

value: skin

value: iHemEC

value: immortalised human cell line

value: sunitinib treated


title: Nsd2 KO2


title: 10763_S3_S6


title: Daudi cells, ENO1_IP_2

city: 大连

first: WenliYan

middle: Wenli

last: Yan

state: 辽宁省

address: 甘井子区

department: 附属第二医院

institute: 大连医科大学

description:
Library name: Sample 4
ENO1_IP_2_peak_info.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by tophat2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak_info values for each Sample

source_name: Daudi cells

growth_protocol: Daudi cells were maintained in 1640 supplemented with 10% fetal bovne serum(FBS)and antibiotics in humidifed atmosphere with 5% CO2 at 37C

extract_protocol:
RNA extraction: The TRIzol method is used to extract RNA according to the manufacturer's instructions. RNA precipitates were washed with 75% ethanol and dissolved in RNase-free water.RNA quality control: RNA concentration is determined using NanoDrop. RNA integrity was measured using Agilent Bioanalyzer (RIN > 7.0).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-SeqLibrary Prep Kit following manufacturer's protocols.

treatment_protocol: Cell treatment: Cell line: Daudi cells. Treatment conditions: Cells were cultured in 1640 medium containing 10% FBS. Crosslinking: Use 1% formaldehyde at room temperature for 10 minutes, followed by 125 mM glycine to terminate the reaction. Cell lysis: Cells were lysed using RIPA lysis buffer containing protease inhibitors and RNase inhibitors and incubated on ice for 15 minutes. The lysate was clarified by centrifugation (12,000 g, 10 min, 4°C). Immunoprecipitation: Anti-ENO1 antibody (1:30 dilution;abcam Catalog:ab227978 Lot:GR3234384-14) was incubated with lysate overnight at 4°C. Protein A/G magnetic beads were added and incubated at 4°C for 2 hours. The magnetic beads were washed 4 times with RIPA buffer to remove unbound proteins. RNA decrosslinking: Add 10% Chelex-100 and 1% SDS and boil for 10 minutes for decrosslinking. RNA was extracted by TRIzol.

value: Daudi cells

value: lymphoma cell

value: Daudi cells(IP)


title: 10763_E3_S9

value: everolimus treated


title: 26-T

description: hippocampus, testosterone group, day14

value: injected with dihydrotestosterone


title: Cmtr1_cKO_CD4_4

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

description: rRNA-depleted

data_processing:
Reads were aligned to mm10 with gencode vM25 annotation, and read counts for each gene calculated using STAR version 2.5.2b.
Gene expression was compared between controls and Cmtr1 cKO in R using EdgeR (Robinson et al., 2010).
Assembly: mm10 (GRCm38)
Supplementary files format and content: *ReadsPerGene.out.tab: Each reads per gene file contains a tab-delimited table of reads per gene counted during alignment in STAR. The first column indicates the Ensembl gene id, the second column shows all alignments, the third shows forwards alignments, and the fourth shows reverse alignments (reverse aligned reads are the reads counts to use for this library strategy).

source_name: 20 hour activated CD4 T cells

growth_protocol: CD4 T cells were sorted from lymph nodes using a MACS mouse CD4 T cell isolation kit (Miltenyi).

extract_protocol:
RNA was prepared using Trizol.
Libraries were constructed by Genewiz for Illumina, strand-specific RNA-seq with rRNA depletion. Libraries underwent 2x150 bp sequencing on an Illumina NovaSeq.

treatment_protocol: CD4 T cells were cultured for 20 hours in T cell culture medium (RPMI + 10% heat inactivated FCS + pen/strep + 50µM 2ME) on anti-CD3/CD28 coated plates prepared by incubating the plates with PBS with 5ug/ml anti-CD3 and 1ug/ml anti-CD28 at 37C for three hours.

value: Cmtr1 fl/fl CD4cre +

tag: Sex

value: Female

value: Activated CD4 T cells


title: 19-T

description: hippocampus, testosterone group, day14


title: Daudi cells, ENO1_IP_1

description:
Library name: Sample 3
ENO1_IP_1_peak_info.txt

value: WT


title: 10763_E2_S8


title: 3-C

description: hippocampus,control group,day 14

value: hippocampus tissue


title: 10763_S2_S5


title: Nsd2 WT1

value: pancreatic cancer cell


title: Cmtr1_cKO_CD4_3

description: rRNA-depleted


title: 10763_E1_S7


title: Daudi cells, ENO1_input_1

description:
Library name: Sample 1
ENO1_IP_1_peak_info.txt

value: Daudi cells(Input)


title: Con_2.

value: CT26 subcutaneous tumors

value: colon cancer cell

value: Solvent treatment


title: Cmtr1_cKO_CD4_2

description: rRNA-depleted


title: 10763_C3_S3

value: skin

value: iHemEC

value: immortalised human cell line

value: control


title: Cmtr1_cKO_CD4_4

description: Library name: Cmtr1_cKO_CD4_4

data_processing:
DNA sequences were called with Guppy basecaller using the dna_r9.4.1_450bps_fast.cfg configuration file.
Sequence data quality was assessed with NanoComp.
Sequences were aligned to the mm10 mouse genome using flair align, splice junctions corrected using flair correct with gencode vM25 annotation, and isoforms collapsed using flair collapse with the stringent option.
Assembly: mm10
Supplementary files format and content: quants.txt contains a tab seperated file with the counts per transcript for each sample

growth_protocol: CD4 T cells were sorted from lymph nodes using a MACS mouse CD4 T cell isolation kit (miltenyi).

extract_protocol:
RNA was prepared using trizol. mRNA was oligo-dT selected using Dynabeads mRNA direct kit and quantified using the qubit high sensitivity RNA assay.
Libraries were generated with a nanopore direct cDNA sequencing with native barcoding kit (SQK-DCS109 with EXP-NBD104 and EXP-NBD114, Oxford Nanopore) and sequenced on R9.4.1 (FLO-MIN106) flow cells on a MinION sequencer (Oxford Nanopore).

value: 20 hour activated CD4 T cells


title: H2Bub_Light_Rep1_input

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

institute: Sorbonne Université

data_processing:
The Trimmomatic tool is used to trim the reads.
STAR was used to map reads to the TAIR10 genome with --alignIntronMax and  --alignEndsType options to 1 and EndToEnd.
Filters are applied using sambamba view. The flag used is 2572.
Problematic regions of the genome were filtered out from the alignment files using the -L option of sambamba view
The bamCoverage command from deeptools was used to produce bigwig tracks. Specifics about spike-in factor normalization can be found at https://github.com/vidal-adrien/ChIP-Rx-Pipeline-Pub
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: Cotyledon

growth_protocol: Seeds were surface sterilized and sown on half-strength Murashige and Skoog media (Duchefa Biochemie, The Netherlands) with 1% (w/v) Phytoagar, pH 5.7. After three days of stratification at 4°C in darkness, seeds were exposed to light for 4-6 hours to synchronize germination.

extract_protocol:
For S2P RNA Pol II and H2Bub ChIP-seq, dark and light-grown seedlings were fixed in 1% formaldehyde under safe green light or white ambient light, respectively. 400 cotyledons were dissected, frozen and ground. For S2P RNA Pol II ChIP, a second crosslinking was performed and chromatin was extracted as in (Bourbousse2018). Chromatin was sheared using a Covaris sonicator. Immunoprecipitation and subsequent steps employed the Abcam Ab5095. For H2Bub ChIP, 400 cotyledons were dissected from fixed seedlings and chromatin spike-in and immunoprecipitation was conducted as previously described earlier ({NassrallaheLife2018}) using the Medimabs MM-0029-P antibodies.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645). The sequencing was performed on the DNBSEQ-G400 platform (BGI) in paired-end mode.

treatment_protocol: Plants were either grown under long-day light condition for 5 days (Light) or under three layers of aluminum foil for five days. Dark samples were collected under a green safe light.

value: Cotyledon

value: Col-0 WT

value: Light


title: H2Bub_Dark_Rep2_input

value: Dark


title: 10763_C2_S2


title: Control_CD4_4

description: rRNA-depleted

value: Cmtr1 fl/fl CD4cre -

value: Female

value: Activated CD4 T cells


title: Cmtr1_cKO_CD4_3

description: Library name: Cmtr1_cKO_CD4_3

value: Cmtr1 fl/fl CD4cre +


title: 10763_C1_S1

value: WT


title: Cmtr1_cKO_CD4_2

description: Library name: Cmtr1_cKO_CD4_2

value: Male


title: H2Bub_Dark_Rep1_input


title: WT_B

city: Boston

first: Claudia

last: Mimoso

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

data_processing:
All custom scripts described are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts). For Figures 2 and 6, the custom script (trim_and_filter_PE.pl) was used to trim FASTQ read pairs to 75 bp per mate and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were aligned to human (hg38) genome using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.
Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.
BedGraphs were depth-normalized using the normalize_bedGraph custom script.
Depth-normalized BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: human embryonic stem cells

growth_protocol: hESCs were cultured using the mTeSR1TM1 kit (STEMCELL technology) and 1% penicillin-streptomycin (Sigma) on Matrigel-coated (CORNING) tissue culture plates and incubated at 37°C in humidified 5% (vol/vol) CO2.

extract_protocol:
Total RNA isolation from SF3B1K700E and WT ES cells was performed using the RNeasy Kit (Qiagen) following manufacturer’s instructions.
Bulk mRNA sequencing of triplicate samples was performed using NEBNext® Ultra™ II RNA Library preparation (NEB #E7775) with PolyA selection

value: human embryonic stem cells

value: H9 ES cells (WA09)

value: SF3B1 WT


title: Control_CD4_3

description: rRNA-depleted


title: S2P_Light_Rep3_input


title: H2Bub_Light_Rep2_input


title: Cmtr1_cKO_CD4_1

description: Library name: Cmtr1_cKO_CD4_1


title: Control_CD4_4

description: Library name: Control_CD4_4


title: S2P_Light_Rep1_input


title: WT_A


title: S2P_Light_Rep2_input


title: Control_CD4_3

description: Library name: Control_CD4_3


title: Cmtr1_cKO_CD4_1

description: rRNA-depleted


title: Mut3_CL5C

value: SF3B1 K700E


title: S2P_Dark_Rep3_input


title: Mut3_CL5B


title: S2P_Dark_Rep2_input


title: Control_CD4_2

description: Library name: Control_CD4_2


title: HEP2

city: Hangzhou

first: Jiaxiong

last: Wu

state: ZHEJIANG

address: Yuhangtang Road 866#

institute: Zhejiang University

description: Library name: SAMPLE5

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp(https://github.com/OpenGene/fastp) with default parameters.
Clean reads were then aligned to the reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2) in strand-specific mode.
Transcript expression levels were quantified as transcripts per million (TPM).
Gene abundance was estimated using RSEM (http://deweylab.github.io/RSEM).
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/stats/bioc/DESeq2).
KEGG pathway analysis was carried out by Python scipy software (https://scipy.org/install/).
Assembly: Transcript assembly for each sample was performed with StringTie (https://github.com/gpertea/stringtie), following a reference-based strategy.
Supplementary files format and content: tab-delimited text file incudes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: inguinal white adipose tissue

extract_protocol:
Total RNA was extracted from the iWAT of HFD group and HEP group using TRIzol® Reagent according the manufacturer’s instructions.
Transcriptome libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) with 1 μg of total RNA. Libraries were size selected for cDNA target fragments of 300 bp on 2 % Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

value: inguinal white adipose tissue

value: High-fat-diet with 0.5% hesperidin


title: HEP1

description: Library name: SAMPLE4


title: Mut3_CL5A


title: WT_C


title: FasL KO 3

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

description: Sample 6

data_processing:
FastQC
Trimgalore
SortMeRNA
Rbowtie2
Rsamtools
Function summarizeOverlaps from GenomicAlignments package
DeSEQ2
Assembly: mm10
Supplementary files format and content: comma-separated file includes raw count for each sample and output DESeq2

growth_protocol: Differentiation was performed in osteogenic media consisting of MEM alpha (Gibco, Waltham, MA, USA), 10% fetal bovine serum (Sigma-Aldrich, Burlington, MA, USA), 1% penicillin/streptomycin (Sigma-Aldrich), 50 mg/ml ascorbate and 4 mM β-glycerophosphate in 37˚C and 5% CO2. For the stimulatory experiment of gld cells, the osteogenic medium was supplemented with 150 ng/ml recombinant human sFas ligand (Peprotech, 310-03H) at day 14 of differentiation. The cells were then cultured for 72 h, the medium/medium+FasL was changed once during this time, wt cells (wt), gld cells (gld) and gld cells treated by FasL (gld+FasL) were cultured in parallel.

extract_protocol:
Samples for RNA isolation were lysed in 350 μl of RLT lysis buffer (Qiagen) with β-ME (Sigma-Aldrich), total RNA was extracted using RNeasy Mini Kit (Qiagen, Germany).
Total RNA samples were sent for QuantSeq analysis to Lexogen GmbH, Campus Vienna Biocenter 5, Vienna, where the samples were processed and sequenced according to the company's standard operating procedure. In brief, the library for sequencing was prepared using the QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and the Lexogen i5 6 nt Unique Dual Indexing Add-on Kit (Lexogen).

value: FasL KO


title: HFD3

description: Library name: SAMPLE3

value: High-fat-diet


title: Normal control chondeocytes, rep1

value: chondrocytes

value: NC


title: Mut2_CL274C


title: 27-T

description: hippocampus, testosterone group, day14

value: hippocampus tissue

value: C57BL/6 mice

value: injected with dihydrotestosterone


title: Control_CD4_2

description: rRNA-depleted

value: Cmtr1 fl/fl CD4cre -

value: Female

value: Activated CD4 T cells


title: HEP3

description: Library name: SAMPLE6

value: WT


title: Daudi cells, ENO1_input_2

description:
Library name: Sample 2
ENO1_IP_2_peak_info.txt

value: Daudi cells

value: lymphoma cell

value: Daudi cells(Input)


title: HFD2

description: Library name: SAMPLE2


title: FasL KO 2

description: Sample 5


title: S2P_Dark_Rep1_input

value: Cotyledon

value: Col-0 WT

value: Dark


title: H2Bub_Light_Rep1_IP

value: Light


title: Control_CD4_1

description: rRNA-depleted


title: FasL KO 1

description: Sample 4

value: FasL KO


title: HFD1

description: Library name: SAMPLE1

value: inguinal white adipose tissue

value: High-fat-diet


title: Mut2_CL274B

value: human embryonic stem cells

value: H9 ES cells (WA09)

value: SF3B1 K700E


title: H2Bub_Dark_Rep2_IP


title: wt 3

description: Sample 3


title: H2Bub_Light_Rep2_IP


title: Control_CD4_1

description: Library name: Control_CD4_1

value: Male

value: Cmtr1 fl/fl CD4cre -

value: 20 hour activated CD4 T cells


title: cdh5-3

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: Library name: cdh5-3

data_processing:
Bioinformatic analysis of transcriptomic data adhere to recommended ENCODE guidelines and best practices for RNA-Seq (Encode Consortium, 2016). Alignment of adapter-trimmed (Skewer v0.1.123; Jiang et al., 2014) 2x150 (paired-end; PE) bp strand-specific Illumina reads to the Mus musculus GRCm39 genome (assembly accession NCBI: GCA_000001635.9) was achieved with the Spliced Transcripts Alignment to a Reference (STAR 2.7.11b) software (Dobin, et al., 2013), a splice-junction aware aligner, using annotation provided by Ensembl release 110. Expression estimation was performed with RSEM v1.3.1 (RNASeq by Expectation Maximization; Li and Dewey, 2011).
Assembly: GRCm39
Supplementary files format and content: TSV of RSEM normalized RNA expression values for each gene

source_name: hematopoietic stem and progenitor cells

extract_protocol:
HSPCs were sorted directly into TRIzol LS (Invitrogen) and stored at -80C until ready for RNA extraction. RNA was extracted following TRIzol LS manufacturer's instruction with GenElute-LPA added to facilitate RNA precipitation.
Total RNA libraries were prepared using the Takara SMARTer Stranded RNA v2 Pico kit.

value: hematopoietic stem and progenitor cells


title: Mut1_CL245C


title: cdh5-2

description: Library name: cdh5-2


title: wt 1

description: Sample 1

value: WT


title: Mut1_CL245B


title: S2P_Light_Rep3_IP


title: Mut1_CL245A


title: Cmtr1 cKO naive CD4 4

data_processing:
Libraries were sequenced on an Illumina Nextseq 500 using a high output 2 X 75bp kit.
Reads were aligned to mm10 with gencode vM12 basic annotation, and read counts for each gene calculated using STAR version 2.5.2b.
Gene expression was compared between controls and Cmtr1 cKO in R using EdgeR (Robinson et al., 2010), using a counts per million (CPM) threshold of 1 in at least three samples.
Assembly: mm10 (GRCm38)
Supplementary files format and content: *ReadsPerGene.out.tab: Each reads per gene file contains a tab-delimited table of reads per gene counted during alignment in STAR. The first column indicates the Ensembl gene id, the second column shows all alignments, the third shows forwards alignments, and the fourth shows reverse alignments (reverse aligned reads are the reads counts to use for this library strategy).

source_name: Naïve CD4 T cells

growth_protocol: Naïve CD4 T cells were FACS sorted (as: TCRb+, CD4+, CD62L+, CD44-, DAPI-) from lymph nodes.

extract_protocol:
RNA was prepared using Trizol.
Libraries were prepared at the Tayside Centre for Genomic Analysis with an Illumina TruSeq kit with Ribozero Gold rRNA depletion.

value: Cmtr1 fl/fl CD4cre +

value: Naive CD4 T cells


title: S2P_Light_Rep2_IP

value: Cotyledon


title: WT-3

description: Library name: WT-2


title: wt 2

description: Sample 2


title: S2P_Light_Rep1_IP

value: Col-0 WT


title: S2P_Dark_Rep3_IP

value: Dark


title: WT-2

description: Library name: WT-1b


title: Sap130_ChIPSeq

city: Pittsburgh

first: Hisato

last: Yagi

state: PA

address: 530 45th street, Rangos Res Center 8162

institute: University of Pittsburgh

description: Library name: Sap130_ChIPSeq

data_processing:
Reads were mapped to the mouse reference genome (GRCm38 from Illumina iGenomes website) using Bowtie1 (Version: 1.1.2) with the commandline options: bowtie -v 2 -t -k 2 -m 1
Peaks were called using MACS2 (Model-based Analysis for ChIP-Seq, version: MACS-2.1.0.20140616) with the command-line options: macs2 callpeak -t sap130File -c ctrlFile -f BOWTIE -g mm -B -q 0.01. (FDR cutoff of 0.01).
Assembly: GRCm38/mm10
Supplementary files format and content: E13.5_heart_Sap130vsInput_peaks
Supplementary files format and content: Chromosome-wise wig files (tar) for each of Sap130 and Input and a BED file with peaks found by comparing Sap130 to Input."

source_name: Heart

extract_protocol:
Chromatin immunoprecipitation of Sap130 was performed with rabbit anti-Sap130 antibody (A302-491A: Bethyl laboratories, 2ug) and iDeal ChIP-seq Kit for Transcription Factors (Diagenode) following the manufacturer’s protocol
ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

value: Heart

tag: age

value: B6 Wild type

tag: antibody


title: Mut2_CL274A


title: WT-1

description: Library name: WT-1


title: Input DNA

description: Library name: Input DNA

value: none; input


title: S2P_Dark_Rep2_IP


title: Cmtr1 cKO naive CD4 1


title: Actr3 KO-1

city: Freiburg

first: Manuel

last: Rogg

address: Breisacher Straße 115a

institute: University Medical Center Freiburg

description:
Library name: Sample 3
featureCounts

data_processing:
The Galaxy Europe resource was used for processing and analysis of sequencing data (https://usegalaxy.eu).
Sequenced reads were quality and adapter trimmed using fastp v0.20.1.
Reads were mapped to mm10 whole genome using HISAT2 v2.2.1 with default settings for single-end libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.7 were applied for differential expression analysis
Assembly: Mouse Dec. 2011 (GRCm38/mm10) (mm10)
Supplementary files format and content: tab-delimited text files include normalized counts for all samples

source_name: Kidney medulla

extract_protocol:
Isolation of total RNA from the medulla of two Actr3 KO and two Actr3 WT animals at p14 was performed using the Qiagen RNAeasy midi Kit (74104, Quiagen) according to the supplier instructions.
Library preparation and Illumina sequencing were performed by Eurofins GATC Biotech.

value: Kidney medulla

value: C57BL/6 mixed

value: Actr3 KO


title: H2Bub_Dark_Rep1_IP


title: Tie2-3

description: Library name: Tie2-3


title: Control naive CD4 2


title: Actr3 WT-2

description:
Library name: Sample 2
featureCounts

value: wild type control

value: Actr3 WT


title: Tie2-2

description: Library name: Tie2-2


title: cdh5-1

description: Library name: cdh5-1


title: Tie2-1

description: Library name: Tie2-1


title: Control naive CD4 1

value: Cmtr1 fl/fl CD4cre -

value: Male


title: Actr3 WT-1

description:
Library name: Sample 1
featureCounts


title: WT_rep5_L

data_processing:
Reads were mapped using Salmon (version 1.9.0) (PatroNat Methods 2017) on a merged reference transcriptome composed of the AtRTD3 (ZhangGenome Biol 2022) Arabidopsis transcriptome and the dmel_r6.48 Drosophila transcriptome and using the Arabidopsis (TAIR10) and Drosophila (dmel_r6.48) genome as a decoy sequence.
The read counts were obtained from the median of those inferential replicates via the tximport R package (version 1.30.0, R version 4.3.2) (SonesonF1000Research 2015) with the 'scaledTPM' option. on TAIR10 genes and transposons with htseq-count
Genome_build: TAIR10
Supplementary_files_format_and_content: txt file containing raw read count per locus

source_name: cotyledon

growth_protocol: 5 days of growth on MS 1/2 in darkness or long days

extract_protocol:
Acetone fixation, dissection of cotyledons, grinding and extraction after adding drosohila cells with Qiagen micro RNeasy kit
DNB-seq paired-end stranded

treatment_protocol: Dark-grown seedlings (D) were further exposed to 1h, 6h or 24h of continuous light

tag: time of light

value: L

tag: bio rep


title: Cmtr1 cKO naive CD4 3


title: Cd19-3

description: Library name: Cd19-3

value: hematopoietic stem and progenitor cells


title: WT_rep5_6h

value: WT


title: HepG2 cells hypoxia

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

institute: Shanghai Jiao Tong University

data_processing:
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: hg38
Supplementary files format and content: tab-delimited includes FPKM for each sample

growth_protocol: Huh7,97H and HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hepatocellular carcinoma

value: hypoxia