title: E7809003-Visit 8-AZD2423 150 mg

description:
Library name: A9421107-40
A9421107-40,E7809003,Visit 8,AZD2423 150 mg,61,F,69,163,25.97,BLACK OR AFRICAN AMERICAN  ,A9421107_40,CKRO220004047-1A,28,Average Pain NRS Last 12 Hours,1.4,Worst Pain NRS Last 12 Hours,1.4,29,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,0,Evoked Pain Sub Score,0.33,NPSI Total Score,1,Pain Attacks,3,Pain Brushing,0,Pain Pins and Needle,0,Pain Present,4,Pain Pressure,1,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,0,Paroxysmal Pain Sub Score,0,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,0,Tingling,0,


title: E7809008-Visit 8-Placebo

status: Public on Jul 16 2025

type: SRA

city: Piscataway

first: Lei Yu

last: Lei Yu

state: New Jersey

address: 145 Bevier Rd

department: Genetics

country: USA

institute: Rutgers University, New Brunswick: School of Arts and Sciences

description:
Library name: A9421105-37
A9421105-37,E7809008,Visit 8,Placebo,77,F,101,168,35.79,BLACK OR AFRICAN AMERICAN  ,A9421105_37,CKRO220003956-1A,28,Average Pain NRS Last 12 Hours,7.3,Worst Pain NRS Last 12 Hours,7.7,29,Burning Pain,8,Burning Superfic. Spont. Pain Sub Score,8,Electric Shock Pain,4,Evoked Pain Sub Score,5,NPSI Total Score,54,Pain Attacks,4,Pain Brushing,4,Pain Pins and Needle,4,Pain Present,0,Pain Pressure,4,Pain Something Cold,7,Paresthesia/Dysesthesia Sub Score,5.5,Paroxysmal Pain Sub Score,4.5,Pressing Deep Spont. Pain Sub Score,5.5,Pressure Pain,5,Squeezing Pain,6,Stabbing Pain,5,Tingling,7,

library_source: transcriptomic

data_processing:
Combined raw data was delivered via FTP in fast q format.
Assembly: GRCh38
Supplementary files format and content: Tab delimited files (tsv) of merged salmon quantification

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
RNA Extraction from Paxgene tube.
GlobinClear with NEBNext Ultra II RNA (directional) with PolyA selection.

tag: tissue

value: blood

tag: treatment

value: painful diabetic neuropathy


title: E7809016-Visit 8-AZD2423 150 mg

description:
Library name: A9421104-37
A9421104-37,E7809016,Visit 8,AZD2423 150 mg,72,F,76,173,25.39,BLACK OR AFRICAN AMERICAN  ,A9421104_37,CKRO220003965-1A,28,Average Pain NRS Last 12 Hours,1.7,Worst Pain NRS Last 12 Hours,1.8,29,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,1,Evoked Pain Sub Score,1.33,NPSI Total Score,8,Pain Attacks,4,Pain Brushing,2,Pain Pins and Needle,1,Pain Present,4,Pain Pressure,2,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,1,Paroxysmal Pain Sub Score,1,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,1,Tingling,1,


title: E7809005-Visit 8-AZD2423 20 mg

description:
Library name: A9421103-37
A9421103-37,E7809005,Visit 8,AZD2423 20 mg,59,M,100,183,29.86,WHITE,A9421103_37,CKRO220004052-1A,28,Average Pain NRS Last 12 Hours,5.2,Worst Pain NRS Last 12 Hours,4.6,29,Burning Pain,2,Burning Superfic. Spont. Pain Sub Score,2,Electric Shock Pain,2,Evoked Pain Sub Score,3.33,NPSI Total Score,41,Pain Attacks,3,Pain Brushing,4,Pain Pins and Needle,8,Pain Present,3,Pain Pressure,4,Pain Something Cold,2,Paresthesia/Dysesthesia Sub Score,8,Paroxysmal Pain Sub Score,4.5,Pressing Deep Spont. Pain Sub Score,2,Pressure Pain,2,Squeezing Pain,2,Stabbing Pain,7,Tingling,8,


title: E7809012-Visit 3-AZD2423 20 mg

description:
Library name: A9421026-41
A9421026-41,E7809012,Visit 3,AZD2423 20 mg,56,F,115,157,46.66,BLACK OR AFRICAN AMERICAN  ,A9421026_41,CKRO220003995-1A,-1,Average Pain NRS Last 12 Hours,6.9,Worst Pain NRS Last 12 Hours,7.25,1,Burning Pain,5,Burning Superfic. Spont. Pain Sub Score,5,Electric Shock Pain,7,Evoked Pain Sub Score,3.33,NPSI Total Score,45,Pain Attacks,2,Pain Brushing,4,Pain Pins and Needle,5,Pain Present,2,Pain Pressure,6,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,5.5,Paroxysmal Pain Sub Score,6.5,Pressing Deep Spont. Pain Sub Score,3,Pressure Pain,6,Squeezing Pain,0,Stabbing Pain,6,Tingling,6,


title: E7809003-Visit 3-AZD2423 150 mg

description:
Library name: A9421024-41
A9421024-41,E7809003,Visit 3,AZD2423 150 mg,61,F,69,163,25.97,BLACK OR AFRICAN AMERICAN  ,A9421024_41,CKRO220004030-1A,-1,Average Pain NRS Last 12 Hours,7.1,Worst Pain NRS Last 12 Hours,8.8,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,2,Evoked Pain Sub Score,4.67,NPSI Total Score,44,Pain Attacks,3,Pain Brushing,5,Pain Pins and Needle,5,Pain Present,3,Pain Pressure,8,Pain Something Cold,1,Paresthesia/Dysesthesia Sub Score,6,Paroxysmal Pain Sub Score,1,Pressing Deep Spont. Pain Sub Score,4.5,Pressure Pain,3,Squeezing Pain,6,Stabbing Pain,0,Tingling,7,


title: E7809005-Visit 3-AZD2423 20 mg

description:
Library name: A9421023-41
A9421023-41,E7809005,Visit 3,AZD2423 20 mg,59,M,100,183,29.86,WHITE,A9421023_41,CKRO220003944-1A,-1,Average Pain NRS Last 12 Hours,8,Worst Pain NRS Last 12 Hours,8.7,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,8,Evoked Pain Sub Score,7.33,NPSI Total Score,76,Pain Attacks,2,Pain Brushing,8,Pain Pins and Needle,9,Pain Present,2,Pain Pressure,8,Pain Something Cold,6,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,6.5,Pressure Pain,7,Squeezing Pain,6,Stabbing Pain,8,Tingling,9,


title: E1004001-Visit 8-Placebo

description:
Library name: A9420980-37
A9420980-37,E1004001,Visit 8,Placebo,57,F,94,160,36.72,WHITE,A9420980_37,CKRO220003904-1A,28,Average Pain NRS Last 12 Hours,8.1,Worst Pain NRS Last 12 Hours,8.1,29,Burning Pain,8,Burning Superfic. Spont. Pain Sub Score,8,Electric Shock Pain,0,Evoked Pain Sub Score,0,NPSI Total Score,33,Pain Attacks,3,Pain Brushing,0,Pain Pins and Needle,0,Pain Present,3,Pain Pressure,0,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,0,Paroxysmal Pain Sub Score,4.5,Pressing Deep Spont. Pain Sub Score,8,Pressure Pain,8,Squeezing Pain,8,Stabbing Pain,9,Tingling,0,


title: RNA-seq of mouse brain tissue from high-fat diet AD-4 model

city: Xiangtan

first: Shen

last: Yang

address: No.100 Shuyuan Road, Yuetang District, Xiangtan City, Hunan Province

country: China

institute: Department of Neurology, The First People's Hospital of Xiangtan City,

description: Library name: AD-HFD-4

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapter sequences and low-quality bases were trimmed using Trimmomatic.
Assembly: GRCr8 (GCA_036323735.1)
Supplementary files format and content: A tab-delimited text file (raw_counts.txt) containing raw gene counts for all samples. Rows represent genes, and columns represent samples. Gene identifiers are in Ensembl format.

organism: Rattus norvegicus

source_name: brain

growth_protocol: Mice were housed in a specific pathogen-free (SPF) facility with a 12-hour light/dark cycle and had ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from mouse brain tissues using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA integrity was assessed by Agilent 2100 Bioanalyzer.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: brain


title: RNA-seq of mouse brain tissue from high-fat diet AD-3 model

description: Library name: AD-HFD-3


title: E7802006-Visit 8-Placebo

description:
Library name: A9420875-37
A9420875-37,E7802006,Visit 8,Placebo,50,M,106,191,29.06,BLACK OR AFRICAN AMERICAN,A9420875_37,CKRO220002259-1A,28,Average Pain NRS Last 12 Hours,0,Worst Pain NRS Last 12 Hours,0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,


title: E1004001-Visit 3-Placebo

description:
Library name: A9420903-41
A9420903-41,E1004001,Visit 3,Placebo,57,F,94,160,36.72,WHITE,A9420903_41,CKRO220004002-1A,-1,Average Pain NRS Last 12 Hours,7.9,Worst Pain NRS Last 12 Hours,8.2,1,Burning Pain,0,Burning Superfic. Spont. Pain Sub Score,0,Electric Shock Pain,8,Evoked Pain Sub Score,0,NPSI Total Score,33,Pain Attacks,2,Pain Brushing,0,Pain Pins and Needle,3,Pain Present,1,Pain Pressure,0,Pain Something Cold,0,Paresthesia/Dysesthesia Sub Score,4.5,Paroxysmal Pain Sub Score,8.5,Pressing Deep Spont. Pain Sub Score,3.5,Pressure Pain,4,Squeezing Pain,3,Stabbing Pain,9,Tingling,6,


title: RNA-seq of mouse brain tissue from high-fat diet AD-2 model

description: Library name: AD-HFD-2


title: E7802009-Visit 8-AZD2423 20 mg

description:
Library name: A9420874-40
A9420874-40,E7802009,Visit 8,AZD2423 20 mg,61,F,107,171,36.59,WHITE,A9420874_40,CKRO220003943-1A,28,Average Pain NRS Last 12 Hours,8.3,Worst Pain NRS Last 12 Hours,8.5,29,Burning Pain,9,Burning Superfic. Spont. Pain Sub Score,9,Electric Shock Pain,8,Evoked Pain Sub Score,9.67,NPSI Total Score,80,Pain Attacks,1,Pain Brushing,10,Pain Pins and Needle,9,Pain Present,1,Pain Pressure,10,Pain Something Cold,9,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,8,Pressing Deep Spont. Pain Sub Score,4,Pressure Pain,8,Squeezing Pain,0,Stabbing Pain,8,Tingling,9,


title: E7807006-Visit 3-AZD2423 150 mg

description:
Library name: A9422976-41
A9422976-41,E7807006,Visit 3,AZD2423 150 mg,53,M,71,173,23.72,BLACK OR AFRICAN AMERICAN  ,A9422976_41,CKRO220004031-1A,-1,Average Pain NRS Last 12 Hours,4.6,Worst Pain NRS Last 12 Hours,5.4,1,Burning Pain,5,Burning Superfic. Spont. Pain Sub Score,5,Electric Shock Pain,8,Evoked Pain Sub Score,6,NPSI Total Score,63,Pain Attacks,2,Pain Brushing,3,Pain Pins and Needle,9,Pain Present,1,Pain Pressure,7,Pain Something Cold,8,Paresthesia/Dysesthesia Sub Score,9,Paroxysmal Pain Sub Score,6,Pressing Deep Spont. Pain Sub Score,5,Pressure Pain,7,Squeezing Pain,3,Stabbing Pain,4,Tingling,9,


title: E7802002-Visit 8-AZD2423 20 mg

description:
Library name: A9420873-37
A9420873-37,E7802002,Visit 8,AZD2423 20 mg,65,M,82,174,27.08,BLACK OR AFRICAN AMERICAN,A9420873_37,CKRO220003939-1A,28,Average Pain NRS Last 12 Hours,1.9,Worst Pain NRS Last 12 Hours,2,29,Burning Pain,4,Burning Superfic. Spont. Pain Sub Score,4,Electric Shock Pain,0,Evoked Pain Sub Score,3.33,NPSI Total Score,24,Pain Attacks,4,Pain Brushing,0,Pain Pins and Needle,3,Pain Present,3,Pain Pressure,5,Pain Something Cold,5,Paresthesia/Dysesthesia Sub Score,4,Paroxysmal Pain Sub Score,1,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,2,Tingling,5,


title: E7802007-Visit 8-AZD2423 150 mg

description:
Library name: A9420872-40
A9420872-40,E7802007,Visit 8,AZD2423 150 mg,74,M,90,186,26.01,WHITE,A9420872_40,CKRO220004044-1A,28,Average Pain NRS Last 12 Hours,3.7,Worst Pain NRS Last 12 Hours,3.8,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,


title: RNA-seq of mouse brain tissue from Alzheimer's-3 model

description: Library name: AD-3


title: RNA-seq of mouse brain tissue from Alzheimer's-4 model

description: Library name: AD-4


title: HT29 3D wt vs PARP13 KO Replicate 3

type: RNA

city: Vilnius

first: Rimvile

last: Prokarenkaite

address: Santariskiu st 1

country: Lithuania

institute: National Cancer Institute

description: HT29 wt and PAR13 KO HT29 cells  were cultivated under 3D cell culture. For differential gene expression analysis wild type cells served as a control. Biological replicate 3 of 3.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes using Gene Expression Hybridization Kit (Agilent) were hybridized to Human 4x44k Oligonucleotide Microarrays (Agilent) using HS 400 hybridization station (Tecan, Switzerland).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

source_name: Colorectal cancer HT29 cells cultivated under 3D cell culture conditions, wt

label_protocol: 100 ng of total RNA was used for cDNA synthesis and amplification using Low Input Quick Amp Gene Expression Labeling Kit (Agilent).

growth_protocol: Cells were cultured in DMEM cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2. For 3D cell culture conditions, cells were plated in 0.5 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose ir a 24-well cell culture plates.

extract_protocol: Total RNA was isolated from harvested cells using Quick-RNA Miniprerp Kit (Zymo Research) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer 2100 (Agilent).

tag: origin

value: colorectal cancer

tag: cell line

source_name: Colorectal cancer HT29 PARP13 knockout cells  cultivated under 3D cell culture conditions


title: HT29 3D wt vs PARP13 KO Replicate 1

description: HT29 wt and PAR13 KO HT29 cells  were cultivated under 3D cell culture. For differential gene expression analysis wild type cells served as a control. Biological replicate 1 of 3.


title: HT29 2D wt vs PARP13 KO Replicate 3

description: HT29 wt and PAR13 KO HT29 cells  were cultivated under 2D cell culture. For differential gene expression analysis wild type cells served as a control. Biological replicate 3 of 3.

source_name: Colorectal cancer HT29 cells cultivated under 2D cell culture conditions, wt

source_name: Colorectal cancer HT29 PARP13 knockout cells  cultivated under 2D cell culture conditions


title: HT29 2D wt vs PARP13 KO Replicate 1

description: HT29 wt and PAR13 KO HT29 cells  were cultivated under 2D cell culture. For differential gene expression analysis wild type cells served as a control. Biological replicate 1 of 3.


title: RNA-seq of mouse brain tissue from Alzheimer's-2 model

description: Library name: AD-2


title: HT29 PARP13 KO 3D Control vs 5x2Gy Replicate 3

description: HT29 PARP13 KO cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

scan_protocol: Microarray slides were scanned using SureScan Microarray scanner (Agilent).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Colorectal cancer HT29 PARP13 KO cells cultivated under 3D cell culture conditions, without irradiation

treatment_protocol: Cells were treated with fractionated 5x2 Gy dose of ionizing radiation

source_name: Colorectal cancer HT29 PARP13 KO cells cultivated under 3D cell culture conditions, irradiated 5x2Gy


title: E7802003-Visit 8-Placebo

description:
Library name: A9420876-37
A9420876-37,E7802003,Visit 8,Placebo,46,M,143,178,45.13,WHITE,A9420876_37,CKRO220004050-1A,28,Average Pain NRS Last 12 Hours,8,Worst Pain NRS Last 12 Hours,9,29,Burning Pain,1,Burning Superfic. Spont. Pain Sub Score,1,Electric Shock Pain,10,Evoked Pain Sub Score,6.33,NPSI Total Score,54,Pain Attacks,0,Pain Brushing,10,Pain Pins and Needle,10,Pain Present,1,Pain Pressure,7,Pain Something Cold,2,Paresthesia/Dysesthesia Sub Score,10,Paroxysmal Pain Sub Score,6,Pressing Deep Spont. Pain Sub Score,1,Pressure Pain,1,Squeezing Pain,1,Stabbing Pain,2,Tingling,10,


title: RNA-seq of mouse brain tissue from Alzheimer's-1 model

description: Library name: AD-1


title: HT29 PARP13 KO 2D Control vs 5x2Gy Replicate 2

description: HT29 PARP13 KO cells were cultivated under 2D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.

source_name: Colorectal cancer HT29 PARP13 KO cells cultivated under 2D cell culture conditions, without irradiation

source_name: Colorectal cancer HT29 PARP13 KO cells cultivated under 2D cell culture conditions, irradiated 5x2Gy


title: SRRM4KO 3

city: Tokyo

first: Iichiroh

last: Onishi

address: 1-5-45 Yushima, Bunkyo-ku

department: Pathology

country: Japan

institute: Institute of Science Tokyo

description: Library name: SRRM4KO3

data_processing:
Mapping: Hisat2 v2.0.5.
Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%). Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Reference genome version:Homo_sapiens_Ensemble_94
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
DEseq2 for differential analysis
Assembly: Reference genome version:Homo_sapiens_Ensemble_94
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Mesenchymal stem cell

growth_protocol: UE7T-9 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, FUJIFILM Wako Pure Chemical Co., Osaka, Japan).

extract_protocol:
Total RNA was extracted  by RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol including DNase I treatment.
NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Targeted genes, SRRM4 was knocked out using CRISPR v2 by infection with lentivirus.

value: Mesenchymal stem cell

tag: genotype

value: SRRM4 KO


title: HT29 3D wt vs PARP13 KO Replicate 2

description: HT29 wt and PAR13 KO HT29 cells  were cultivated under 3D cell culture. For differential gene expression analysis wild type cells served as a control. Biological replicate 2 of 3.


title: HT29 PARP13 KO 3D Control vs 5x2Gy Replicate 2

description: HT29 PARP13 KO cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: HT29 PARP13 KO 2D Control vs 5x2Gy Replicate 3

description: HT29 PARP13 KO cells were cultivated under 2D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.


title: SRRM4KO 2

description: Library name: SRRM4KO2


title: HT29 PARP13 KO 3D Control vs 5x2Gy Replicate 1

description: HT29 PARP13 KO cells were cultivated under 3D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: RNA-seq of mouse brain tissue from high-fat diet AD-1 model

description: Library name: AD-HFD-1


title: Control3

description: Library name: Control3

value: WT


title: RNA-seq of mouse brain tissue from Sham-3 group

description: Library name: Sham-3


title: RNA-seq of mouse brain tissue from Sham-2 group

description: Library name: Sham-2


title: RNA-seq of mouse brain tissue from Sham-1 group

description: Library name: Sham-1


title: Control2

description: Library name: Control2


title: Control1

description: Library name: Control1


title: E7802003-Visit 3-Placebo

description:
Library name: A9420795-41
A9420795-41,E7802003,Visit 3,Placebo,46,M,143,178,45.13,WHITE,A9420795_41,CKRO220003970-1A,-1,Average Pain NRS Last 12 Hours,6.3,Worst Pain NRS Last 12 Hours,8.7,1,Burning Pain,1,Burning Superfic. Spont. Pain Sub Score,1,Electric Shock Pain,3,Evoked Pain Sub Score,7,NPSI Total Score,47,Pain Attacks,3,Pain Brushing,8,Pain Pins and Needle,10,Pain Present,3,Pain Pressure,8,Pain Something Cold,5,Paresthesia/Dysesthesia Sub Score,10,Paroxysmal Pain Sub Score,2.5,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,2,Tingling,10,


title: BNPMT-3

city: hangzhou

first: Zhao

last: lan

state: Zhejiang Province

address: Dinglan Street

institute: Hangzhou Traditional Chinese Medicine Hospital

description: Library name: sample9

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
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: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

molecule: polyA RNA

source_name: Nucleus pulposus

growth_protocol: Nucleus pulposus cells were cultured in a high-glucose DMEM medium containing 10% serum at 37°C and 5% CO2 in an incubator.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: Nucleus pulposus cells were incubated with 200 nM doxorubicin for 24 h and then replaced with fresh complete medium for another 6 days to induce senescence of nucleus pulposus cells.

value: Nucleus pulposus

tag: cell type

value: Primary nucleus pulposus cells

value: BNPMT intervenes in doxorubicin-induced senescence of nucleus pulposus cells


title: BNPMT-2

description: Library name: sample8


title: E7802002-Visit 3-AZD2423 20 mg

description:
Library name: A9420793-41
A9420793-41,E7802002,Visit 3,AZD2423 20 mg,65,M,82,174,27.08,BLACK OR AFRICAN AMERICAN,A9420793_41,CKRO220003971-1A,-1,Average Pain NRS Last 12 Hours,4.6,Worst Pain NRS Last 12 Hours,5.4,1,Burning Pain,7,Burning Superfic. Spont. Pain Sub Score,7,Electric Shock Pain,7,Evoked Pain Sub Score,5,NPSI Total Score,42,Pain Attacks,1,Pain Brushing,5,Pain Pins and Needle,7,Pain Present,1,Pain Pressure,5,Pain Something Cold,5,Paresthesia/Dysesthesia Sub Score,6.5,Paroxysmal Pain Sub Score,3.5,Pressing Deep Spont. Pain Sub Score,0,Pressure Pain,0,Squeezing Pain,0,Stabbing Pain,0,Tingling,6,


title: SEN-3

description: Library name: sample6

value: Doxorubicin-induced senescence


title: BNPMT-1

description: Library name: sample7


title: SEN-2

description: Library name: sample5


title: SRRM4KO 1

description: Library name: SRRM4KO1


title: RNA-seq of mouse brain tissue from Sham-4 group

description: Library name: Sham-4


title: HC-MYCN-OE1-2

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

description: Library name: Sample36

data_processing:
Raw reads were aligned to the mouse reference genome UCSC mm10 (GRCm38) or the human reference genome (GRCh38/hg38) using salmon for quasi-mapping-based transcript quantification. Transcript abundance was reported as transcripts per million (TPM)
Assembly: mm10, hg38
Supplementary files format and content: CSV file includes TPM values from mouse liver tissues
Supplementary files format and content: CSV file includes TPM values from huaman HCC cells

source_name: Hc

extract_protocol:
Total RNA was extracted using a FastGene RNA Basic Kit (NIPPON Genetics) and quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific)
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol

value: Hc

tag: time point

value: hepatocyte

value: MYCN overexpression


title: HC-MYCN-OE1-1

description: Library name: Sample35


title: HC-MYCN-OE2-1

description: Library name: Sample37


title: HC-WT2

description: Library name: Sample34


title: SEN-1

description: Library name: sample4


title: Neutrophil RNA-seq from trauma patient T32 at 72h

city: Los Angeles

first: Jinyao

last: Tian

state: CA

address: 3185 Wilshire Blvd

department: Keck Medicine of USC

institute: University of Southern California

description: Library name: Pt_32_72h_S61

data_processing:
Raw FASTQ files were quality-checked using FastQC. Adapter trimming and low-quality base removal performed using Trimmomatic.
Assembly: GRCh38 (GENCODE release 38)
Supplementary files format and content: Tab-delimited gene expression matrix (.txt or .csv) containing Ensembl gene IDs and raw read counts for each sample.

source_name: Peripheral blood CD66b+ neutrophils

extract_protocol:
Neutrophils were isolated from whole blood using CD66b+ magnetic bead-based positive selection. Total RNA was extracted using Qiagen RNeasy Mini Kit following manufacturer’s instructions.
PolyA-enriched mRNA libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit v2 according to manufacturer’s protocol.

value: Peripheral blood CD66b+ neutrophils

tag: time

tag: injury type

value: Severe

tag: patient id

value: Trauma


title: NC3

description: Library name: sample3


title: HC-WT1

description: Library name: Sample33


title: Neutrophil RNA-seq from trauma patient T23 at 72h (S10)

description: Library name: Pt_23_72h_S10

value: Mild


title: NC1

description: Library name: sample1


title: NC2

description: Library name: sample2


title: Neutrophil RNA-seq from trauma patient T22 at 8h

description: Library name: Pt_22_8h_S12


title: Cardiomyocyte,Cardiacfibroblats,Bonemarrow derived-macrophages

city: Beijing

first: Xiangning

last: Liu

address: Chaoyang District, N.3rd Ring Rd East

institute: Beijing University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Rnor_6.0  and  mm10
Supplementary files format and content: tab-delimited text files include raw conuts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
mRNA was extracted using trizol
NEB library, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand-specific library, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Primary cell


title: 3D Coculture Cardiomyocyte,Cardiacfibroblats,Bonemarrow derived-macrophages


title: RM_2

city: Parma

first: Alessia

last: Caputo

state: Parma

address: Parco Area delle Scienze 23/A

country: Italy

institute: University of Parma

data_processing:
Data processing steps were conducted following the LeXogen suggested pipeline https://www.lexogen.com/quantseq-data-analysis/
The adapter contamination, polyA read through, and low quality tails were removed using bbduk
Reads were aligned to the Rattus norvegicus genome (v. mRatBN7.2) using STAR (v. 2.7.10a)
Counts were generated using HTSeq (v. 0.11.3)
Assembly: rn6
Supplementary files format and content: The tab-delimited text file includes the raw counts for each sample

source_name: heart_right ventricle

extract_protocol:
The fresh ventricles were immediately separated from the atria and flash frozen. Subsequently, the ventricles were homogenised with pestle and mortar in liquid nitrogen and RNA was extracted using miRNeasy Tissue/Cells Advanced Mini Kit (QIAGEN, The Netherlands), including the DNase digestion protocol.
Libraries for massive parallel RNA sequencing (RNA-seq) were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) and sequenced, in two runs, with the use of a HiSeq X Ten platform, which generated at least 20 million reads/sample (150 bp Paired End).

treatment_protocol: Methods: Male rats, upon reaching a weight of 250g, were injected with a dose of monocrotaline (MCT) 60 mg/kg or saline solution and sacrificed upon reaching a discomfort score (DS) greater than or equal to 7. Transcriptome profiling by RNAseq was performed on total RNA extracted from the right and left ventricles.

value: heart_right ventricle

value: monocrotaline


title: Neutrophil RNA-seq from trauma patient T39 at 72h

description: Library name: Pt39_72h_S76


title: HC-MYCN-OE2-2

description: Library name: Sample38


title: HT29 2D wt vs PARP13 KO Replicate 2

description: HT29 wt and PAR13 KO HT29 cells  were cultivated under 2D cell culture. For differential gene expression analysis wild type cells served as a control. Biological replicate 2 of 3.

value: colorectal cancer


title: RM_1


title: Neutrophil RNA-seq from trauma patient T39 at 24h

description: Library name: Pt39_24h_S75


title: Neutrophil RNA-seq from trauma patient T39 at 8h

description: Library name: Pt39_8h_S74


title: RM_3


title: Neutrophil RNA-seq from trauma patient T39 at 0h

description: Library name: Pt39_0h_S73


title: RM_5


title: Neutrophil RNA-seq from trauma patient T36 at 72h

description: Library name: Pt36_72h_S70


title: Neutrophil RNA-seq from trauma patient T36 at 24h

description: Library name: Pt36_24h_S69


title: Neutrophil RNA-seq from healthy control HC37

description: Library name: Pt37_control_S71

value: Healthy Control


title: Neutrophil RNA-seq from healthy control HC38

description: Library name: Pt38_control_S72


title: LM_1

source_name: heart_left ventricle

value: heart_left ventricle


title: Neutrophil RNA-seq from trauma patient T3 at 72h

description: Library name: Pt_3_72h_S3


title: LM_3


title: LM_5


title: RP_5

value: saline solution


title: RP_2


title: Neutrophil RNA-seq from trauma patient T36 at 8h

description: Library name: Pt36_8h_S68


title: Neutrophil RNA-seq from trauma patient T36 at 0h

description: Library name: Pt36_0h_S67


title: Neutrophil RNA-seq from trauma patient T32 at 24h

description: Library name: Pt32_24h_S60


title: Neutrophil RNA-seq from trauma patient T32 at 0h

description: Library name: Pt32_0h_S58


title: RP_1


title: RP_3


title: RP_4


title: Neutrophil RNA-seq from trauma patient T30 at 24h

description: Library name: Pt30_24h_S51


title: Neutrophil RNA-seq from trauma patient T30 at 8h

description: Library name: Pt30_8h_S52


title: LP_2


title: LP_5


title: Neutrophil RNA-seq from trauma patient T28 at 72h

description: Library name: Pt28_72h_S26


title: Neutrophil RNA-seq from trauma patient T28 at 24h

description: Library name: Pt28_24h_S25


title: RM_4


title: Neutrophil RNA-seq from trauma patient T28 at 8h

description: Library name: Pt28_8h_S24


title: LM_2


title: LP_3


title: LP_4


title: Neutrophil RNA-seq from trauma patient T32 at 8h

description: Library name: Pt32_8h_S59


title: LM_4


title: THRAA, uninjured entire heart, biological rep2

city: Shatin

first: Man Yee

last: CHEUNG

address: Lo Kwee-Seong Integrated Biomedical Sciences  Building, Area 39

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: THRAA2_entireheart

data_processing:
QC and adapters trimming were performed by Trim Galore (v.0.6.10) and aligned with the reference genome of zebrafish (Genome assembly of Danio Rerio: GRCz11) using STAR (v2.7.9). The output files in BAM format were passed to RSEM (v1.3.3) for quantifying gene expression level. DESeq2 (v1.42.0) was used for differential expression analysis, genes with |log2FC| ≥ 1 and adjusted p-value < 0.05 are defined as differentially expressed genes (DEGs) for downstream analysis. Enrichment of Gene Ontology (GO), pathway analysis, motif analysis, ligand-receptor interaction, protein-protein interaction network (PPI) and Gene Set Enrichments Analysis (GSEA) were conducted by clusterProfiler (v.4.10.0), HOMER (v4.11), DanioTalk (v.2.0.1), STRING database and GSEA software (v.4.1.0). Mitochondrial and metabolic genes used in this study were referred from the mitoXplorer 2.0 database.
Assembly: GRCz11
Supplementary files format and content: a tab-delimited TPM matrix file for all samples

organism: Danio rerio

source_name: heart

growth_protocol: WT and transgenic zebrafish lines were housed in animal core facility of The Chinese University of Hong Kong. Zebrafish were maintained at 28.5°C and pH 7.0-7.5, and under a 14-hour light and 10-hour dark cycle according to the suggested protocol [258]. Zebrafish were fed 3 times a day with dry feeds.

extract_protocol:
Ventricles from at least five zebrafish ventricles were pooled together for each biological replicate. Total RNA was extracted from the pooled apex tissue collected in TRIzol™ Reagent as previously described [105]. At least 500 ng of extracted RNA was then reverse-transcribed with EasyScript® First-Strand cDNA Synthesis SuperMix (TransGen Biotech, AE301-02) according to manufacturer’s instructions
Two biological replicates were prepared for each genotype. Extracted RNA was sent to Novogene Ltd. (Beijing, China) for library construction and bulk RNA-sequencing. Constructed libraries were sequenced on NovaSeq 6000 PE150 system and ~6 GB of raw data was collected from each sample

treatment_protocol: Ventricles were collected to study heart development in this study. The experimental procedures of ventricle collection were performed as previously described. In brief, adult zebrafish at 4- to 6-month-old were euthanized by overdose Tricaine solution (Sigma-Aldrich, E15021) and subsequently transferred to a wet sponge with ventral side up.  Zebrafish hearts were collected by micro-scissor and stored in TRIzol™ Reagent (Thermo Fisher Scientific, #15596026) for total RNA extraction and sequencing in later steps.

value: heart

value: THRAA hom

value: no injury and homeostasis


title: WT, uninjured entire heart, biological rep1

description: Library name: WT1_entireheart

value: WT


title: Neutrophil RNA-seq from trauma patient T30 at 72h

description: Library name: Pt30_72h_S53


title: Neutrophil RNA-seq from trauma patient T27 at 72h

description: Library name: Pt27_72h_S22


title: Neutrophil RNA-seq from trauma patient T28 at 0h

description: Library name: Pt28_0h_S23


title: Neutrophil RNA-seq from trauma patient T26 at 24h

description: Library name: Pt26_24h_S17


title: Neutrophil RNA-seq from trauma patient T27 at 24h

description: Library name: Pt27_24h_S21


title: THRAA, uninjured entire heart, biological rep1

description: Library name: THRAA1_entireheart


title: Neutrophil RNA-seq from trauma patient T26 at 0h

description: Library name: Pt26_0h_S15


title: WT, uninjured entire heart, biological rep2

description: Library name: WT2_entireheart


title: Neutrophil RNA-seq from trauma patient T26 at 8h

description: Library name: Pt26_8h_S16


title: Homozygous cdkl5sa21938 zebrafish, biol rep 3, 5 days post-fertilization

city: Faro

first: Tatiana

last: Varela

email: tatianacdv@gmail.com, a44770@ualg.pt

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

description: Library name: Homo_3_5dpf

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Raw reads were first trimmed to obtain clean reads using Novogene perl scripts through the elimination of low-quality reads, adapter-containing reads, and ploy-N-containing reads.
After filtering, clean reads were aligned to the zebrafish reference genome (Danio rerio GRCz11) using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the number of reads mapped to each gene. FPKM for each gene were then calculated, considering the gene length and the total number of mapped reads.
Assembly: GRCz11
Supplementary files format and content: one csv file include raw count values for 5dpf  samples (raw_counts_5dpf.csv)
Supplementary files format and content: one csv file include raw count values for 35dpf  samples (raw_counts_35dpf.csv)
Supplementary files format and content: one csv file include FPKM values for 5dpf  samples (FPKM_5dpf.csv)
Supplementary files format and content: one csv file include FPKM values for 35dpf  samples (FPKM_35dpf.csv)

source_name: whole zebrafish

extract_protocol:
Total RNA was isolated using the NZYOL reagent. DNase treatment was then performed using the RNase-Free DNase set from QIAGEN. RNA samples were subjected to the RNeasy kit (QIAGEN) clean-up protocol.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and subjected to fragmentation. Then, the first strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase, followed by the second strand cDNA synthesis using DNA polymerase I, RNase H and dUTP for directional library. The lasting overhangs were transformed into blunt ends through polymerase and exonuclease reactions. To prepare for hybridization, adaptors containing a hairpin loop structure were ligated to the previously 3’ ends adenylated DNA fragments. The AMPure XP system was used to purify the cDNA fragments with 370~420 bp in length that were then digested with USER enzyme. PCR was carried out using Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. The PCR products were purified, and the Agilent Bioanalyzer 2100 system was used to evaluate the library quality.

value: whole zebrafish

value: Homozygous cdkl5sa21938


title: Neutrophil RNA-seq from trauma patient T24 at 24h

description: Library name: Pt24_24h_S44

value: Peripheral blood CD66b+ neutrophils


title: Neutrophil RNA-seq from trauma patient T27 at 8h

description: Library name: Pt27_8h_S20

value: Severe


title: WT zebrafish, biol rep 4, 5 days post-fertilization

description: Library name: WT_4_5dpf


title: Neutrophil RNA-seq from trauma patient T24 at 0h

description: Library name: Pt24_0h_S42

value: Trauma


title: Neutrophil RNA-seq from trauma patient T27 at 0h

description: Library name: Pt27_0h_S19


title: WT zebrafish, biol rep 3, 5 days post-fertilization

description: Library name: WT_3_5dpf


title: Neutrophil RNA-seq from trauma patient T26 at 72h

description: Library name: Pt26_72h_S18


title: Homozygous cdkl5sa21938 zebrafish, biol rep 4, 5 days post-fertilization

description: Library name: Homo_5_5dpf


title: LP_1


title: Homozygous cdkl5sa21938 zebrafish, biol rep 2, 5 days post-fertilization

description: Library name: Homo_2_5dpf


title: Neutrophil RNA-seq from trauma patient T24 at 72h

description: Library name: Pt24_72h_S45


title: WT zebrafish, biol rep 5, 5 days post-fertilization

description: Library name: WT_5_5dpf


title: Neutrophil RNA-seq from trauma patient T24 at 8h

description: Library name: Pt24_8h_S43


title: Neutrophil RNA-seq from trauma patient T23 at 72h (S9)

description: Library name: Pt23_72h_S9

value: Mild


title: Neutrophil RNA-seq from trauma patient T23 at 0h

description: Library name: Pt23_0h_S7


title: Neutrophil RNA-seq from trauma patient T23 at 8h

description: Library name: Pt23_8h_S8


title: Neutrophil RNA-seq from trauma patient T22 at 72h

description: Library name: Pt22_72h_S14


title: Zebrafish Testis scRNAseq replicate 2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

description: Library name: Zebrafish_Testis_scRNA_rep2

library_source: transcriptomic single cell

data_processing:
Data processing with CellRanger (v7.2.0) pipeline.
Assembly: danRer11
Supplementary files format and content: scRNAseq count matrices

source_name: Testis

growth_protocol: Wild Type Adult zebraifsh were used.

extract_protocol:
Adult transgenic zebrafish (Danio rerio), aged six months, were prepared and anesthetized with 0.25% tricaine methanesulfonate (MS-222) on ice for 15 minutes prior to experimentation. Testes samples were dissected from these zebrafish and rinsed three times with PBS. The samples were then digested in 10 ml of 0.25% trypsin at 37°C for 15 minutes, with gentle pipetting every 3 minutes to break down the tissue. The digestion process was stopped using DMEM containing 10% FBS, and the resulting cell suspension was passed through a 70 μm nylon mesh filter. The cells were centrifuged at 1,000 rpm for 10 minutes. After centrifugation, the cells were resuspended in 1 ml of DMEM (with 10% FBS) and subsequently filtered through a 40 μm nylon mesh.
Libraries were constructed using 10X Genomics Chromium Single Cell 3' (v3.1) kit.

value: Testis

tag: developmental stage

value: Adult


title: Homozygous cdkl5sa21938 zebrafish, biol rep 5, 5 days post-fertilization

description: Library name: Homo_4_5dpf


title: WT zebrafish, biol rep 2, 5 days post-fertilization

description: Library name: WT_2_5dpf


title: Zebrafish Testis scRNAseq replicate 1

description: Library name: Zebrafish_Testis_scRNA_rep1


title: Neutrophil RNA-seq from trauma patient T22 at 24h

description: Library name: Pt22_24h_S13


title: thraa, 15 dpi, biological rep2

description: Library name: thraa2_15dpi

extract_protocol:
Uninjured apex tissue or injured zone from at least five zebrafish ventricles were pooled together for each biological replicate. Total RNA was extracted from the pooled apex tissue collected in TRIzol™ Reagent as previously described [105]. At least 500 ng of extracted RNA was then reverse-transcribed with EasyScript® First-Strand cDNA Synthesis SuperMix (TransGen Biotech, AE301-02) according to manufacturer’s instructions
Total RNA was extracted with from uninjured ventricles and injured tissues as described above. At least five ventricles and injured tissues were pooled to together for RNA extraction and serve as one biological replicate. Two biological replicates were prepared for each time point and genotype. Extracted RNA was sent to Novogene Ltd. (Beijing, China) for library construction and bulk RNA-sequencing. Constructed libraries were sequenced on NovaSeq 6000 PE150 system and ~6 GB of raw data was collected from each sample

treatment_protocol: Ventricular amputation method was utilized to study heart regeneration in this study. The experimental procedures of ventricular amputation were performed as previously described. In brief, adult zebrafish at 4- to 6-month-old were anesthetized with 0.02% of Tricaine solution (Sigma-Aldrich, E15021) and subsequently transferred to a wet sponge with ventral side up.  Zebrafish hearts were exposed by a small incision and ~20% of ventricular apex was resected. Injured zebrafish were then returned to aquarium system with fresh water and feed supplied. Uninjured zebrafish (as control group) and injured zebrafish at designated time points were euthanized by overdose Tricaine solution. Injured zone from injured zebrafish and ventricular apex from uninjured zebrafish were collected by micro-scissor and stored in TRIzol™ Reagent (Thermo Fisher Scientific, #15596026) for total RNA extraction and sequencing in later steps.

value: thraa KO

value: apex amputation


title: Homozygous cdkl5sa21938 zebrafish, biol rep 1, 5 days post-fertilization

description: Library name: Homo_1_5dpf


title: Neutrophil RNA-seq from trauma patient T22 at 0h

description: Library name: Pt22_0h_S11


title: Neutrophil RNA-seq from trauma patient T19 at 72h

description: Library name: Pt19_72h_S63


title: Neutrophil RNA-seq from trauma patient T19 at 24h

description: Library name: Pt19_24h_S29


title: HT29 PARP13 KO 2D Control vs 5x2Gy Replicate 1

description: HT29 PARP13 KO cells were cultivated under 2D cell culture and irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.

value: colorectal cancer


title: WT, 15 dpi, biological rep1

description: Library name: wt1_15dpi

value: Wild-type


title: WT, 15 dpi, biological rep2

description: Library name: wt2_15dpi


title: Neutrophil RNA-seq from trauma patient T19 at 8h

description: Library name: Pt19_10h_S28


title: thraa, 7 dpi, biological rep1

description: Library name: thraa1_7dpi


title: Neutrophil RNA-seq from trauma patient T18 at 72h

description: Library name: Pt18_72h_S57


title: Neutrophil RNA-seq from trauma patient T19 at 0h

description: Library name: Pt19_0h_S27


title: thraa, 7 dpi, biological rep2

description: Library name: thraa2_7dpi


title: WT, 7 dpi, biological rep2

description: Library name: wt2_7dpi


title: WT zebrafish, biol rep 1, 5 days post-fertilization

description: Library name: WT_1_5dpf


title: WT, 7 dpi, biological rep1

description: Library name: wt1_7dpi


title: Neutrophil RNA-seq from trauma patient T18 at 24h

description: Library name: Pt18_24h_S56


title: Neutrophil RNA-seq from trauma patient T18 at 8h

description: Library name: Pt18_8h_S55


title: Neutrophil RNA-seq from trauma patient T18 at 0h

description: Library name: Pt18_0h_S54


title: thraa, 3 dpi, biological rep1

description: Library name: thraa1_3dpi


title: Neutrophil RNA-seq from trauma patient T15 at 0h

description: Library name: Pt15_0h_S49


title: WT, 3 dpi, biological rep1

description: Library name: wt1_3dpi


title: Neutrophil RNA-seq from trauma patient T14 at 72h

description: Library name: Pt14_72h_S41


title: thraa, 1 dpi, biological rep1

description: Library name: thraa1_1dpi


title: thraa, 15 dpi, biological rep1

description: Library name: thraa1_15dpi


title: WT, 3 dpi, biological rep2

description: Library name: wt2_3dpi


title: Neutrophil RNA-seq from trauma patient T15 at 8h

description: Library name: Pt15_8h_S50


title: Neutrophil RNA-seq from trauma patient T14 at 24h

description: Library name: Pt14_24h_S40


title: thraa, 1 dpi, biological rep2

description: Library name: thraa2_1dpi


title: Neutrophil RNA-seq from trauma patient T14 at 8h

description: Library name: Pt14_8h_S39


title: WT, 1 dpi, biological rep2

description: Library name: wt2_1dpi


title: WT, 1 dpi, biological rep1

description: Library name: wt1_1dpi


title: Neutrophil RNA-seq from trauma patient T13 at 24h

description: Library name: Pt13_24h_S36


title: Neutrophil RNA-seq from trauma patient T14 at 0h

description: Library name: Pt14_0h_S38


title: thraa, 8 hpi, biological rep1

description: Library name: thraa1_8hpi


title: thraa, 8 hpi, biological rep2

description: Library name: thraa2_8hpi


title: Neutrophil RNA-seq from trauma patient T13 at 72h

description: Library name: Pt13_72h_S37


title: thraa, 3 dpi, biological rep2

description: Library name: thraa2_3dpi


title: WT, 8 hpi, biological rep2

description: Library name: wt2_8hpi


title: Neutrophil RNA-seq from trauma patient T12 at 0h

description: Library name: Pt12_0h_S46


title: Neutrophil RNA-seq from trauma patient T12 at 24h

description: Library name: Pt12_24h_S48


title: Neutrophil RNA-seq from trauma patient T13 at 8h

description: Library name: Pt13_8h_S35


title: Neutrophil RNA-seq from trauma patient T12 at 8h

description: Library name: Pt12_8h_S47


title: thraa, uninjured, biological rep1

description: Library name: thraa1_uninj

value: no injury


title: thraa, uninjured, biological rep2

description: Library name: thraa2_uninj

value: heart


title: Neutrophil RNA-seq from trauma patient T10 at 72h

description: Library name: Pt10_72h_S33


title: WT, uninjured, biological rep2

description: Library name: wt2_uninj


title: Neutrophil RNA-seq from trauma patient T10 at 24h

description: Library name: Pt10_24h_S32


title: WT, uninjured, biological rep1

description: Library name: wt1_uninj


title: Neutrophil RNA-seq from trauma patient T7 at 72h

description: Library name: Pt7_72h_S5


title: Neutrophil RNA-seq from trauma patient T7 at 24h

description: Library name: Pt7_24h_S4


title: Neutrophil RNA-seq from trauma patient T10 at 0h

description: Library name: Pt10_0h_S30


title: 39

city: Vienna

first: Dietmar

last: Pils

address: Spitalgasse 23

department: Dept. of General Surgery

country: Austria

institute: Medical Univ. of Vienna

description: Library name: S118036

data_processing:
unitas V.1.8.0 (PMID: 28830358)
Assembly: hg38
Supplementary files format and content: raw reads for tRNA-fragments; tab-delimited

source_name: CRLM

extract_protocol:
AllPrep DNA/RNA FFPE Kit (QIAGEN); RNA fraction
NEBNext® Small RNA Library Prep Set for Illumina®

value: CRLM

tag: Sex

value: male

tag: timing of_metastasis

value: metachronous

tag: tnm

tag: grading

tag: ras

value: wt


title: Neutrophil RNA-seq from trauma patient T10 at 8h

description: Library name: Pt10_8h_S31


title: 26

description: Library name: S118037

tag: primary tumor_sidedness

value: Left

value: mut


title: Neutrophil RNA-seq from trauma patient T7 at 8h

description: Library name: Pt7_8h_S66

tag: tissue

value: Peripheral blood CD66b+ neutrophils

value: Severe


title: 3

description: Library name: S118041

value: female

value: synchronous


title: Neutrophil RNA-seq from trauma patient T4 at 24h

description: Library name: Pt4_24h_S64

tag: treatment

value: Trauma


title: 1

description: Library name: S118039


title: 37

description: Library name: S118034


title: 20

description: Library name: S118035


title: 42

description: Library name: S118033


title: Neutrophil RNA-seq from trauma patient T4 at 72h

description: Library name: Pt4_72h_S62


title: WT, 8 hpi, biological rep1

description: Library name: wt1_8hpi


title: Neutrophil RNA-seq from trauma patient T4 at 8h

description: Library name: Pt4_8h_S6


title: 14

description: Library name: S118029

value: Right


title: 25

description: Library name: S118031


title: Neutrophil RNA-seq from trauma patient T7 at 0h

description: Library name: Pt7_0h_S65


title: 158

description: Library name: S118028


title: Neutrophil RNA-seq from trauma patient T3 at 0h

description: Library name: Pt3_0h_S1

value: Mild


title: 29

description: Library name: S118026


title: Neutrophil RNA-seq from cardiac surgery patient CT1 at 72h

description: Library name: CT1_72h_S79

value: Cardiac Surgery


title: Neutrophil RNA-seq from trauma patient T13 at 0h

description: Library name: P13_0h_S34


title: Neutrophil RNA-seq from trauma patient T3 at 24h

description: Library name: Pt3_24h_S2


title: 102

description: Library name: S118022


title: 28

description: Library name: S118024


title: Neutrophil RNA-seq from cardiac surgery patient CT1 at 24h

description: Library name: CT1_24h_S80


title: 23

description: Library name: S118021


title: 7

description: Library name: S118019


title: Neutrophil RNA-seq from cardiac surgery patient CT1 at 8h

description: Library name: CT1_6h_S78


title: Neutrophil RNA-seq from cardiac surgery patient CT1 at 0h

description: Library name: CT1_0h_S77


title: 45

description: Library name: S118016


title: 155

description: Library name: S118015


title: Raw264.7_LB+LPS

city: Wen zhou

first: haoyi

last: han

address: Ou hai Cha shan

institute: Wenzhou Medical University

description: Library name: sample3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Mouse macrophage

growth_protocol: Cells were incubated at 37 ℃ in 5% CO2 and maintained in DMEM medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: RAW 264.7 cells were seeded in 100 mm dishes at a density of 1 × 107 cells per well.Three experimental groups, Control, LPS, and LB+ LPS, were set up, and 0.5 μg/mL LPS was added to stimulate for 6 h after LB was activated for 30 min. After treatment, the cells were collected, and total RNA from each group was extracted using TRIzol (TaKaRa, Japan). Paired-end sequencing was ultimately carried out on an Illumina HiSeq 4000 platform at LC-BIO Technologies (Hangzhou, China).

value: Macrophage

value: WT

value: with LB and LPS


title: Raw264.7_LPS

description: Library name: sample2

value: with LPS


title: 35

description: Library name: S118014

value: CRLM

value: male


title: Raw264.7_Control

description: Library name: sample1

value: without any drugs


title: 49

description: Library name: S118010

value: metachronous

value: Left

value: wt


title: siMTHFD2-11_TGFb_2

city: Chicago

first: Kun Woo

last: Shin

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

description: Library name: GM-1324

data_processing:
RNA-seq reads were pseudoaligned using Kallisto v.0.46.1
The Kallisto index was made with default parameters and the GENCODE (Release 45 (GRCh38.14) and was run in quant mode with default parameters
Assembly: hg38
Supplementary files format and content: .csv file reports TPM values for all samples

source_name: Lung

growth_protocol: primary normal human lung fibroblasts (HLFs) were grown in DMEM containing 0.1% bovine serum albumin, 5.5mM glucose, 2 mM glutamine, and 1mM pyruvate for 24 hours

extract_protocol:
Total RNA was isolated from fibroblasts using, GenElute™ Mammalian Total RNA Miniprep Kit
Oligo-dT mRNA directional

treatment_protocol: For inhibition of MTHFD2, HLFs were transfected with ON-TARGETplus siRNA (Dharmacon). Cells were plated on 10cm dishes for 24 hours and then replated for experiments as growth protocol. HLFs were treated with TGF-beta (Peprotech) or left untreated.

value: Lung

value: Primary Fibroblast

value: Fibroblast

value: MTHFD2 KD + TGFb


title: 13

description: Library name: S118012

value: female

value: synchronous

value: mut


title: 47

description: Library name: S118009


title: siMTHFD2-11_UT_3

description: Library name: GM-1322

value: MTHFD2 KD Untreated


title: 4

description: Library name: S118011


title: siMTHFD2-11_UT_2

description: Library name: GM-1321


title: siMTHFD2-11_TGFb_1

description: Library name: GM-1323


title: siMTHFD2-11_UT_1

description: Library name: GM-1320


title: 327

description: Library name: S117997


title: 19

description: Library name: S118005


title: 8

description: Library name: S118017


title: 21

description: Library name: S117994


title: siMTHFD2-9_TGFb_3

description: Library name: GM-1319


title: 46

description: Library name: S117992


title: 18

description: Library name: S118002


title: 322

description: Library name: S117995


title: siMTHFD2-9_UT_3

description: Library name: GM-1316


title: siMTHFD2-9_TGFb_1

description: Library name: GM-1317


title: siMTHFD2-9_TGFb_2

description: Library name: GM-1318


title: siMTHFD2-9_UT_2

description: Library name: GM-1315


title: 31

description: Library name: S117991

value: 2 ypN1


title: siMTHFD2-11_TGFb_3

description: Library name: GM-1325


title: siMTHFD2-9_UT_1

description: Library name: GM-1314


title: 2

description: Library name: S117988


title: siControl_TGFb_3

description: Library name: GM-1313

value: Control + TGFb


title: 30

description: Library name: S117987


title: 101

description: Library name: S117981


title: siControl_UT_3

description: Library name: GM-1310

value: Control Untreated


title: siControl_TGFb_1

description: Library name: GM-1311


title: 24

description: Library name: S117982

value: CRLM

value: Right


title: siControl_UT_2

description: Library name: GM-1309


title: 50

description: Library name: S117985


title: siControl_TGFb_2

description: Library name: GM-1312


title: siControl_UT_1

description: Library name: GM-1308


title: 43

description: Library name: S117977


title: 51

description: Library name: S117973


title: 40

description: Library name: S117972

value: male


title: Serie1, RAW 264.7, 24h ML, ChIP H3.3, REP2

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description:
Library name: serie1_raw_ML_H3.3_rep2
Serie1

library_source: genomic

data_processing:
reads were aligned on mm10 or hg38 with bowtie2
alignments were filtered with samtools on MAPQ30.
PCR ducplicates were removed with Picard tools
Bigwig werer generated with Deeptools BamCoverage with CPM normalization
Assembly: hg38
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: RAW 264.7 mouse macrophages were maintained in DMEM+Glutamax (GIBCO) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin. When indicated, cells were treated with the SUMOylation inhibitor (SUMOi) ML-792(MedChemExpress) at a final concentration of 2,5uM. WT, IFNAR1-/- IFNAR2-/- and IFNAR1-/- IFNAR2-/-MORC3-/- BlaER1 cell lines were previously described in {Gaidt et.al DOI 10.1038/s41586-021-04054-5}. They were maintained in suspension at approximately 10e6 cells per mL in RPMI+Glutamax (GIBCO) supplemented with 10% FBS, penicillin/streptomycin, 25mM HEPES, 1mM sodium pyruvate and 2-mercaptoethanol. When indicated, cells were treated with the SUMOi TAK-981 at a final concentration of 100nM.

extract_protocol:
Cells were collected and fixed in 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched using glycine at a final concentration of 125mM for 5 minutes. Cells were washed twice in ice cold PBS. For fragmentation by sonication, cells were lysed in nuclei extraction buffer (250mM sucrose, 10mM Tris-HCl, 10mM MgCl2, 1% Triton X-100, 5mM 2-mercaptoethanol, and cOmplete protease inhibitor cocktail (Roche)) for 10 minutes on ice. The extracted nuclei were resuspended in nuclei lysis buffer (50mM Tris-HCl, 10mM EDTA, 0,2% SDS, and cOmplete protease inhibitor cocktail (Roche)), and sonicated with a Bioruptor Pico (Diagenode) using 6 cycles (30 sec on, 30 sec off), until chromatin fragments reached a size of around 300 base pairs (bp). For fragmentation by Micrococcal Nuclease (Mnase) digestion, cells were lysed with SimpleChIP® Enzymatic Cell Lysis Buffers A & B (Cell signaling) following manufacturer’s instructions. Nuclei were incubated with Mnase (Cell signaling) for 20 minutes at 37°C, until the chromatin fragments were digested to the size of 150 to 450 bp.
ChIP-seq libraries were prepared using Diagenode MicroPlex kit following manufacturer’s instructions

value: WT

tag: batch

value: Abcam ab176840


title: 44

description: Library name: S117989

value: metachronous

value: Left

value: wt


title: Serie1, RAW 264.7, 24h ML, ChIP H3.3, REP1

description:
Library name: serie1_raw_ML_H3.3_rep1
Serie1

tag: cell line


title: AAVS1 sg1 D N=3

city: Leuven

first: Sophie

last: Vlayen

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven

description:
Library name: Sample 25
AAVS1sg1DN_3

data_processing:
Illumina sequencing on a NovaSeq 6000 (100 bp paired-end reads) were performed for 27 samples. Twenty-million paired reads were generated per sample. Reads were confirmed as high quality using FastQC prior to downstream analysis. Feature count tables were generated using Kallisto with an index created for the human transcriptome (version GRCh38.96). Association of gene expression with gene KO and compound treatments was estimated using DESeq2 with a model that allowed for an interaction effect between KO and compound treatment. Significance of the model coefficients was estimated using a Wald test, with p-values corrected for multiple testing using Benjamini-Hochberg’s procedure.
Assembly: GRCh38.96
Supplementary files format and content: Excel file

source_name: Bone marrow

extract_protocol:
RNeasy mini kit (Qiagen)
Library preparation using TruSeq stranded mRNA

treatment_protocol: NUDCD2 KO and control cell lines were treated with bortezomib or carfilzomib for two days. DMSO was used as control treatment. Samples were collected from three repeated experiments.

value: Bone marrow

value: Plasma cell

tag: genotype

value: AAVS1 KO

value: DMSO


title: AAVS1 sg1 C N=3

description:
Library name: Sample 27
AAVS1sg1CN_3

tag: cell type

value: Carfilzomib


title: NUDCD2 sg2 C N=3

description:
Library name: Sample 24
NUDCD2sg2CN_3

value: NUDCD2 KO


title: NUDCD2 sg2 B N=3

description:
Library name: Sample 23
NUDCD2sg2BN_3

value: Bortezomib


title: Serie1,RAW 264.7, DMSO, ChIP H3.3, REP1

description:
Library name: serie1_raw_ctrl_H3.3_rep1
Serie1


title: Serie1, RAW 264.7, DMSO, ChIP H3.3, REP2

description:
Library name: serie1_raw_ctrl_H3.3_rep2
Serie1


title: NUDCD2 sg1 C N=3

description:
Library name: Sample 21
NUDCD2sg1CN_3


title: AAVS1 sg1 B N=3

description:
Library name: Sample 26
AAVS1sg1BN_3


title: NUDCD2 sg2 D N=3

description:
Library name: Sample 22
NUDCD2sg2DN_3


title: Serie1, RAW 264.7, 24h ML, Input, REP2

description:
Library name: serie1_raw_ML_input_rep2
Serie1


title: NUDCD2 sg1 B N=3

description:
Library name: Sample 20
NUDCD2sg1BN_3


title: 22

description: Library name: S117983

value: synchronous

value: mut


title: NUDCD2 sg1 D N=3

description:
Library name: Sample 19
NUDCD2sg1DN_3


title: Serie1, RAW 264.7, Input, REP2

description:
Library name: serie1_raw_ctrl_input_rep2
Serie1


title: AAVS1 sg1 C N=2

description:
Library name: Sample 18
AAVS1sg1CN_2


title: Serie1, RAW 264.7, Input, REP1

description:
Library name: serie1_raw_ctrl_input_rep1
Serie1


title: NUDCD2 sg2 B N=2

description:
Library name: Sample 14
NUDCD2sg2BN_2


title: AF.PR8 rep 2

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Hisat2 sequence alignment programs. Reads were mapped to the mm10 genome reference to identify transcripts.
Count value were calculated by featureCount
Normalized by DESeq2 with rlogTransformed
Assembly: mm10
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample ...

source_name: Neutrophils

growth_protocol: Wild-type (WT) C57BL/6J mice (6-8 weeks old) were purchased from Jackson Laboratory (Bar Harbor, ME) and bred in-house. Age- and sex-matched mice were used for experiments and received food and water ad libitum.

extract_protocol:
Neutrophils were magnetically sorted from pooled BALF from mock, single (Af, IAV), and IAV-Af co-infected mice at 48 hours after single/co-infection. RNA extraction was performed using Qiagen RNA extraction kit. Libraries were prepared with a NEBNext Ultra II RNA-Seq library kit following the manufacturer’s instructions as described earlier. DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neutrophils

value: Day 7


title: NUDCD2 sg2 C N=2

description:
Library name: Sample 15
NUDCD2sg2CN_2


title: AAVS1 sg1 B N=2

description:
Library name: Sample 17
AAVS1sg1BN_2


title: AF.PR8 rep 1


title: AAVS1 sg1 D N=2

description:
Library name: Sample 16
AAVS1sg1DN_2


title: AF.PR8 rep 3


title: AF rep 3

value: AF


title: NUDCD2 sg2 D N=2

description:
Library name: Sample 13
NUDCD2sg2DN_2


title: AF rep 2


title: PR8 rep 2

value: IAV


title: NUDCD2 sg1 D N=2

description:
Library name: Sample 10
NUDCD2sg1DN_2


title: AAVS1 sg1 C N=1

description:
Library name: Sample 9
AAVS1sg1CN_1


title: AF rep 1


title: NUDCD2 sg1 C N=2

description:
Library name: Sample 12
NUDCD2sg1CN_2


title: AAVS1 sg1 B N=1

description:
Library name: Sample 8
AAVS1sg1BN_1


title: NUDCD2 sg2 C N=1

description:
Library name: Sample 6
NUDCD2sg2CN_1


title: NUDCD2 sg1 B N=2

description:
Library name: Sample 11
NUDCD2sg1BN_2


title: WT_Mock rep 2

value: PBS


title: PR8 rep 1


title: WT_Mock rep 3


title: AAVS1 sg1 D N=1

description:
Library name: Sample 7
AAVS1sg1DN_1


title: Serie1, RAW 264.7, 24h ML, Input, REP1

description:
Library name: serie1_raw_ML_input_rep1
Serie1

value: WT


title: WT_Mock rep 1


title: NUDCD2 sg2 B N=1

description:
Library name: Sample 5
NUDCD2sg2BN_1


title: MullerControl, replicate 1, scRNAseq

city: Shanghai

first: Jinhai

last: Huang

address: 83 Fenyang Road, Xuhui District

institute: EYE & ENE Hospital of Fudan University

description: 10x Genomics

data_processing:
The mRNA library(10x Genomics) was processed by CellRanger(v.4.0.0) and aligned to the GRCh38(provided by 10x Genomics) with default alignment parameters.
The gene-barcode matrices was generated by the 'count' command from the mRNA library
Seurat(v.4.0.5) was then applied for further data analysis of clustering and dimensionally reduction. For filtering, cells with more than 4000 or less than 200 detected genes, as well as those with mitochondrial transcripts proportion higher than 30% were excluded
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
8 weeks after injection with AAV virus, the eyeballs were immersed in 4°C pre-cooled PBS. After rinsing, the cornea, lens, and vitreous were removed, and retinal tissue was separated. The retina was dissected in fresh and cold 1x HBSS and transferred to a 5ml polypropylene round-bottomed test tube containing 1ml of digestion solution. The sample was then incubated at 8°C for 40 min, followed by a second incubation at 28°C for 10 min. The test tube was inverted gently every 5 min. The retina was piped up and down in 700µl of preheated (10 min at 28°C) inactivation solution. When the retina was dissociated, pipetting was stopped and 700 µl of ice-cold washing solution was added. The cell suspension was centrifuged at 300× g for 5 min at 4°C using a swinging bucket rotor. After removing the supernatant, the cells were resuspended in 500 μL DPBS containing 0.04% BSA and passed through a 100 μm cell strainer (pluriSelect). 50μl cells were taken from each tube for a vitality test. Tdtamato positive cells were collected by fluorescence activated cell sorting (FACS) using a BD FACS Aria Fusion instrument. The positive rate of the Control-tdtamato positive group was about 10%; around 120000 control- Tdtamato positive cells per sample were collected by FACS. The positive rate of Test-Tdtamato positive group was about 4.9%; 60000 Test Tdtamato positive cells per sample were collected by FACS. The cells were immediately centrifuged at 600g at 4°C for 5 min. 27,000 cell samples of Control/Test -Tdtamato positive cells were used for scRNA-seq which followed the manufacturer’s instructions of the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1(cat. No. CG000204).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: retina

tag: strain

tag: age

value: 14 weeks


title: PR8 rep 3

tag: time


title: NUDCD2 sg1 Carflzomib N=1

description:
Library name: Sample 3
NUDCD2sg1CN_1

value: Bone marrow


title: Muller, replicate 1, scRNAseq

description: 10x Genomics


title: NUDCD2 sg1 Bortezomib N=1

description:
Library name: Sample 2
NUDCD2sg1BN_1

value: Plasma cell


title: Mo-AM KO-1

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

department: Dermatology

institute: Henry Ford Health System

data_processing:
bcl2fastq v2.17.1.14 conversion software used for basecalling.
The RNA-Seq reads were aligned to the mouse GRCm38/mm10 reference genome using Biomedical Genomics Workbench 4 (QIAGEN).
The expression levels for each sample were quantified and normalized usingBiomedical Genomics Workbench 4 (QIAGEN).
Assembly: mm10
Supplementary files format and content: Excel file includes gene name, chromosome, region, identifier, KO vs. WT-Max group means, KO vs. WT-Fold change, KO vs. WT-Log fold change, KO vs. WT-P-value, KO vs. WT-FDR p-value, KO vs. WT- FDR-Bonferroni; Total counts and RPKM values for each sample

source_name: Monocyte-derived alveolar macrophage (Mo-AM)

extract_protocol:
Resting TR-AMs (CD45+CD11chiSiglec-Fhi) from naïve mice and TR-AMs (CD45+CD64+Siglec-FhiCD11blo) and Mo-AMs (CD45+CD64+Siglec-FloCD11bhi) from bleomycin-treated mice were sorted using the BD FACSAria™ II cell sorter. Total RNA was extracted from purified AM cells using the miRNeasy Mini Kit (QIAGEN). cDNA library was generated using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
cDNA was pre-amplified by a thermal cycler (Applied Biosystem) using 12-14 cycles and sheered into 150-400 bp fragments using Bioruptor Pico sonicator (Diagenode). The DNA ends were repaired using End-It™ DNA End-Repair Kit (Epicentre). The end repaired DNA fragments were ligated to adaptors by T4 ligase (NEB) after a single “A” was added at 3’ by Klenow Fragment (3’→5’ Exo-) (NEB). MinElute Reaction Cleanup Kit (Qiagen) was used for DNA cleanup after each step. Illumina P5 and P7 primers with individual adaptors were used for final library amplification. The 150-400 bp final product was purified on a 2% E-gel (Thermo Fisher Scientific).

treatment_protocol: Mice were intratracheally treated with 1.0 U/kg bleomycin on day 0 and lungs were harvested on day 14 after treatment.

value: B6129F1 backcross to C57BL/6 over 10 generations

value: Lung

value: 6-18 weeks

value: Dicer knockout


title: NUDCD2 sg1 DMSO N=1

description:
Library name: Sample 1
NUDCD2sg1DN_1

value: NUDCD2 KO

value: DMSO


title: K562 dBRD9 treatment, RNase H1-Mnase

city: Chuncheon

first: JaeJin

last: Kim

state: Kangwon

address: 1 Hallymdaehak-gil

country: South Korea

institute: Hallym University

description: Library name: K562_dBRD9_RnaseH1MNase

data_processing:
library strategy: MapR-seq
All samples were pooled in equimolar ratio and sequenced on one NovaSeq 6000, PE for 2 × 101 cycles for the index read.
Assembly: GRCh38
Supplementary files format and content: bigwig (Processed data provided as supplementary file)

source_name: blood

extract_protocol:
Concanavalin-A-coated beads (Polysciences Europe GmbH) were activated in binding buffer (20 mM Hepes-KOH pH 7.9, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂). Cells were washed with Wash Buffer (Hepes-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 mM protease inhibitor) at room temperature and subsequently immobilized on the activated beads in 50 μl Wash Buffer containing 0.05% Digitonin. pA-MNase or RHΔ-MNase fusion protein was added to the cells and incubated overnight at 4°C on a rotating wheel. After three washes with Wash Buffer containing 0.05% Digitonin (Millipore), samples resuspended in 100 μl Dig-Wash-Buffer were equilibrated on ice. The activity of the MNase was triggered by adding 2 mM CaCl₂ to the samples for 30 minutes. The reaction was stopped by adding 2× Stop Buffer (68 μl 5 M NaCl, 40 μl 0.5 M EDTA, 20 μl 0.2 M EGTA, 10 μl 5% digitonin, 5 μl 10 mg/ml RNase A). Chromatin fragments were released by incubating the samples for 20 minutes at 37°C and centrifugation at 16,000×g for 10 minutes at 4°C. Supernatants were incubated at 70°C in the presence of 0.1% SDS and 5 μg proteinase K. Before library preparation, the DNA was recovered by DNA Purification Buffers and Spin Columns kit (Cell Signaling #14209).
NGS library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (NEB, E7103). Libraries were prepared with a starting amount of 1 ng of DNA and were amplified in 12 PCR cycles. Libraries were profiled in a D1000 ScreenTape on a TapeStation 4200 (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).

treatment_protocol: K562 cells were treated with either dBRD9 (100 nM) or DMSO control for 3 days.

value: blood

value: myeloid leukemia cell


title: Mo-AM WT-3

value: Monocyte-derived alveolar macrophage (Mo-AM)

value: wild-type


title: K562 DMSO control, RNase H1-Mnase

description: Library name: K562_DMSO_RnaseH1MNase


title: TR-AM KO-3

source_name: Tissue-resident alveolar macrophage (TR-AM)


title: Mo-AM WT-1


title: K562 dBRD9 treatment, pA-Mnase

description: Library name: K562_dBRD9_pAMNase


title: SCCOHT-RNAseq V1_3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description: Library name: Sample18

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2
Assembly: hg38
Supplementary files format and content: CUT&RUN: peak file per sample
Supplementary files format and content: RNA-seq: txt count file for all samples

growth_protocol: BIN-67 cells were maintained in RPMI supplemented with 10% FBS and 1%Penicillin/Streptomycin. This maintenance media was also the same media that DMSO, dTAGV-1 and dTAGV-1-NEG was diluted in.

extract_protocol:
For RNA-seq, RNA was extracted from 2-3 million cells using Trizol and the Direct-zol RNA mini prep kit by Zymo Research. For CUT&RUN, 500,000 cells were bound to ConA beads and processed following the Cell Signaling CUT&RUN kit protocol. For MYC and IgG three separate reactions, equivalent to 1.5 million cells, was pooled together during the DNA purification step before library generation. For H3K4me3, one reaction was sufficient to achieve signal.
For RNA-seq, libraries were made at Novogene using their standard methods with polyA-enrichment. For CUT&RUN, we made libraries of purified DNA fragments using the NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: All cells were treated with 500 nM dTAGV-1, 500 nM dTAGV-1-NEG, or matched DMSO control for 24 hr (RNA-seq). For CUT&RUN, no treatment was performed prior to collection.

value: Cell Line

tag: genetic modification

value: N-terminal HA-FKBPF36V dTAG module on MYC

value: 500 nM dTAGv-1, 24 hr


title: TR-AM KO-2

value: Tissue-resident alveolar macrophage (TR-AM)


title: K562 DMSO control, pA-Mnase

description: Library name: K562_DMSO_pAMNase


title: TR-AM KO-1


title: SCCOHT-RNAseq NEG_2

description: Library name: Sample14

value: 500 nM dTAGv-1-NEG, 24 hr


title: TR-AM WT-3


title: SCCOHT-RNAseq V1_2

description: Library name: Sample17


title: SCCOHT-RNAseq NEG_3

description: Library name: Sample15


title: Mo-AM KO-2


title: SCCOHT-RNAseq V1_1

description: Library name: Sample16


title: TR-AM WT-2


title: SCCOHT-RNAseq NEG_1

description: Library name: Sample13


title: SCCOHT-RNAseq DMSO_3

description: Library name: Sample12

value: DMSO, 24 hr


title: SCCOHT-RNAseq DMSO_2

description: Library name: Sample11


title: TR-AM WT-1


title: fyn_randomization_output2

city: Barcelona

first: Albert

last: Escobedo

state: Catalonia

address: Carrer Dr Aiguader 88

department: Systems and synthetic biology

institute: CRG

description: Library name: FYN_random_o2

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Supplementary files format and content: All in tabular format. sparse_DTS_core_mutagenesis_scores.csv contains a list of variants, each linked to the protein they are related to (Protein), its Uniprot identifier (UniprotCode), their complete amino acid sequence (aa_seq), the sequence in core positions (core), the hamming distance to the WT protein they are related to (Nham_aa), whether they were used as the reference in DiMSUM processing (WT), and their fitness and error values as obtained directly from DiMSum (fitness_raw and sigma_raw) and after scaling in the 0-1 range (fitness_scaled and sigma_scaled). The FYN-SH3_buried_n_exposed_randomization_scores.csv file contains equivalent aa_seq, Nham_aa, WT, fitness_scaled, sigma_scaled, fitness_raw and sigma_raw fields for all variants in the FYN-SH3 buried and exposed residue randomization libraries, plus an additional column specifying the library they belong to (library). The FYN-SH3_core_DTS_binding_scores_PDR1super.csv file contains equivalent aa_seq, core, Nham_aa, WT, fitness_scaled, sigma_scaled, fitness_raw and sigma_raw fields for all variants related to FYN SH3 binding to PDR1super. The FYN-SH3_core_permissivity_scores contains equivalent aa_seq, WT, fitness_scaled, sigma_scaled, fitness_raw and sigma_raw fields for variants in the permissivity library.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: We performed four large-scale competitive selection experiments: (i) the bottlenecked FYN-SH3, CI-2A and CspA seven-site core DTS randomization libraries in pGJJ162 containing a random subsample of the sequence space were selected together in a pooled experiment; (ii) the bottlenecked FYN-SH3 buried and exposed residue randomization libraries in pGJJ162 were selected together in a second pooled experiment; and each the FYN-SH3 core transplant failure suppression in pGJJ162 and FYN-SH3 seven-site core DTS randomization binding to PRD1-super in pGJJ159 libraries were selected independently [(iii) and (iv)]. Library pools and full complexity libraries were transformed into BY4741 yeast cells by heat shock. The number of transformation reactions was scaled depending on the final selection volume, which was in turn scaled to achieve a 100X coverage at the most stringent selection step in terms of cell count bottlenecking (inoculation in selection medium, see below). An individual transformation was performed per 200 ml of selection culture. For each individual transformation, 25 ml YPDA were inoculated with BY4741 colonies from a freshly streaked YPDA plate and grown overnight at 30°C. The process was performed in parallel for each independent biological replicate, starting from a different BY4741 colony (two replicates for the subsample DTS core library pool, three replicates for the other experiments). The precultures were used to inoculate 180 ml of YPDA to an OD600 of 0.3, which was grown for 4 hours at 30°C. Cells were harvested by 5 min centrifugation at 3,000 g, washed in water and treated with 8.6 ml SORB for 30 min. 3.5 μg of plasmid DNA were then added along with 175 μl of 10 mg/ml sonicated salmon sperm DNA (Santa Clara, CA, USA), and the mixture was agitated at room temperature for 10 min followed by addition of 35 ml of plate mixture plus another 30 min incubation. 3.5 ml of DMSO were then added and the mixture was heat- shocked at 42°C for 20 min. After the heat-shock, cells were harvested by 5 min centrifugation at 3,000 g, resuspended in recovery media and incubated at 30°C for 1 hour. Cells were then harvested again and resuspended in 200 ml of SC -URA selective medium. A 10- μl aliquot was serially diluted and plated in SC -URA to assess transformation efficiency. All biological replicate transformation cultures were grown in parallel at 30°C for ~24 hours. Then, the selection input cultures were inoculated by resuspending water washed harvested cell pellets in SC -URA -ADE to an OD600 of 0.1 (800 ml in 5-liter flasks in the cases of the subsampled DTS core library pool, the subsampled FYN-SH3 buried and exposed residue randomization library pool, and the FYN SH3 binding library; 400 ml in 2-liter flasks in the case of the FYN SH3 suppression library). The input cultures were grown at 30°C and harvested upon reaching an OD600 of 1.6 (five generations), which typically occurred from 12 to 15 hours after inoculation. Cell pellets were stored at −-20°C. Aliquots of the input culture were used to inoculate the selection (output) cultures (SC -URA -ADE, 200 μg/ml methotrexate) at an OD600 of 0.05. The output cultures were grown at 30°C for ~30 hours (subsampled DTS core library pool and FYN-SH3 binding library) or until they reached an OD600 of 1.6 (subsampled FYN-SH3 buried and exposed residue randomization library pool 31.42 hours, FYN-SH3 suppression library 24.92 hours). At that time, cells were harvested by 5 min centrifugation at 3,000 g, thoroughly washed in water and stored at −20°C.

extract_protocol:
Input and output culture cell pellets were resuspended in DNA extraction buffer (10 mM Tris-HCl, 100 mM NaCl, 2% Triton-X, 1% SDS, pH 8). Volumes were scaled depending on the volume of cell pellets to process. For pellets from 100- ml cultures harvested at OD600 1.6, 1 ml of DNA extraction buffer was used. Cells were lysed by cyclically freezing in liquid nitrogen followed by incubation in a 62°C water bath twice. Total DNA was extracted by adding 1 ml of a 25:24:1 phenol:chloroform:isoamyl alcohol mixture (Merck, Darmstadt, Germany) along with 1 g of acid washed glass beads (Sigma-Aldrich, Saint Louis, MO, USA) and vortexing for 10 min. The mixture was centrifuged at room temperature for 30 min at 3,300 g and the aqueous phase (upper layer) was recovered in a separate tube. 1 ml of the phenol:chloroform:isoamyl alcohol was added to it and the mixture was vortexed for 2 min followed by 45 min centrifugation at 3,300 g. The aqueous phase was again transferred to a new tube and mixed with 0.1 volumes of 3 M sodium acetate and 2.2 volumes of pure ethanol previously cooled down at −-80°C. The mixture was kept at −-20°C for 30 min and spun down at 3,300 g for 30 min at 4°C. The DNA pellets were dried overnight in a fume extraction hood. Plasmid DNA from total DNA extracts was quantified by qPCR using the oGJJ152- oGJJ153 oligo pair that anneals at the origin of replication of all pGJJ vector series. The qPCR reaction was performed in a LightCycler 400 instrument (Roche, Basel, Switzerland) using the SYBR green qPCR 2X master mix from Thermo Fisher Scientific (Waltham, MA, USA). Quantification was achieved by measuring a standard curve on a serial dilution of a control sample of known concentration in the same qPCR run as the query samples, and subtracting blank measurements. Library preparation for sequencing in Illumina instruments followed a two-step PCR protocol. Frameshifts and a segment of the Illumina adapter overhangs were introduced in PCR1. For each sample, 8x50 μl PCR1 reactions were performed using 31.25 million plasmid molecules as a template as quantified by qPCR. PCR1 used the oGJJ595 and the oGJJ748 frameshifting oligo pools (table S1) and consisted of 11 cycles. Next, all reactions corresponding to the same sample were pooled and treated with 16 μl ExoSAP for 30 min at 37°C, then for 20 min at 80°C. Samples were cleaned-up using MinElute columns, eluted in 30 μl of pre-warmed water (55°C) and 1.5 μl were used as template for each PCR2 reaction.16x50 μl 8-cycle PCR2 reactions were performed per sample to introduce the rest of the Illumina adapters and the dual index barcodes. PCR2 reactions corresponding to the same sample were pooled, concentrated using a MinElute column, and run in a 2% agarose gel. Bands of the correct sizes were excised from the gel and sequencing-ready DNA was recovered by using a centrifugal filter unit followed by MinElute clean-up.
Oligonucleotides, plasmids and media used are listed in tables S1, S2 and S3, respectively. Combinatorial core libraries using a reduced alphabet of hydrophobic amino acids (F, L, I, M, V) were built by multiple segment Gibson assembly of oligonucleotides bearing the DTS degenerate codon at core residue-encoding positions (oligos used in this study are detailed in table S1 and were all obtained from IDT, Coralville, IA, USA). Each of the genes encoding the FYN SH3 domain, CI-2A and CspA were codon optimized for expression in S cerevisiae and divided in two segments smaller than 200 bp each. These two segments had internal homology regions of at least 25 nt. FYN-SH3 buried and exposed residue randomization libraries were instead purchased as 233- nt single-stranded DNA oligonucleotides, with degenerate codons optimized ad hoc for each randomized position. For all libraries, both the 5′ and the 3′ gene segments contained a homology region of at least 25 nt to the linearized pGJJ191 mutagenesis vector. Double stranded Gibson assembly inserts were produced from single stranded commercial oligonucleotides via a single cycle PCR reaction using a 3′ annealing reverse primer specific to each segment (see table S1). The pGJJ191 vector was linearized via a 25-cycle PCR reaction using primers oGJJ311 and oGJJ406, followed by 1 hour DpnI (NEB) treatment at 37°C plus inactivation at 80°C for 20 min (1 μl enzyme per 50 μl PCR reaction). Both inserts and vector PCR reactions were cleaned-up in MinElute columns (Qiagen, Hilden, Germany). Gibson assembly mixtures contained 300 ng of linearized pGJJ191 plus the two insert segments at a 5:1 molar ratio each, along with a Gibson enzyme mixture produced in house by the Protein Technologies core facility at the CRG. Conversely, the FYN SH3 suppression library was purchased as an oligo pool from Twist Bioscience (San Francisco, CA, USA). The oligo pool was amplified in a 13- cycle PCR reaction with primers oAE018 and oAE227, which was cleaned up using a MinElute column. The insert amplified oligo pool contained 25-bp homology regions at both ends and was mixed at a 5 to 1 molar ratio with 300 ng of linearized pGJJ191 and subsequently with the Gibson enzyme mixture. All Gibson assembly reactions were incubated at 50°C for 8 hours, dialyzed against water using 0.025- μm filters (Millipore, Burlington, MA, USA) for 1.5 hours, concentrated using a SpeedVac and transformed into E. coli C3020 cells (NEB, Ipswich, MA, USA). The number of transformants was assessed by colony count in serial dilutions of transformation outgrowth aliquots in LB plates supplemented with 50 μg/ml spectinomycin, and 1 to 5 equivalent transformation reactions were pooled to reach at least 20X variant coverage per library as required. Plasmid DNA was extracted using the Qiagen Plasmid Plus Midi kit and the library inserts were obtained through double endonuclease digestion (HindIII-HF and NheI-HF, NEB) followed by agarose gel purification achieved by a combined use of centrifugal filter units (Millipore) and MinElute clean-up. Inserts were introduced in double-restricted, Quick CIP- trated (NEB) pGJJ162 (AbundancePCA) or pGJJ159-PRD1super (BindingPCA) vectors by overnight thermal-cyclic ligation using T4 DNA ligase. The pGJJ159-PRD1super vector was previously obtained by introducing the S. cerevisiae codon-optimized PRD1super encoding gene from commercial oligo synthesis (IDT) into BamHI-SpeI double restriction-linearized pGJJ159 via Gibson assembly. Ligation mixtures were dialyzed against water, SpeedVac-concentrated and transformed into E. coli C3020 electrocompetent cells. Equivalent transformations were combined to reach at least 20X variant coverage, and selection-ready libraries in PCA vectors were Midi-prep extracted.

value: lab strain BY4741

value: Saccharomyces cerevisiae


title: fyn_randomization_output3

description: Library name: FYN_random_o3

treatment_protocol: All biological replicate transformation cultures were grown in parallel at 30°C for ~24 hours. Then, the selection input cultures were inoculated by resuspending water washed harvested cell pellets in SC -URA -ADE to an OD600 of 0.1 (800 ml in 5-liter flasks in the cases of the subsampled DTS core library pool, the subsampled FYN-SH3 buried and exposed residue randomization library pool, and the FYN SH3 binding library; 400 ml in 2-liter flasks in the case of the FYN SH3 suppression library). The input cultures were grown at 30°C and harvested upon reaching an OD600 of 1.6 (five generations), which typically occurred from 12 to 15 hours after inoculation. Cell pellets were stored at −-20°C. Aliquots of the input culture were used to inoculate the selection (output) cultures (SC -URA -ADE, 200 μg/ml methotrexate) at an OD600 of 0.05. The output cultures were grown at 30°C for ~30 hours (subsampled DTS core library pool and FYN-SH3 binding library) or until they reached an OD600 of 1.6 (subsampled FYN-SH3 buried and exposed residue randomization library pool 31.42 hours, FYN-SH3 suppression library 24.92 hours). At that time, cells were harvested by 5 min centrifugation at 3,000 g, thoroughly washed in water and stored at −20°C.


title: NUDCD2 sg2 D N=1

description:
Library name: Sample 4
NUDCD2sg2DN_1

value: Bone marrow

value: Plasma cell


title: fyn_randomization_output1

description: Library name: FYN_random_o1


title: Mo-AM KO-3

value: B6129F1 backcross to C57BL/6 over 10 generations

value: Lung

value: 6-18 weeks

value: Dicer knockout


title: fyn_randomization_input1

description: Library name: FYN_random_i1


title: fyn_randomization_input2

description: Library name: FYN_random_i2


title: Mo-AM WT-2


title: BIN67-CnR IgG-3

description: Library name: Sample7

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2
Assembly: hg38
Supplementary files format and content: CUT&RUN: peak file per sample
Supplementary files format and content: RNA-seq: txt count file for all samples
Library strategy: CUT&Run

tag: cut&run antibody

value: Normal igG, Cell Signaling, 2729

value: No treatment


title: fyn_randomization_input3

description: Library name: FYN_random_i3


title: BIN67-CnR H3K4me3-3

description: Library name: Sample8

value: H3K4me3, included in Cell Signaling kit


title: BIN67-CnR MYC-3

description: Library name: Sample9

value: MYC, Cell Signaling, 13987

value: Cell Line


title: ycg1-2_Input_3hr_Rep1

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: Library name: ycg1-2_Input_3hr_Rep1

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) (for single-end data) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Assembly: SK1 (Yue et al., 2017)
Supplementary files format and content: bedGraph files

source_name: Nucleus

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606 which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
ChIP samples were processed as described in Blitzblau et al., 2012. The quality of the libraries was assessed using the 2100 Bioanalyzer or 2200 Tapestation. Library concentrations were quantified using qPCR prior to pooling. Sequencing was performed on Illumina NextSeq 500 instruments at the NYU Biology Genomics Core.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

value: Nucleus

value: Meiosis Hour 3

value: WT


title: smc2-8_ChIP_3hr_antiHop1_Rep1

description: Library name: smc2-8_ChIP_3hr_antiHop1_Rep1


title: BIN67-CnR H3K4me3-1

description: Library name: Sample2

value: N-terminal HA-FKBPF36V dTAG module on MYC


title: ycg1-2_ChIP_3hr_antiHop1_Rep1

description: Library name: ycg1-2_ChIP_3hr_antiHop1_Rep1


title: BIN67-CnR MYC-2

description: Library name: Sample6


title: BIN67-CnR IgG-2

description: Library name: Sample4


title: SCCOHT-RNAseq DMSO_1

description: Library name: Sample10

value: DMSO, 24 hr


title: WT_ChIP_3hr_antiHop1_Rep1

description: Library name: WT_ChIP_3hr_antiHop1_Rep1


title: TET2_LPS_rep3

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: T3_LPS

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: hg38
Supplementary files format and content: .csv, salmon raw gene counts and median-ratios normalized gene counts

source_name: iMG (induced Microglia)

growth_protocol: iPSCs were differentiated into iMGLs

extract_protocol:
200,000 iMGLs were collected and RNA extraction was performed with the RNeasy mini kit (QIAGEN).
RNA sequencing libraries were prepared by Azenta Life Sciences using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions

treatment_protocol: NS/ LPS

value: iMG (induced Microglia)

value: LPS-treated

value: TET2 delE3-11/WT


title: TET2_LPS_rep2

description: Library name: T2_LPS