title: 293-WT-V_Rep3

description:
Grown under regular culture condition, no treatment.
S45

source_name: 293-WT-V cells (WT cells transduced with pHIV-Luc-Blast control vector), biological replicate-#3


title: 293-dKO-19M_2_Rep1

status: Public on Jun 30 2023

type: SRA

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

country: USA

institute: University of South Carolina

description:
Grown under regular culture condition, no treatment.
S40

library_source: transcriptomic

data_processing:
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HEK293_dKO_WT_expression_derivatives_GeneCounts.txt: Space-delimited text file includes gene counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: 293-dKO-19M_2 cells (dKO cells transduced with pHIV-Blast-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#1

growth_protocol: HEK293 derivatives (dKO-V, dKO-8, dKO-8M, dKO-19, dKO-19M, dKO-V_2, dKO-8_2, dKO-8M_2, dKO-19_2, dKO-19M_2, WT-V, WT-8, WT-8M, WT-19 and WT-19M) were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent).
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit.

treatment_protocol: Cells were cultured in regular culture media and grown to 80~90% confluent before being lysed for RNA extraction.

tag: cell line

value: HEK293 (ATCC)

tag: genotype

tag: treatment

value: No treatment


title: Glomeruli, biol rep 1

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.8 (Andrews 2010) and multiQC v1.7 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using bbduk from the bbmap package v38.69 (Bushnell 2015) and filtered for a minimum length of 17nt and phred quality of 30.
Alignment steps were performed with STAR v2.7 (Dobin et al. 2013) using samtools v1.9 (Li et al. 2009) for indexing, whereas reads were mapped against the genomic reference GRCm38.p6 provided by Ensembl (Zerbino et al. 2018).
Assignment of features to the mapped reads was done with htseq-count v0.13 (Anders, Pyl, and Huber 2015).
Assembly: GRCm39 Assembly GCA_000001635.9
Supplementary files format and content: CSV file containing gene read counts from featureCount

organism: Mus musculus

source_name: Kidney

extract_protocol: Lexogen Quantseq according to manufacturer's protocol

tag: tissue

value: Kidney

tag: strain

value: WT

tag: seks

value: male

tag: laser microdissected

value: Yes

tag: microvascular compartment

value: Glomeruli


title: Ume6(T99N)-3v5,  0HR,  Rep1

city: Berkeley

first: Anthony

last: Harris

state: CA

address: 622 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

description:
Ume6(T99N)-3v5,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

data_processing:
Sequencing reads were mapped to a reference genome using HISAT2, samtools, and Stringtie
Mapped reads were visualized to IGV_2.12.3.app
Counts and TPM tables were generated from sequencing reads using pseudoalignment with kallisto
Assembly: SK1 Reference Genome from Saccharomyces Genome Resequencing Project at Sanger Institute
Supplementary files format and content: Excel tables include counts and TPMs for each sample.

organism: Saccharomyces cerevisiae

growth_protocol:
(Mitotic) – SK1 cells were grown overnight in rich media (YPD) at 30˚C before being back diluted to 0.2 OD600 and allowed to grow to log phase (0.5 OD600) at 30˚C.
(Meiotic) – SK1 cells were grown overnight first in rich media (YPD), then in presporulation media, before being transferred to sporulation media (SPO) at 1.85 OD600 all at 30˚C.

extract_protocol:
RNA was harvested using phenol chloroform precipitation and DNA was cleared using TURBO DNA-free kit (Thermo Fisher) according to manufacturer’s protocol.
RNA libraries were prepared for RNA-Seq using NEXTFLEX Rapid Direction RNA-seq kit (PerkinElmer) according to the provided manual.

treatment_protocol:
(Mitotic Depletion) Log phase cells were treated with ß-estradiol (40µM; t = -30min). This expressed OsTIR in cells with 4xLexO-OsTIR. Then, 30 min later auxin was added to cells (200µM; t = 0). This initiated Ume6 depletion in 4xLexO-OsTIR cells.
(Meiotic Depletion) Cells transferred to SPO were allowed to normalize for 30 min (t = 0.5 h). All cells were treated with ß-estradiol (5nM) and Auxin (200µM), but Ume6 depletion only occurred in 8xLexO-OsTIR containing cells. Cells were incubated in SPO for an additional 1.5 h before IME1 and IME4 were induced by CuSO4 (50µM).

tag: time

tag: condition

value: Meiotic


title: single cell Plasma cell  [17.3]

city: PARIS

first: Marion

last: Espeli

address: 1 avenue Claude Vellefaux, Inserm U1160, Institut de Recherche Saint Louis

country: France

institute: Inserm U1160

library_source: transcriptomic single cell

data_processing:
Reads adapters were trimmed using trim_galore, with parameters --paired --nextera --quality 20 --stringency 3 --length 20
Reads were mapped using STAR (v2.4) with default parameters. Only primary alignment and properly mapped read pairs were kept.
Read count were obtained with featureCounts, counts only reads pairs with fragment length < 2000 , excluding chimeric reads.
Assembly: mm10 + ERCC
Supplementary files format and content: full counttable 1 geo
Supplementary files format and content: rawcount2 geo

source_name: Bone marrow

extract_protocol:
RNA was extracted on C1 array in presence of spike-in (Invitrogen) to normalize gene expression
cDNA-seq libraries have been prepared using the Illumina Nextera XT DNA Prep Kit which employs a transposon to shear genomic DNA and simultaneously introduce adapter sequences

value: Bone marrow

tag: cell type

value: Plasma cell


title: 293-dKO-19_2_Rep3

description:
Grown under regular culture condition, no treatment.
S39

source_name: 293-dKO-19_2 cells (dKO cells transduced with pHIV-Blast-based CDK19-WT expressing vector), biological replicate-#3


title: Arterioles, biol rep 4

value: Arterioles


title: Ume6-3v5,  6HR,  Rep3

description:
Ume6-3v5,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: IME1; UME6-3V5


title: single cell Plasma cell  [16.3]


title: 293-dKO-19_2_Rep2

description:
Grown under regular culture condition, no treatment.
S38

source_name: 293-dKO-19_2 cells (dKO cells transduced with pHIV-Blast-based CDK19-WT expressing vector), biological replicate-#2


title: 293-dKO-19M_2_Rep3

description:
Grown under regular culture condition, no treatment.
S42

source_name: 293-dKO-19M_2 cells (dKO cells transduced with pHIV-Blast-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#3


title: Arterioles, biol rep 3


title: Ume6-3v5,  4HR,  Rep3

description:
Ume6-3v5,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [15.3]


title: Arterioles, biol rep 2


title: 293-dKO-19_2_Rep1

description:
Grown under regular culture condition, no treatment.
S37

source_name: 293-dKO-19_2 cells (dKO cells transduced with pHIV-Blast-based CDK19-WT expressing vector), biological replicate-#1


title: Ume6-3v5,  2HR,  Rep3

description:
Ume6-3v5,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [74.3]


title: single cell Plasma cell  [14.2]


title: Arterioles, biol rep 1


title: 293-dKO-8M_2_Rep3

description:
Grown under regular culture condition, no treatment.
S36

source_name: 293-dKO-8M_2 cells (dKO cells transduced with pHIV-Blast-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#3


title: Ume6-3v5,  0HR,  Rep3

description:
Ume6-3v5,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [13.3]


title: 293-dKO-8M_2_Rep2

description:
Grown under regular culture condition, no treatment.
S35

source_name: 293-dKO-8M_2 cells (dKO cells transduced with pHIV-Blast-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#2


title: Ume6(T99N)-3v5,  4HR,  Rep1

description:
Ume6(T99N)-3v5,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: Ume6-3v5,  6HR,  Rep2

description:
Ume6-3v5,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: 293-dKO-8M_2_Rep1

description:
Grown under regular culture condition, no treatment.
S34

source_name: 293-dKO-8M_2 cells (dKO cells transduced with pHIV-Blast-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#1


title: Ad-OSCAR + 5-ASA treatment rep 3

city: Seoul

first: Gina

last: Ryu

address: Seodaemun-gu

country: South Korea

institute: Ewha

data_processing:
The sequencing quality of FASTQ raw files was assessed using FastQC.
RNA sequencing reads were trimmed by BBDuk and aligned to the GRCm38 genome reference using STAR v2.7.1a.
Raw read counts were obtained by RSEM v.1.3.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene id, transcript id, gene length, effective length, expected count, TPM, and FPKM values for each gene.

source_name: Articular cartilage

growth_protocol: Primary articular chondrocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
For primary cell culture, chondrocytes were isolated from the femoral condyles and tibial plateaus of postnatal day 5 WT mice. RNA was harvested using PureLink RNA Mini Kit (Invitrogen). 1.9 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit).

treatment_protocol: Mouse articular chondrocytes were cultured for 3 days, infected with an adenovirus for 2 h at 400 MOI and cultured for 36 h before further treatment of 5-ASA.

value: Articular cartilage

value: Mouse articular chondrocyte

value: Ad-OSCAR + 5-ASA treatment


title: Ad-OSCAR + 5-ASA treatment rep 2


title: 293-dKO-8_2_Rep3

description:
Grown under regular culture condition, no treatment.
S33

source_name: 293-dKO-8_2 cells (dKO cells transduced with pHIV-Blast-based CDK8-WT expressing vector), biological replicate-#3


title: 293-dKO-8_2_Rep2

description:
Grown under regular culture condition, no treatment.
S32

source_name: 293-dKO-8_2 cells (dKO cells transduced with pHIV-Blast-based CDK8-WT expressing vector), biological replicate-#2


title: Ume6-3v5,  2HR,  Rep2

description:
Ume6-3v5,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [H7]


title: single cell Plasma cell  [H6]


title: Ad-OSCAR + 5-ASA treatment rep 1


title: Ad-OSCAR rep 3

value: Ad-OSCAR


title: Ume6-3v5,  0HR,  Rep2

description:
Ume6-3v5,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [H5]


title: 293-dKO-8_2_Rep1

description:
Grown under regular culture condition, no treatment.
S31

source_name: 293-dKO-8_2 cells (dKO cells transduced with pHIV-Blast-based CDK8-WT expressing vector), biological replicate-#1


title: Ad-OSCAR rep 2


title: single cell Plasma cell  [H4]


title: 293-dKO-V_2_Rep3

description:
Grown under regular culture condition, no treatment.
S30

source_name: 293-dKO-V_2 cells (dKO cells transduced with pHIV-Luc-Blast control vector), biological replicate-#3


title: single cell Plasma cell  [H3]


title: 293-dKO-V_2_Rep2

description:
Grown under regular culture condition, no treatment.
S29

source_name: 293-dKO-V_2 cells (dKO cells transduced with pHIV-Luc-Blast control vector), biological replicate-#2


title: Ume6-3v5,  4HR,  Rep1

description:
Ume6-3v5,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [H2]


title: single cell Plasma cell  [11.1]


title: Control rep 2

value: Control


title: Control rep 3


title: single cell Plasma cell  [H1]


title: Ume6-3v5,  4HR,  Rep2

description:
Ume6-3v5,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: Ume6-3v5,  2HR,  Rep1

description:
Ume6-3v5,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: Ume6-3v5,  0HR,  Rep1

description:
Ume6-3v5,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: Ad-OSCAR rep 1


title: Control rep 1


title: Wild-Type,  6HR,  Rep3

description:
Wild-Type,  6HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue

value: IME1; UME6


title: 655

city: Toulouse

first: Liliana

middle: Elisa

last: Lucca

address: 2 Avenue Hubert Curien

department: Immunology

institute: CRCT

data_processing:
Fastq files were aligned to the NCBI GRCm38 mice reference genome using STAR (version 2.3.0, (Dobin et al., 2013))
Gene expression summary was obtained using the Subread featurecount algorithm (version 1.4.6, (Liao et al., 2014)).
Patient gene expression was then normalized using standard procedure from the limma R package(Ritchie et al., 2015), retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6
Supplementary files format and content: tab-delimited text files include normalized gene expression values retaining only genes expressed in at least 50% of patients.

source_name: Total bone marrow cells

extract_protocol:
otal RNA was extracted from total BM at the indicated time points using RNeasy micro kit (Qiagen) according to the manufacturer’s instruction. The quality of the isolated total RNA from each sample was checked on 2200 Tapestation System (Agilent, Santa Clara, USA) using the RNA ScreenTape assay and the quantitation was performed using the NanoVue Plus Spectrophotometer (Biochrom Ltd, Cambridge, UK).
100-300 ng of total RNA per sample with a RNA integrity number >8 were used for library preparation. The RNA-Seq library preparation was performed using TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, Calif) according to the manufacturer’s instructions (High Sample Protocol). The RNA-Seq libraries were checked on the 2200 Tapestation System (Agilent) using the High-Sensitivity DNA 1000 ScreenTape.assay. Libraries were quantified by qPCR on a LightCycler 480 System (Roche Molecular Diagnostics, Pleasanton, Calif) using KAPA Library Quantification Kit for Illumina platforms (Kapa BiosysTem cells, Boston, Massachusetts). Libraries were then pooled in equal quantities, checked and quantified using same techniques (2200 Tapestation and LightCycler 480).
Paired-end sequencing (2 x 150 bps) of these libraries was performed on a  Novaseq 6000 S4 Illumina sequencing using NextSeq 500 High Output kit v2 (Illumina) generating in average 20 million pairs of reads per sample.

treatment_protocol: anti-CD137 (3H3, i.p twice a week)

value: Total bone marrow cells

tag: mice

value: D28 VK12653 bearing mice

tag: treatment kinetic


title: 293-dKO-19M_Rep6

description:
Grown under regular culture condition, no treatment.
S27

source_name: 293-dKO-19M cells (dKO cells transduced with pHIV-dTomato-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#6

value: HEK293 (ATCC)

value: No treatment


title: Wild-Type,  4HR,  Rep3

description:
Wild-Type,  4HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [G7]

value: WT


title: 293-dKO-19M_Rep5

description:
Grown under regular culture condition, no treatment.
S26

source_name: 293-dKO-19M cells (dKO cells transduced with pHIV-dTomato-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#5


title: single cell Plasma cell  [G6]

source_name: Bone marrow


title: Ume6-3v5,  6HR,  Rep1

description:
Ume6-3v5,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: 293-dKO-19M_Rep4

description:
Grown under regular culture condition, no treatment.
S25

source_name: 293-dKO-19M cells (dKO cells transduced with pHIV-dTomato-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#4


title: 653


title: Wild-Type,  2HR,  Rep3

description:
Wild-Type,  2HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [G5]


title: 293-dKO-19M_Rep3

description:
Grown under regular culture condition, no treatment.
S24

source_name: 293-dKO-19M cells (dKO cells transduced with pHIV-dTomato-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#3


title: 648


title: 293-dKO-V_2_Rep1

description:
Grown under regular culture condition, no treatment.
S28

source_name: 293-dKO-V_2 cells (dKO cells transduced with pHIV-Luc-Blast control vector), biological replicate-#1


title: single cell Plasma cell  [G4]


title: 293-dKO-19M_Rep2

description:
Grown under regular culture condition, no treatment.
S23

source_name: 293-dKO-19M cells (dKO cells transduced with pHIV-dTomato-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#2


title: Wild-Type,  0HR,  Rep3

description:
Wild-Type,  0HR,  Rep3
gene_count_matrix_Ume6T99N_Rescue


title: Wild-Type,  6HR,  Rep2

description:
Wild-Type,  6HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [G3]


title: Wild-Type,  4HR,  Rep2

description:
Wild-Type,  4HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [G2]


title: 293-dKO-19_Rep6

description:
Grown under regular culture condition, no treatment.
S21

source_name: 293-dKO-19 cells (dKO cells transduced with pHIV-dTomato-based CDK19-WT expressing vector), biological replicate-#6


title: single cell Plasma cell  [G1]


title: Wild-Type,  0HR,  Rep2

description:
Wild-Type,  0HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: Wild-Type,  2HR,  Rep2

description:
Wild-Type,  2HR,  Rep2
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [F7]


title: 293-dKO-19_Rep3

description:
Grown under regular culture condition, no treatment.
S18

source_name: 293-dKO-19 cells (dKO cells transduced with pHIV-dTomato-based CDK19-WT expressing vector), biological replicate-#3


title: single cell Plasma cell  [F6]


title: Wild-Type,  6HR,  Rep1

description:
Wild-Type,  6HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: 694

value: D14 VK12653 bearing mice


title: 293-dKO-19_Rep5

description:
Grown under regular culture condition, no treatment.
S20

source_name: 293-dKO-19 cells (dKO cells transduced with pHIV-dTomato-based CDK19-WT expressing vector), biological replicate-#5


title: 664

value: D21 VK12653 bearing mice


title: single cell Plasma cell  [F5]

value: Bone marrow


title: 293-dKO-19_Rep2

description:
Grown under regular culture condition, no treatment.
S17

source_name: 293-dKO-19 cells (dKO cells transduced with pHIV-dTomato-based CDK19-WT expressing vector), biological replicate-#2


title: 684


title: 683


title: 646

value: D10 VK12653 bearing mice

value: No Treatment


title: Wild-Type,  4HR,  Rep1

description:
Wild-Type,  4HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue

value: Meiotic


title: 669


title: 665


title: single cell Plasma cell  [F4]

value: Plasma cell


title: Wild-Type,  2HR,  Rep1

description:
Wild-Type,  2HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: 644


title: 293-dKO-19_Rep1

description:
Grown under regular culture condition, no treatment.
S16

source_name: 293-dKO-19 cells (dKO cells transduced with pHIV-dTomato-based CDK19-WT expressing vector), biological replicate-#1


title: Wild-Type,  0HR,  Rep1

description:
Wild-Type,  0HR,  Rep1
gene_count_matrix_Ume6T99N_Rescue


title: single cell Plasma cell  [F3]


title: 293-dKO-8M_Rep6

description:
Grown under regular culture condition, no treatment.
S15

source_name: 293-dKO-8M cells (dKO cells transduced with pHIV-dTomato-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#6


title: 293-dKO-19M_Rep1

description:
Grown under regular culture condition, no treatment.
S22

source_name: 293-dKO-19M cells (dKO cells transduced with pHIV-dTomato-based CDK19-D173A kinase-inactive mutant expressing vector), biological replicate-#1


title: 643


title: 293-dKO-19_Rep4

description:
Grown under regular culture condition, no treatment.
S19

source_name: 293-dKO-19 cells (dKO cells transduced with pHIV-dTomato-based CDK19-WT expressing vector), biological replicate-#4


title: 293-dKO-8M_Rep5

description:
Grown under regular culture condition, no treatment.
S14

source_name: 293-dKO-8M cells (dKO cells transduced with pHIV-dTomato-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#5


title: single cell Plasma cell  [F2]


title: single cell Plasma cell  [F1]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_4.5h, Rep3

description:
U+Tag_LexA_LexO_Replicate_3_4.5HR
gene_count_matrix_meiotic_depletion

value: ß-estradiol + Auxin


title: 293-dKO-8M_Rep4

description:
Grown under regular culture condition, no treatment.
S13

source_name: 293-dKO-8M cells (dKO cells transduced with pHIV-dTomato-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#4


title: HFD, replicate 2, scRNAseq

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: sciatic nerve

extract_protocol:
Schwann cells (SCs) were isolated from the sciatic nerves of 23-week-old SD and HFD mice following a modification of the previously described protocol by Wolbert et al.  (PMID: 32295886). Briefly, sciatic nerves were extracted from mice intracardially perfused with Hank’s buffered salt solution (HBSS, Invitrogen ThermoFisher, Waltham, MA). Nerve segments were finely chopped, incubated in HBSS at 37oC, and then digested in Dulbecco’s Modified Eagles Medium (DMEM, Lonza, Basel, Switzerland) containing trypsin (Gibco ThermoFisher, Waltham, MA; 0.25%) and collagenase II (Worthington Biochemical, Freehold, NJ; 1.62 U/μl) at 37°C for 20 minutes. Cells were triturated using fire-polished Pasteur pipettes, filtered through a 70-μm cell strainer (Falcon, Ontario, Canada), and centrifuged at 300 rpm for 10 minutes. They were then re-suspended in 120 μl of phosphate buffered saline (PBS) supplemented with 5% fetal bovine serum (FBS) and 20 μl of Anti-O4 magnetic beads (Miltenyi Biotec, Bergisch Gladbach, Germany) to ensure selective purification of SCs. SC magnetic enrichment step was performed as per the manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, SCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Schwann cells

value: sciatic nerve

tag: age

value: 23 weeks old

value: HFD


title: SD, replicate 3, scRNAseq

description: 10x Genomics

value: SD


title: single cell Plasma cell  [E6]


title: single cell Plasma cell  [E7]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_2.5h, Rep3

description:
U+Tag_LexA_LexO_Replicate_3_2.5HR
gene_count_matrix_meiotic_depletion


title: 293-dKO-8M_Rep3

description:
Grown under regular culture condition, no treatment.
S12

source_name: 293-dKO-8M cells (dKO cells transduced with pHIV-dTomato-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#3


title: LexA-ER-GAL4AD,8xLexO-OsTIR_3h, Rep3

description:
U+Tag_LexA_LexO_Replicate_3_3HR
gene_count_matrix_meiotic_depletion


title: SD, replicate 2, scRNAseq

description: 10x Genomics


title: single cell Plasma cell  [43.2]

source_name: Bone marrow


title: single cell Plasma cell  [E5]


title: 293-dKO-8M_Rep2

description:
Grown under regular culture condition, no treatment.
S11

source_name: 293-dKO-8M cells (dKO cells transduced with pHIV-dTomato-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#2


title: 293-dKO-8M_Rep1

description:
Grown under regular culture condition, no treatment.
S10

source_name: 293-dKO-8M cells (dKO cells transduced with pHIV-dTomato-based CDK8-D173A kinase-inactive mutant expressing vector), biological replicate-#1


title: LexA-ER-GAL4AD,8xLexO-OsTIR_2h, Rep3

description:
U+Tag_LexA_LexO_Replicate_3_2HR
gene_count_matrix_meiotic_depletion


title: LexA-ER-GAL4AD,8xLexO-OsTIR_0.5h, Rep3

description:
U+Tag_LexA_LexO_Replicate_3_0.5HR
gene_count_matrix_meiotic_depletion


title: 293-dKO-8_Rep6

description:
Grown under regular culture condition, no treatment.
S9

source_name: 293-dKO-8 cells (dKO cells transduced with pHIV-dTomato-based CDK8-WT expressing vector), biological replicate-#6


title: single cell Plasma cell  [E4]


title: SD, replicate 1, scRNAseq

description: 10x Genomics


title: HFD, replicate 1, scRNAseq

description: 10x Genomics


title: LexA-ER-GAL4AD,8xLexO-OsTIR_6h, Rep3

description:
U+Tag_LexA_LexO_Replicate_3_6HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [E3]


title: 293-dKO-8_Rep5

description:
Grown under regular culture condition, no treatment.
S8

source_name: 293-dKO-8 cells (dKO cells transduced with pHIV-dTomato-based CDK8-WT expressing vector), biological replicate-#5


title: HFD, replicate 3, scRNAseq

description: 10x Genomics


title: single cell Plasma cell  [E2]


title: 293-WT-19_Rep2

description:
Grown under regular culture condition, no treatment.
S53

source_name: 293-WT-19 cells (WT cells transduced with pHIV-Blast-based CDK19-WT expressing vector), biological replicate-#2


title: NEC + ST266 ip 4

city: Baltimore

first: David

middle: J.

last: Hackam

address: 733 North Broadway

department: Surgery

institute: Johns Hopkins University School of Medicine

data_processing:
Basecalls performed using Illumina CASAVA after sequencing on IlluminaNovaseq™6000
read trimming and filtering were performed using Cutadapt 1.9
Quality control was performed using FastQC 0.11.9
Read alignment and transcript quantification were performed using Salmon 1.3.0. A mouse reference genome was constructed using the mm10 mouse genome for Salmon analysis. Fragment-level GC biases were corrected for by using the “--gcBias” option in Salmon.
Gene expression values were adjusted for sequencing depth and RNA composition using median of ratios method using the R Package DESeq2 version 1.32.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of transcript counts from Salmon alignment and quantification
Supplementary_files_format_and_content: Matrix of normalized transcript counts from DESeq2 median of ratios method

source_name: ileum

growth_protocol: Breast-fed (control) animals remained with their mothers and received breast milk ad libitum. To induce NEC, mice were gavage fed (40μL/g) five times/day (7 am to 7 pm) with formula supplemented with bacterial stock that had been cultured from the stool of an infant with severe NEC (12.5μl stool slurry in 1ml formula). The stool mixed formula (50µl per gram of mouse body weight) was administered using a 24-French angiocatheter placed into the mouse esophagus. Mice were exposed to hypoxia (5% O2, 95% N2) for 10 minutes in a chamber (Billups-Rothenberg INC. Del Mar, CA), twice daily for 4 days.

extract_protocol:
Total RNA was purified and DNAse I treated using RNeasy mini kit (Qiagen)
The total RNA quantity and purity were analyzed using the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511), and high-quality RNA samples with RIN number > 7.0 were used to construct sequencing libraries. After total RNA was extracted, mRNA was purified from total RNA (5μg) 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) at 94℃ for 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, cat # 1896649, USA), which were next used to synthesize 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 heat-labile UDG enzyme (NEB, cat. # M0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR in 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 libraries was 300 ± 50 bp.

treatment_protocol: The ST266 Amnion-derived Multipotent Progenitor cell secretome (Noveome Biotherapeutics, Pittsburgh, PA)(26) was either added to the NEC formula (20μL/ml/mice/day) or administrated via intraperitoneal route (20μL/mice/day).

tag: name


title: LexA-ER-GAL4AD,8xLexO-OsTIR_6h, Rep2

description:
U+Tag_LexA_LexO_Replicate_2_6HR
gene_count_matrix_meiotic_depletion


title: NEC + ST266 ip 3


title: 293-dKO-8_Rep4

description:
Grown under regular culture condition, no treatment.
S7

source_name: 293-dKO-8 cells (dKO cells transduced with pHIV-dTomato-based CDK8-WT expressing vector), biological replicate-#4


title: LexA-ER-GAL4AD,8xLexO-OsTIR_4.5h, Rep2

description:
U+Tag_LexA_LexO_Replicate_2_4.5HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [E1]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_3h, Rep2

description:
U+Tag_LexA_LexO_Replicate_2_3HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [D8]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_2.5h, Rep2

description:
U+Tag_LexA_LexO_Replicate_2_2.5HR
gene_count_matrix_meiotic_depletion


title: 293-dKO-8_Rep2

description:
Grown under regular culture condition, no treatment.
S5

source_name: 293-dKO-8 cells (dKO cells transduced with pHIV-dTomato-based CDK8-WT expressing vector), biological replicate-#2


title: 293-dKO-8_Rep3

description:
Grown under regular culture condition, no treatment.
S6

source_name: 293-dKO-8 cells (dKO cells transduced with pHIV-dTomato-based CDK8-WT expressing vector), biological replicate-#3


title: NEC + ST266 ip 1


title: NEC + ST266 oral 4


title: 293-dKO-8_Rep1

description:
Grown under regular culture condition, no treatment.
S4

source_name: 293-dKO-8 cells (dKO cells transduced with pHIV-dTomato-based CDK8-WT expressing vector), biological replicate-#1


title: LexA-ER-GAL4AD,8xLexO-OsTIR_2h, Rep2

description:
U+Tag_LexA_LexO_Replicate_2_2HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [D6]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_0.5h, Rep2

description:
U+Tag_LexA_LexO_Replicate_2_0.5HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [D5]


title: NEC + ST266 ip 2


title: 293-dKO-V_Rep3

description:
Grown under regular culture condition, no treatment.
S3

source_name: 293-dKO-V cells (dKO cells transduced with pHIV-dTomato control vector), biological replicate-#3


title: 293-dKO-V_Rep2

description:
Grown under regular culture condition, no treatment.
S2

source_name: 293-dKO-V cells (dKO cells transduced with pHIV-dTomato control vector), biological replicate-#2


title: NEC + ST266 oral 3


title: single cell Plasma cell  [D4]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_6h, Rep1

description:
U+Tag_LexA_LexO_Replicate_1_6HR
gene_count_matrix_meiotic_depletion


title: LexA-ER-GAL4AD,8xLexO-OsTIR_4.5h, Rep1

description:
U+Tag_LexA_LexO_Replicate_1_4.5HR
gene_count_matrix_meiotic_depletion


title: 293-dKO-V_Rep1

description:
Grown under regular culture condition, no treatment.
S1

source_name: 293-dKO-V cells (dKO cells transduced with pHIV-dTomato control vector), biological replicate-#1


title: NEC + ST266 oral 2


title: NEC + ST266 oral 1


title: single cell Plasma cell  [D3]


title: LexA-ER-GAL4AD,8xLexO-OsTIR_3h, Rep1

description:
U+Tag_LexA_LexO_Replicate_1_3HR
gene_count_matrix_meiotic_depletion


title: 293-dKO_15w_72h_Rep3

description:
293-dKO cells treated with 1uM 15w for 72 hours.
S18

data_processing:
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HEK293_dCA_15w_geneCounts.txt: Tab-delimited text file includes gene counts for each sample.

source_name: 293-dKO cells treated with 1μM 15w for 72 hours, biological replicate-#3

growth_protocol: 293-WT and 293-dKO cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 5x10^4 cells per well.  24 hours post seeding, cells were treated as indicated.

treatment_protocol: Cells were treated with vehicle control (0.1% DMSO) or 1 μM dCA or 1 μM 15w for 72 hours.

value: CDK8/19 dKO

value: 1uM 15w for 72 hours


title: NEC 4


title: single cell Plasma cell  [D7]


title: 293-dKO_15w_72h_Rep2

description:
293-dKO cells treated with 1uM 15w for 72 hours.
S17

source_name: 293-dKO cells treated with 1μM 15w for 72 hours, biological replicate-#2


title: NEC 3


title: LexA-ER-GAL4AD,8xLexO-OsTIR_2.5h, Rep1

description:
U+Tag_LexA_LexO_Replicate_1_2.5HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [D1]


title: single cell Plasma cell  [D2]


title: 293-dKO_15w_72h_Rep1

description:
293-dKO cells treated with 1uM 15w for 72 hours.
S16

source_name: 293-dKO cells treated with 1μM 15w for 72 hours, biological replicate-#1


title: NEC 2


title: single cell Plasma cell  [C8]

source_name: Bone marrow


title: LexA-ER-GAL4AD,8xLexO-OsTIR_0.5h, Rep1

description:
U+Tag_LexA_LexO_Replicate_1_0.5HR
gene_count_matrix_meiotic_depletion


title: 293-dKO_dCA_72h_Rep3

description:
293-dKO cells treated with 1uM dCA for 72 hours.
S15

source_name: 293-dKO cells treated with 1μM dCA for 72 hours, biological replicate-#3

value: 1uM dCA for 72 hours


title: LexA-ER-GAL4AD_6h, Rep3

description:
U+Tag_LexA_Replicate_3_6HR
gene_count_matrix_meiotic_depletion

value: UME6-AID-3V5; lexA-ER-GAL4AD


title: single cell Plasma cell  [C7]

value: WT


title: single cell Plasma cell  [C6]


title: 293-dKO_dCA_72h_Rep2

description:
293-dKO cells treated with 1uM dCA for 72 hours.
S14

source_name: 293-dKO cells treated with 1μM dCA for 72 hours, biological replicate-#2


title: 293-dKO_dCA_72h_Rep1

description:
293-dKO cells treated with 1uM dCA for 72 hours.
S13

source_name: 293-dKO cells treated with 1μM dCA for 72 hours, biological replicate-#1


title: LexA-ER-GAL4AD_4.5h, Rep3

description:
U+Tag_LexA_Replicate_3_4.5HR
gene_count_matrix_meiotic_depletion


title: NEC 1


title: LexA-ER-GAL4AD_3h, Rep3

description:
U+Tag_LexA_Replicate_3_3HR
gene_count_matrix_meiotic_depletion


title: Breast-fed Control 3


title: single cell Plasma cell  [C5]


title: 293-dKO_Ctrl_72h_Rep3

description:
293-dKO cells treated with 0.1% DMSO (vehicle control) for 72 hours.
S12

source_name: 293-dKO cells treated with 0.1% DMSO (vehicle control) for 72 hours, biological replicate-#3


title: Breast-fed Control 2


title: single cell Plasma cell  [C4]


title: Breast-fed Control 1


title: 293-dKO_Ctrl_72h_Rep2

description:
293-dKO cells treated with 0.1% DMSO (vehicle control) for 72 hours.
S11

source_name: 293-dKO cells treated with 0.1% DMSO (vehicle control) for 72 hours, biological replicate-#2


title: LexA-ER-GAL4AD,8xLexO-OsTIR_2h, Rep1

description:
U+Tag_LexA_LexO_Replicate_1_2HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [C3]


title: LexA-ER-GAL4AD_2h, Rep3

description:
U+Tag_LexA_Replicate_3_2HR
gene_count_matrix_meiotic_depletion


title: 293-dKO_Ctrl_72h_Rep1

description:
293-dKO cells treated with 0.1% DMSO (vehicle control) for 72 hours.
S10

source_name: 293-dKO cells treated with 0.1% DMSO (vehicle control) for 72 hours, biological replicate-#1


title: ZRS08_11_OT2_thy_r2_111

first: Zoë

last: Steier

address: 378 Stanley Hall

description: OT-II TCR transgenic replicate 2

data_processing:
Library strategy: CITE-seq
Sequencing reads were processed with CellRanger v3.1.0 with feature barcoding to produce UMI count matrices.
Cellranger was used to aggregate samples without read depth normalization (e.g., ZRS06_ZRS07_matrix.mtx.gz, ZRS08_matrix.mtx.gz).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Cell barcodes.
Supplementary_files_format_and_content: *_features.tsv.gz: Genes and proteins.
Supplementary_files_format_and_content: *_matrix.mtx.gz: UMI count matrix for all cell barcodes and features.

molecule: polyA RNA

source_name: thymus

extract_protocol:
Stained and washed cells from one sample were loaded into a single lane of the 10x Genomics Chromium Single Cell 3' v3 kit.
CITE-seq library construction was performed following the 10x Genomics Chromium Single Cell 3' v3 protocol to prepare RNA and antibody-derived-tag (ADT) libraries.

treatment_protocol: Cells were stained in RPMI + 10% FBS with pooled BioLegend TotalSeq-A antibodies according to the manufacturer's instructions.

value: thymus

value: OT-II

value: 4-8 weeks

tag: molecule subtype

value: polyA RNA and protein

tag: sort population


title: 293-WT_15w_72h_Rep3

description:
293-WT cells treated with 1uM 15w for 72 hours.
S9

source_name: 293-WT cells treated with 1μM 15w for 72 hours, biological replicate-#3

tag: cell line


title: LexA-ER-GAL4AD_0.5h, Rep3

description:
U+Tag_LexA_Replicate_3_0.5HR
gene_count_matrix_meiotic_depletion

tag: genotype

value: Meiotic


title: LexA-ER-GAL4AD_6h, Rep2

description:
U+Tag_LexA_Replicate_2_6HR
gene_count_matrix_meiotic_depletion

tag: treatment


title: Breast-fed Control 4

source_name: ileum


title: single cell Plasma cell  [C1]

tag: tissue

value: Bone marrow

value: Plasma cell


title: LexA-ER-GAL4AD_4.5h, Rep2

description:
U+Tag_LexA_Replicate_2_4.5HR
gene_count_matrix_meiotic_depletion

tag: strain

value: ß-estradiol + Auxin


title: ZRS08_10_OT1_thy_r2_111

description: OT-I TCR transgenic replicate 2

value: OT-I


title: 293-WT_15w_72h_Rep2

description:
293-WT cells treated with 1uM 15w for 72 hours.
S8

source_name: 293-WT cells treated with 1μM 15w for 72 hours, biological replicate-#2


title: ZRS08_9_B6_thy_r5_111

description: Wild-type replicate 5 sample 2

value: B6 (WT)


title: LexA-ER-GAL4AD_3h, Rep2

description:
U+Tag_LexA_Replicate_2_3HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [B8]


title: 293-WT_dCA_72h_Rep3

description:
293-WT cells treated with 1uM dCA for 72 hours.
S6

source_name: 293-WT cells treated with 1μM dCA for 72 hours, biological replicate-#3


title: LexA-ER-GAL4AD_2.5h, Rep3

description:
U+Tag_LexA_Replicate_3_2.5HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [B7]


title: LexA-ER-GAL4AD_2.5h, Rep2

description:
U+Tag_LexA_Replicate_2_2.5HR
gene_count_matrix_meiotic_depletion


title: 293-WT_dCA_72h_Rep2

description:
293-WT cells treated with 1uM dCA for 72 hours.
S5

source_name: 293-WT cells treated with 1μM dCA for 72 hours, biological replicate-#2


title: single cell Plasma cell  [B6]


title: ZRS08_4_OT2_thy_r1_111

description: OT-II TCR transgenic replicate 1


title: ZRS08_8_B6_thy_r5_111

description: Wild-type replicate 5 sample 1


title: ZRS08_3_OT1_thy_r1_111

description: OT-I TCR transgenic replicate 1


title: LexA-ER-GAL4AD_2h, Rep2

description:
U+Tag_LexA_Replicate_2_2HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [B5]


title: 293-WT_dCA_72h_Rep1

description:
293-WT cells treated with 1uM dCA for 72 hours.
S4

source_name: 293-WT cells treated with 1μM dCA for 72 hours, biological replicate-#1


title: single cell Plasma cell  [C2]


title: ZRS08_2_B6_thy_r4_111

description: Wild-type replicate 4 sample 2


title: LexA-ER-GAL4AD_0.5h, Rep2

description:
U+Tag_LexA_Replicate_2_0.5HR
gene_count_matrix_meiotic_depletion


title: 293-WT_Ctrl_72h_Rep3

description:
293-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours.
S3

source_name: 293-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours, biological replicate-#3


title: ZRS08_1_B6_thy_r4_111

description: Wild-type replicate 4 sample 1


title: single cell Plasma cell  [B3]


title: LexA-ER-GAL4AD_4.5h, Rep1

description:
U+Tag_LexA_Replicate_1_4.5HR
gene_count_matrix_meiotic_depletion


title: ZRS07_8_F5_r2

description: F5 TCR transgenic replicate 2


title: 293-WT_15w_72h_Rep1

description:
293-WT cells treated with 1uM 15w for 72 hours.
S7

source_name: 293-WT cells treated with 1μM 15w for 72 hours, biological replicate-#1


title: 293-WT_Ctrl_72h_Rep1

description:
293-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours.
S1

source_name: 293-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours, biological replicate-#1


title: single cell Plasma cell  [B2]

source_name: Bone marrow


title: LexA-ER-GAL4AD_3h, Rep1

description:
U+Tag_LexA_Replicate_1_3HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [A8]


title: LexA-ER-GAL4AD_2.5h, Rep1

description:
U+Tag_LexA_Replicate_1_2.5HR
gene_count_matrix_meiotic_depletion


title: ZRS07_6_MHC2_r1

description: MHCII knockout replicate 1 enriched for positive selection

value: MHCII-/-


title: single cell Plasma cell  [B1]


title: ZRS07_5_B6_r3

description: Wild-type replicate 3 enriched for positive selection


title: single cell Plasma cell  [A7]


title: ZRS07_4_AND_r2

description: AND TCR transgenic replicate 2

value: AND


title: LexA-ER-GAL4AD_0.5h, Rep1

description:
U+Tag_LexA_Replicate_1_0.5HR
gene_count_matrix_meiotic_depletion


title: LexA-ER-GAL4AD_2h, Rep1

description:
U+Tag_LexA_Replicate_1_2HR
gene_count_matrix_meiotic_depletion


title: single cell Plasma cell  [B4]


title: HEK293_PMA24h_SnxB_Rep1

data_processing:
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HEK293_PMA24h_SnxB_geneCounts.txt: Space-delimited text file includes gene counts for each sample.

source_name: HEK293 cells treated with 30nM PMA and 1µM Senexin B for 24 hours, biological replicate-#1

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 2x10^5 cells per well. 24 hours post seeding, cells were treated as indicated.

treatment_protocol: Cells were treated with vehicle control (0.1% DMSO), 1 μM Senexin B, 30nM PMA or combination for 24 hours.

value: HEK293 (ATCC)

value: 30nM PMA and 1uM Senexin B for 24 hours


title: HEK293_PMA24h_SnxB_Rep2

source_name: HEK293 cells treated with 30nM PMA and 1µM Senexin B for 24 hours, biological replicate-#2


title: HEK293_PMA24h_Rep3

source_name: HEK293 cells treated with 30nM PMA for 24 hours, biological replicate-#3

value: 30nM PMA for 24 hours


title: HEK293_PMA24h_SnxB_Rep3

source_name: HEK293 cells treated with 30nM PMA and 1µM Senexin B for 24 hours, biological replicate-#3


title: single cell Plasma cell  [A5]


title: HEK293_PMA24h_Rep2

source_name: HEK293 cells treated with 30nM PMA for 24 hours, biological replicate-#2


title: ZRS07_3_B2M_r2

description: MHCI knockout replicate 2 enriched for positive selection

value: MHCI-/-


title: LexA-ER-GAL4AD_6h, Rep1

description:
U+Tag_LexA_Replicate_1_6HR
gene_count_matrix_meiotic_depletion

value: UME6-AID-3V5; lexA-ER-GAL4AD


title: 293-WT_Ctrl_72h_Rep2

description:
293-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours.
S2

source_name: 293-WT cells treated with 0.1% DMSO (vehicle control) for 72 hours, biological replicate-#2

value: WT


title: ume6∆,(Rep3),Rep3

description:
U6Del(Rep3)
gene_count_matrix_mitotic_depletion

value: Mitotic


title: ume6∆,(Rep2),Rep2

description:
U6Del(Rep2)
gene_count_matrix_mitotic_depletion


title: ZRS07_7_MHC2_r2

description: MHCII knockout replicate 2 enriched for positive selection

source_name: thymus

value: thymus

value: 4-8 weeks


title: HEK293_PMA24h_Rep1

source_name: HEK293 cells treated with 30nM PMA for 24 hours, biological replicate-#1


title: single cell Plasma cell  [A4]


title: ZRS07_1_B6_r2

description: Wild-type replicate 2 enriched for positive selection

value: polyA RNA and protein


title: single cell Plasma cell  [A6]

value: Bone marrow


title: ume6∆,(Rep1),Rep1

description:
U6Del(Rep1)
gene_count_matrix_mitotic_depletion


title: HEK293_SnxB_24h_Rep3

source_name: HEK293 cells treated with 1μM Senexin B for 24 hours, biological replicate-#3

value: 1uM Senexin B for 24 hours


title: single cell Plasma cell  [A3]

value: Plasma cell


title: Wildtype,(Rep3),Rep3

description:
WT (Rep3)
gene_count_matrix_mitotic_depletion

value: ß-estradiol + Auxin


title: ZRS06_3_F5_r1

description: F5 TCR transgenic replicate 1


title: Wildtype,(Rep2),Rep2

description:
WT (Rep2)
gene_count_matrix_mitotic_depletion


title: ZRS06_2_AND_r1

description: AND TCR transgenic replicate 1


title: HEK293_SnxB_24h_Rep1

source_name: HEK293 cells treated with 1μM Senexin B for 24 hours, biological replicate-#1


title: single cell Plasma cell  [A1]


title: Wildtype,(Rep1),Rep1

description:
WT (Rep1)
gene_count_matrix_mitotic_depletion


title: ZRS06_1_B6_r1

description: Wild-type replicate 1 enriched for positive selection

value: B6 (WT)


title: HEK293_Ctrl_24h_Rep3

source_name: HEK293 cells treated with vehicle control (0.1% DMSO) for 24 hours, biological replicate-#3

value: 0.1% DMSO (vehicle control) for 24 hours


title: MEFs, NELFB-AID, Δ-C60, +IAA, Pol II ChIP-seq, biol rep 2

city: Washington

first: Haihui

last: Pan

state: DC

address: 2121 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

library_source: genomic

data_processing:
Raw ChIP-seq data in FASTQ format was aligned to mm10 reference genome using bowtie2
The Sequence Alignment Map (SAM) file was converted to a Binary Alignment Map (BAM) file, and then sorted by Samtools. Alignments with MAPQ score smaller than 30 were skipped.
The coverage (the number of reads per bin) track was generated by deepTools. The size of each bin was set at 1bp and the coverage was normalized by Reads Per Kilobase per Million mapped reads (RPKM).
Scores for each gene were calculated by computeMatrix command. The gene bodies were scaled to 3kb and the region between 1kb upstream to TSS and 1.5kb downstream of TES were included in the analysis.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Embryos

growth_protocol: 10% FBS in DMEM

extract_protocol:
Cells were treated with IAA at 0.5mM for 6 hours, if indicated, and then fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented with micrococcal nuclease and immunoprecipitated with Pol II or flag antibodies.
ChIP-seq libraries were prepared using the KAPA Hyperprep Library Preparation Kit complemented with Roche SeqCap Adapter Kit A.  Post amplification libraries were size selected at 0.7-0.9X using Kapa cleanup beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

value: Fibroblasts

tag: chip antibody

value: Pol II (8wg16, Santa Cruz #56767)

value: Nelfb -/-; NELFB-AID

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-{delta}-C60; +IAA; Pol II ChIP


title: KD

city: Zunyi

first: Juan

middle: Juan

last: Zhao

state: Guizhou

address: 6 Xuefu west Road

country: China

institute: Zunyi medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.   FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: colon tissue

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: colon

tag: disease state

value: DSS-induced IBD mice model

value: miR-7 deficiency


title: LexA-ER-B112,120min,Rep3

description:
+Tag; +LexA (120min) Rep3
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112

value: Mitotic


title: MEFs, NELFB-AID, Δ-C60, +IAA, Pol II ChIP-seq, biol rep 1


title: LexA-ER-B112,60min,Rep3

description:
+Tag; +LexA (60min) Rep3
gene_count_matrix_mitotic_depletion


title: MEFs, NELFB-AID, WT, +IAA, Pol II ChIP-seq, biol rep 2

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-WT-NELFB; +IAA; Pol II ChIP


title: HEK293_Ctrl_24h_Rep1

source_name: HEK293 cells treated with vehicle control (0.1% DMSO) for 24 hours, biological replicate-#1

value: HEK293 (ATCC)


title: WT

value: wild type


title: TNFR1and2KO_2_Liver_RNA-seq

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description: TNFR1/2 KO_3

data_processing:
RNA-seq data were aligned to mm10 using STAR v2.5.4a (default parameter, except: --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical).
Differential gene expression analysis was performed using the Cuffdiff function in the Cufflinks v2.2.1. Analysis was performed on the gene level.
A significant change is defined by a q value (adjusted p value using the Benjamini-Hochberg Procedure) < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each sample with differential gene expression test results

source_name: liver

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEB RNA Ultra

value: TNFR1/2 KO

value: liver


title: LexA-ER-B112,30min,Rep3

description:
+Tag; +LexA (30min) Rep3
gene_count_matrix_mitotic_depletion

value: ß-estradiol + Auxin


title: HEK293_Serum_SnxB_Rep3

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: Serum-starved HEK293 cells, treated with 10% FBS (with presence of 1µM Senexin B) for 30 min, biological replicate-#3

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 2x10^5 cells per well.  24 hours post seeding, cells were washed with serum-free media twice and serum-starved in serum-free DMEM (high-glucose) media for 48 hours before the treatment.

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: Cells were first pre-treated with 1μM Senexin B or 0.1% DMSO (control) for 1 hour and then treated with or without 10% FBS for 30 minutes.

value: Serum-starved for 48 hours, pre-treated with 1microM Senexin B for 60 minutes and then treated with 10percent FBS for 30 minutes


title: TNFR1and2KO_1_Liver_RNA-seq

description: TNFR1/2 KO_2


title: MEFs, NELFB-AID, WT, +IAA, Pol II ChIP-seq, biol rep 1

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)


title: HEK293_SnxB_24h_Rep2

source_name: HEK293 cells treated with 1μM Senexin B for 24 hours, biological replicate-#2

value: 1uM Senexin B for 24 hours


title: HEK293_Serum_SnxB_Rep2

source_name: Serum-starved HEK293 cells, treated with 10% FBS (with presence of 1µM Senexin B) for 30 min, biological replicate-#2


title: single cell Plasma cell  [A2]

source_name: Bone marrow

value: Bone marrow

value: Plasma cell

value: WT


title: TNFR1and2KO_0_Liver_RNA-seq

description: TNFR1/2 KO_1


title: LexA-ER-B112,0min,Rep3

description:
+Tag; +LexA (0min) Rep3
gene_count_matrix_mitotic_depletion


title: MEFs, NELFB-AID, EV, +IAA, Pol II ChIP-seq, biol rep 1

value: Fibroblasts

value: Pol II (8wg16, Santa Cruz #56767)

value: Nelfb -/-; NELFB-AID

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-EV; +IAA; Pol II ChIP


title: RiPK1D138N_2_Liver_RNA-seq

value: RIPK1 D138N


title: LexA-ER-B112,-30min,Rep3

description:
+Tag; +LexA (-30min) Rep3
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112

value: Mitotic


title: MEFs, NELFB-AID, EV, -IAA, Pol II ChIP-seq, biol rep 2

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-EV; -IAA; Pol II ChIP


title: RiPK1D138N_1_Liver_RNA-seq

value: liver


title: MEFs, NELFB-AID, EV, -IAA, Pol II ChIP-seq, biol rep 1


title: HEK293_Ctrl_24h_Rep2

source_name: HEK293 cells treated with vehicle control (0.1% DMSO) for 24 hours, biological replicate-#2

value: HEK293 (ATCC)

value: 0.1% DMSO (vehicle control) for 24 hours


title: HEK293_Serum_Rep3

source_name: Serum-starved HEK293 cells, treated with 10% FBS for 30 min, biological replicate-#3

value: Serum-starved for 48 hours, pre-treated with 0.1percent DMSO (vehicle control) for 60 minutes and then treated with 10percent FBS for 30 minutes


title: HEK293_Serum_Rep2

source_name: Serum-starved HEK293 cells, treated with 10% FBS for 30 min, biological replicate-#2


title: LexA-ER-B112; 4xLexO-TIR,60min,Rep3

description:
+Tag; +LexA; +LexO-TIR (60min) Rep3
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112; 4xLexO-TIR

value: ß-estradiol + Auxin


title: HEK293_Serum_Rep1

source_name: Serum-starved HEK293 cells, treated with 10% FBS for 30 min, biological replicate-#1


title: WT_2_Liver_RNA-seq


title: LexA-ER-B112; 4xLexO-TIR,30min,Rep3

description:
+Tag; +LexA; +LexO-TIR (30min) Rep3
gene_count_matrix_mitotic_depletion


title: MEFs, NELFC-AID, +IAA, Pol II ChIP-seq, biol rep 2

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

value: Nelfcd -/-; NELFC-AID

value: pLenti-NELFC-AID; pCDH-osTIR1-mCherry; Crispr sgNelfcd; single clone isolation; IAA; Pol II ChIP


title: LexA-ER-B112,15min,Rep3

description:
+Tag; +LexA (15min) Rep3
gene_count_matrix_mitotic_depletion


title: MEFs, NELFB-AID, EV, +IAA, Pol II ChIP-seq, biol rep 2

value: Fibroblasts

value: Pol II (8wg16, Santa Cruz #56767)


title: HEK293_SnxB_Rep3

source_name: Serum-starved HEK293 cells, treated with 1μM Senexin B for 90 min, biological replicate-#3

value: Serum-starved for 48 hours, treated with 1microM Senexin B for 90 minutes


title: WT_1_Liver_RNA-seq

value: WT


title: MEFs, NELFC-AID, -IAA, Pol II ChIP-seq, biol rep 2

value: pLenti-NELFC-AID; pCDH-osTIR1-mCherry; Crispr sgNelfcd; single clone isolation; Pol II ChIP


title: LexA-ER-B112; 4xLexO-TIR,15min,Rep3

description:
+Tag; +LexA; +LexO-TIR (15min) Rep3
gene_count_matrix_mitotic_depletion

value: Mitotic


title: HEK293_SnxB_Rep2

source_name: Serum-starved HEK293 cells, treated with 1μM Senexin B for 90 min, biological replicate-#2


title: HEK293_Serum_SnxB_Rep1

source_name: Serum-starved HEK293 cells, treated with 10% FBS (with presence of 1µM Senexin B) for 30 min, biological replicate-#1

value: Serum-starved for 48 hours, pre-treated with 1microM Senexin B for 60 minutes and then treated with 10percent FBS for 30 minutes


title: WT_0_Liver_RNA-seq

value: liver


title: LexA-ER-B112; 4xLexO-TIR,0min,Rep3

description:
+Tag; +LexA; +LexO-TIR (0min) Rep3
gene_count_matrix_mitotic_depletion


title: MEFs, NELFC-AID, -IAA, Pol II ChIP-seq, biol rep 1


title: Sham_2_Liver_RNA-seq


title: HEK293_SnxB_Rep1

source_name: Serum-starved HEK293 cells, treated with 1μM Senexin B for 90 min, biological replicate-#1

value: HEK293 (ATCC)


title: LexA-ER-B112; 4xLexO-TIR,-30min,Rep3

description:
+Tag; +LexA; +LexO-TIR (-30min) Rep3
gene_count_matrix_mitotic_depletion


title: LexA-ER-B112; 4xLexO-TIR,120min,Rep3

description:
+Tag; +LexA; +LexO-TIR (120min) Rep3
gene_count_matrix_mitotic_depletion


title: Sham_1_Liver_RNA-seq


title: HEK293_Ctrl_Rep3

source_name: Serum-starved HEK293 cells, treated with vehicle control (0.1% DMSO) for 90 min, biological replicate-#3

value: Serum-starved for 48 hours, treated with 0.1percent DMSO (vehicle control) for 90 minutes


title: MEFs, NELFB-AID, +IAA, Pol II ChIP-seq, biol rep 2

source_name: Embryos

value: Nelfb -/-; NELFB-AID

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; IAA; Pol II ChIP


title: LexA-ER-B112; 4xLexO-TIR,120min,Rep2

description:
+Tag; +LexA; +LexO-TIR (120min) Rep2
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112; 4xLexO-TIR

value: ß-estradiol + Auxin


title: MEFs, NELFB-AID, +IAA, Pol II ChIP-seq, biol rep 1

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)


title: RiPK1D138N_0_Liver_RNA-seq

value: RIPK1 D138N


title: HEK293_Ctrl_Rep2

source_name: Serum-starved HEK293 cells, treated with vehicle control (0.1% DMSO) for 90 min, biological replicate-#2


title: Sham_0_Liver_RNA-seq


title: ZRS07_2_B2M_r1

description: MHCI knockout replicate 1 enriched for positive selection

source_name: thymus

value: thymus

value: MHCI-/-

value: 4-8 weeks

value: polyA RNA and protein


title: LexA-ER-B112; 4xLexO-TIR,60min,Rep2

description:
+Tag; +LexA; +LexO-TIR (60min) Rep2
gene_count_matrix_mitotic_depletion


title: MEFs, NELFC-AID, +IAA, Pol II ChIP-seq, biol rep 1

value: Fibroblasts

value: Pol II (8wg16, Santa Cruz #56767)

value: Nelfcd -/-; NELFC-AID

value: pLenti-NELFC-AID; pCDH-osTIR1-mCherry; Crispr sgNelfcd; single clone isolation; IAA; Pol II ChIP


title: MEFs, NELFB-AID, -IAA, Pol II ChIP-seq, biol rep 2

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; Pol II ChIP


title: HEK293_Ctrl_Rep1

source_name: Serum-starved HEK293 cells, treated with vehicle control (0.1% DMSO) for 90 min, biological replicate-#1

value: HEK293 (ATCC)

value: Serum-starved for 48 hours, treated with 0.1percent DMSO (vehicle control) for 90 minutes


title: LexA-ER-B112; 4xLexO-TIR,30min,Rep2

description:
+Tag; +LexA; +LexO-TIR (30min) Rep2
gene_count_matrix_mitotic_depletion

value: Mitotic


title: MEFs, NELFB-AID, -IAA, Pol II ChIP-seq, biol rep 1

value: Nelfb -/-; NELFB-AID


title: PERK_KO_Day10_rep3

city: Guangzhou

first: Weisheng

last: Cheng

address: 2nd Zhongshan Road

institute: Sun yat-sen University

data_processing:
Illumina Casava software used for basecalling.
Raw RNA-seq sequenced reads were quality tested using FASTQC
Data were aligned to GRCh38/hg38 Homo sapiens reference genome using STAR aligner with ENCODE standard options for long RNA-seq pipeline
RSEM was used to estimate gene expression abundance and calculate TPM values
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using the NucleoZol reagent and quantified by NanoDrop spectrophotometer.
mRNA libraries were prepared using the VAHTS® mRNA-seq V2 Library Prep Kit for Illumina from Vazyme protocols

value: human embryonic stem cells (hESCs)

tag: genotype/variation

value: PERK KO

tag: differentiation time


title: LexA-ER-B112; 4xLexO-TIR,15min,Rep2

description:
+Tag; +LexA; +LexO-TIR (15min) Rep2
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112; 4xLexO-TIR

tag: time

value: ß-estradiol + Auxin

tag: condition


title: gARID_gsnf2(-)_pfg(-)_INPUT_2

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: Peak-calling, text.

organism: Plasmodium berghei ANKA

growth_protocol: Balb/c mice were infected with transgenic parasites.

extract_protocol:
Whole blood was withdrawn from infected mice, diluted in medium, and filtered with Plasmodipur to remove lymphocytes. The samples were then fixed with 1% formaldehyde for 60 min at 30 °C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were lysed in SDS lysis buffer. The lysates were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power. After centrifugation of the sonicated lysates, the supernatants were subjected to immunoprecipitation with anti-GFP antibodies conjugated on Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Infected mice were treated with sulfadiazine for 2 days.

tag: Stage

value: Gametocyte

value: ANKA

value: GFP-fused gARID expressing, gsnf2 and pfg knockout


title: gARID_gsnf2(-)_pfg(-)_IP(anti-GFP)_2

value: anti-GFP


title: gARID_gsnf2(-)_pfg(-)_INPUT_1


title: LexA-ER-B112; 4xLexO-TIR,0min,Rep2

description:
+Tag; +LexA; +LexO-TIR (0min) Rep2
gene_count_matrix_mitotic_depletion


title: MEFs, Δ-C60, flag ChIP-seq, biol rep 1

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

tag: cell type

value: Fibroblasts

value: flag (M2, Sigma #F1804)

value: Nelfb -/-; {delta}-C60-NELFB

value: pLenti-{delta}-C60-3Xflag; Ad-Cre; single clone isolation; flag ChIP


title: MEFs, Δ-C60, flag ChIP-seq, biol rep 2


title: PERK_KO_Day10_rep1


title: gARID_gsnf2(-)_pfg(-)_IP(anti-GFP)_1


title: MEFs, WT, flag ChIP-seq, biol rep 2

value: Nelfb -/-; WT-NELFB

value: pLenti-WT-NELFB-3Xflag; Ad-Cre; single clone isolation; flag ChIP


title: gARID_gsnf2(-)_INPUT_2

value: GFP-fused gARID expressing, gsnf2 knockout


title: PERK_KO_Day5_rep3

value: human embryonic stem cells (hESCs)


title: LexA-ER-B112,120min,Rep2

description:
+Tag; +LexA (120min) Rep2
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112

value: Mitotic


title: PERK_KO_Day10_rep2

value: PERK KO


title: LexA-ER-B112,60min,Rep2

description:
+Tag; +LexA (60min) Rep2
gene_count_matrix_mitotic_depletion

value: ß-estradiol + Auxin


title: MEFs, Δ-C60, Pol II ChIP-seq, biol rep 4

value: Pol II (8wg16, Santa Cruz #56767)

value: Nelfb -/-; {delta}-C60

value: pLenti-{delta}-C60-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: PERK_KO_Day5_rep2


title: PERK_KO_Day5_rep1


title: gARID_gsnf2(-)_INPUT_1

value: Gametocyte

value: ANKA


title: LexA-ER-B112,30min,Rep2

description:
+Tag; +LexA (30min) Rep2
gene_count_matrix_mitotic_depletion


title: LexA-ER-B112,15min,Rep2

description:
+Tag; +LexA (15min) Rep2
gene_count_matrix_mitotic_depletion


title: PERK_KO_Day3_rep3


title: PERK_KO_Day3_rep2


title: MEFs, WT, Pol II ChIP-seq, biol rep 4

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

value: Fibroblasts

value: pLenti-WT-NELFB-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: MEFs, Δ-C60, Pol II ChIP-seq, biol rep 3


title: MEFs, WT, flag ChIP-seq, biol rep 1

value: flag (M2, Sigma #F1804)

value: Nelfb -/-; WT-NELFB


title: PERK_KO_Day3_rep1


title: MEFs, WT, Pol II ChIP-seq, biol rep 3


title: LexA-ER-B112; 4xLexO-TIR,-30min,Rep2

description:
+Tag; +LexA; +LexO-TIR (-30min) Rep2
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112; 4xLexO-TIR


title: gARID_IP(anti-GFP)_2

value: GFP-fused gARID expressing

value: anti-GFP


title: gARID_INPUT_2


title: gARID_gsnf2(-)_IP(anti-GFP)_1

value: GFP-fused gARID expressing, gsnf2 knockout


title: LexA-ER-B112,-30min,Rep2

description:
+Tag; +LexA (-30min) Rep2
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112

value: Mitotic


title: MEFs, Δ-C60, Pol II ChIP-seq, biol rep 2

value: Pol II (8wg16, Santa Cruz #56767)


title: gARID_INPUT_1


title: PERK_KO_Day2_rep3

value: human embryonic stem cells (hESCs)

value: PERK KO


title: LexA-ER-B112; 4xLexO-TIR,120min,Rep1

description:
+Tag; +LexA; +LexO-TIR (120min) Rep1
gene_count_matrix_mitotic_depletion

value: ß-estradiol + Auxin


title: MEFs, Δ-C60, Pol II ChIP-seq, biol rep 1

value: Nelfb -/-; {delta}-C60

value: pLenti-{delta}-C60-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: PERK_KO_Day2_rep2


title: gARID_IP(anti-GFP)_1

value: Gametocyte

value: ANKA


title: gARID_gsnf2(-)_IP(anti-GFP)_2


title: PERK_KO_Day2_rep1


title: MEFs, MT486, Pol II ChIP-seq, biol rep 2

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

value: Fibroblasts

value: Nelfb -/-; MT486

value: pLenti-MT486-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: LexA-ER-B112; 4xLexO-TIR,60min,Rep1

description:
+Tag; +LexA; +LexO-TIR (60min) Rep1
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112; 4xLexO-TIR


title: LexA-ER-B112; 4xLexO-TIR,30min,Rep1

description:
+Tag; +LexA; +LexO-TIR (30min) Rep1
gene_count_matrix_mitotic_depletion


title: MEFs, MT486, Pol II ChIP-seq, biol rep 1


title: LexA-ER-B112; 4xLexO-TIR,15min,Rep1

description:
+Tag; +LexA; +LexO-TIR (15min) Rep1
gene_count_matrix_mitotic_depletion


title: MEFs, MT194, Pol II ChIP-seq, biol rep 2

value: Nelfb -/-; MT194

value: pLenti-MT194-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: LexA-ER-B112,0min,Rep2

description:
+Tag; +LexA (0min) Rep2
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112

value: Mitotic


title: PERK_KO_Day1_rep2

value: human embryonic stem cells (hESCs)


title: LexA-ER-B112; 4xLexO-TIR,0min,Rep1

description:
+Tag; +LexA; +LexO-TIR (0min) Rep1
gene_count_matrix_mitotic_depletion


title: MEFs, MT194, Pol II ChIP-seq, biol rep 1

value: Pol II (8wg16, Santa Cruz #56767)


title: MEFs, WT, Pol II ChIP-seq, biol rep 2

value: Nelfb -/-; WT-NELFB

value: pLenti-WT-NELFB-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: LexA-ER-B112; 4xLexO-TIR,-30min,Rep1

description:
+Tag; +LexA; +LexO-TIR (-30min) Rep1
gene_count_matrix_mitotic_depletion

value: ß-estradiol + Auxin


title: PERK_KO_Day1_rep1

value: PERK KO


title: LexA-ER-B112,120min,Rep1

description:
+Tag; +LexA (120min) Rep1
gene_count_matrix_mitotic_depletion


title: PERK_KO_Day0_rep3


title: MEFs, MT144, Pol II ChIP-seq, biol rep 2

value: Nelfb -/-; MT144

value: pLenti-MT144-3Xflag; Ad-Cre; single clone isolation; Pol II ChIP


title: PERK_KO_Day0_rep2


title: PERK_KO_Day0_rep1


title: PERK_KO_Day1_rep3


title: LexA-ER-B112,30min,Rep1

description:
+Tag; +LexA (30min) Rep1
gene_count_matrix_mitotic_depletion


title: H1_Day10_rep3

value: Wild type


title: HD 1

type: RNA

city: Prague

first: Zuzana

last: Parackova

address: V Uvalu

country: Czech Republic

institute: Charles University

hyb_protocol: protocol nanostring Immunology panel

scan_protocol: protocol nanostring Immunology panel

data_processing: nCounter and Rosalind

source_name: PBMC RNA

label_protocol: protocol nanostring Immunology panel

extract_protocol: Ficoll density centrifugation isolation method

treatment_protocol: no treatment

tag: group

value: HD

value: PBMC


title: MEFs, MT144, Pol II ChIP-seq, biol rep 1

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

value: Fibroblasts


title: HD 4


title: HD 3


title: JIA 10

value: articul


title: HD 2


title: JIA 9


title: JIA 8

value: ERA


title: H1_Day10_rep2


title: JIA 6


title: LexA-ER-B112,0min,Rep1

description:
+Tag; +LexA (0min) Rep1
gene_count_matrix_mitotic_depletion

value: UME6-AID-3V5; LexA-ER-B112

value: Mitotic


title: MEFs, WT, Pol II ChIP-seq, biol rep 1

value: Pol II (8wg16, Santa Cruz #56767)


title: H1_Day10_rep1

value: human embryonic stem cells (hESCs)


title: LexA-ER-B112,60min,Rep1

description:
+Tag; +LexA (60min) Rep1
gene_count_matrix_mitotic_depletion


title: LexA-ER-B112,-30min,Rep1

description:
+Tag; +LexA (-30min) Rep1
gene_count_matrix_mitotic_depletion


title: MEFs, WT, Cre, RNA-seq, biol rep2

data_processing:
Raw RNA-seq data in FASTQ format were aligned to mm10 reference genome using bowtie2. The Sequence Alignment Map (SAM) file was converted to a Binary Alignment Map (BAM) file, and then sorted by Samtools. Alignments with MAPQ score smaller than 30 were skipped.
HTSeq was used to calculate the number of mapped reads to each gene. The count matrix was imported to DESeq2 for normalization, visualization and analysis of differential gene expression. Empirical Bayes shrinkage estimators were applied to shrink the limit fold change (LFC). The shrinkage of effect size (LFC estimates) was then used for visualization and ranking of genes.
The significantly differentially expressed genes (DEGs) were identified by two thresholds: (1) the absolute value of log2 fold change (LFC) greater than 0.5; (2) the adjust p-value (p-adj) less than 0.05.
These DEGs were used for further GO term enrichment analysis by R package clusterProfiler
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: Embryo

extract_protocol:
RNA was harvested using RNeasy kit
RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide.

value: Embryo

value: Nelfb flox/-

value: pLenti-WT-NELFB; 7 days after Ad-Cre-GFP


title: MEFs, WT, GFP, RNA-seq, biol rep1

value: pLenti-WT-NELFB; 7 days after Ad-GFP


title: H1_Day5_rep3


title: JIA 5


title: MEFs, WT, GFP, RNA-seq, biol rep2


title: MEFs, WT, Cre, RNA-seq, biol rep1


title: H1_Day5_rep2


title: LexA-ER-B112,15min,Rep1

description:
+Tag; +LexA (15min) Rep1
gene_count_matrix_mitotic_depletion

data_processing:
Sequencing reads were mapped to a reference genome using HISAT2, samtools, and Stringtie
Mapped reads were visualized to IGV_2.12.3.app
Counts and TPM tables were generated from sequencing reads using pseudoalignment with kallisto
Assembly: SK1 Reference Genome from Saccharomyces Genome Resequencing Project at Sanger Institute
Supplementary files format and content: Excel tables include counts and TPMs for each sample.

value: ß-estradiol + Auxin


title: MEFs, DMT, GFP, RNA-seq, biol rep2

value: pLenti-DMT(MT194&486); 7 days after AdGFP


title: JIA 7


title: JIA 3


title: H1_Day5_rep1

value: Wild type


title: MEFs, DMT, GFP, RNA-seq, biol rep1


title: 24h-V2

city: OSLO

first: Xuan

last: Jiang

department: Department of Medical Genetics

country: Norway

institute: University of Oslo

description: μParaflo MicroRNA Microarray Assay. The microarray synthesis is based on a µParaflo microfluidic chip technology.

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After hybridization detection used fluorescence labeling using tag-specific Cy5 dyes.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter2 (Locally-weighted Regression).

source_name: primary human neural progenitor cells

label_protocol: The assay started from 5 μg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.

growth_protocol: Human primary NPCs were maintained in culture medium as neurospheres in uncoated dishes or as monolayer in human fibronectin- or poly-D-lysine-coated dishes.

extract_protocol: Virus-infected NPCs were harvested at 2, 4, 12, and 24 hpi and mock-infected cells were harvested at 12 hours post mock infection. Culture medium was removed and cells were rinsed with RNase-free PBS, then lysed using 1 mL of Trizol reagent. Total RNA was extracted using an miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Prior to infection, NPCs were seeded onto poly-D-lysine-coated dishes and allowed to attach overnight. For microarray experiments, NPCs were seeded at a density of 5×106 cells per 10 cm-dish and infected with HCMV at an MOI of 3. For mock infection, an equivalent volume of conditioned medium collected from cultured HFFs was added to the cells. After incubation with virus stock or conditioned medium for 3 h the medium was replaced with half-fresh growth medium/half-conditioned medium collected from cultured NPCs.

tag: tag

value: HCMV infected at a MOI of 3 at 24 hours post infection


title: H1_Day3_rep3


title: 24h-V1


title: MEFs, DMT, Cre, RNA-seq, biol rep2

value: pLenti-DMT(MT194&486); 7 days after Ad-Cre-GFP


title: JIA 2

value: PBMC


title: MEFs, DMT, Cre, RNA-seq, biol rep1

value: Mouse Embryonic Fibroblasts (MEFs)


title: JIA 1


title: H1_Day3_rep1


title: 12h-V2

value: HCMV infected at a MOI of 3 at 12 hours post infection


title: H1_Day2_rep3


title: H1_Day2_rep2


title: MEFs, MT486, GFP, RNA-seq, biol rep2

value: pLenti-MT486; 7 days after Ad-GFP


title: ASC48-old-KO-total-RNA-rep2

city: Hong Kong

first: Gexin

last: Liu

state: Sha Tin

address: 503, Li Ka Shing Medical Science Building, PWH, Yin Cheng Street

country: Hong Kong

institute: Chinese University of Hong Kong

data_processing:
Adaptor sequence trimming using Trimmomatic were first conducted.
Remaining reads were aligned to the mouse genome mm10 using HISAT2 software with default parameters.
Cufflinks was then used to derive the fragments per kilobase per million (FPKM) values.
The subsequent mapped reads were quantified byfeatureCounts.
Genes were identified as differentially expressed genes (DEGs) if the change of expression level is greater than 1 folds and the p-value is less than 0.05 between two stages/conditions using DESeq2.
Assembly: mm10
Supplementary files format and content: *_fpkm_tracking.txt: Tab-delimited files from Cufflinks containing FPKM values.

growth_protocol: FACS sorted ASCs were cultured in F10+20%FBS+1%Pen/Strep+b-FGF. All cells were grown in 5% CO2 37°C incubator.

extract_protocol:
For total RNA-seq, 1ml Trizol(Invitogen) were added to cells and RNA were extracted according to manufacturer's protocol. For subcelluar RNA-seq, cells were treated with buffer A (HEPES-KOH 50 mM pH 7.5, 10 mM KCl, 350 mM sucrose, 1 mM EDTA, 1 mM DTT, 0.1% Triton X-100) for 5 min on ice and then homogenized with a T 10 basic ULTRA-TURRAX® homogenizer at 4th gear for 1min. The nuclei were harvested by brief centrifugation (2000g, 5 min), while the supernatant was collected as the cytoplasmic fraction. Nuclei pelltet were resuspended with same volume buffer A. Then 1ml Trizol were added to both nuclear and cytoplasmic fraction and subjected for RNA extracion. All RNA were subjected to polyA selection (Ambion, 61006) before library preparation.
RNA libraries were prepared with about 1μg RNA according to the manufacturer's protocol (NEB UltraII RNA library kit for illumina). The libraries were sequenced in 2 × 150 nt manner on HiSeq X ten (Illumina).

value: KO

value: Sugt1 Knock Out

tag: age

value: old


title: ASC48-old-WT-total-RNA-rep1

value: WT

value: Ctrl


title: ASC48-young-WT-total-RNA-rep2

value: young


title: ASC48-old-KO-total-RNA-rep1


title: JIA 4

value: articul


title: H1_Day2_rep1

value: human embryonic stem cells (hESCs)


title: 4h-V1

value: HCMV infected at a MOI of 3 at 4 hours post infection


title: H1_Day3_rep2


title: 2h-V2

value: HCMV infected at a MOI of 3 at 2 hours post infection


title: 2h-V1


title: 12h-V1


title: 4h-V2


title: MEFs, MT486, Cre, RNA-seq, biol rep1

value: Embryo

value: Nelfb flox/-

value: pLenti-MT486; 7 days after Ad-Cre-GFP


title: H1_Day1_rep3

value: Wild type


title: MEFs, MT486, Cre, RNA-seq, biol rep2

value: Mouse Embryonic Fibroblasts (MEFs)


title: H1_Day1_rep2


title: MEFs, MT194, GFP, RNA-seq, biol rep2

value: pLenti-MT194; 7 days after Ad-GFP


title: ASC48-young-WT-total-RNA-rep1


title: ASC48-young-KO-total-RNA-rep1


title: MEFs, MT486, GFP, RNA-seq, biol rep1

value: pLenti-MT486; 7 days after Ad-GFP


title: MEFs, MT194, GFP, RNA-seq, biol rep1


title: H1_Day1_rep1


title: ASC48-young-KO-total-RNA-rep2

value: KO


title: MEFs, MT194, Cre, RNA-seq, biol rep2

value: pLenti-MT194; 7 days after Ad-Cre-GFP


title: Zscan4 OE ESC IP of H3K9me3

city: Tianjin

state: Tianjin

address: No. 38 Tongyan Road, Haihe Education Park, Tianjin

department: State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutdadpt, then sequence reads were mapped to mm10 genome using Bowtie2.
Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

growth_protocol: Mouse J1 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma). .

extract_protocol:
Cells were lysed and chromatin was extracted. Anti-H3K9me3 antibodies were used to immunoprecipiate FLAG-Zscan4 in mESCs. Proteins on chromatin associated with Zscan4 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Zscan4-assocated chromatin DNA was used in ChIP-seq library preparation.  Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.

treatment_protocol: The CDS region of Zscan4c was cloned into pCMV-FLAG vector.WT mESCs were transfected with 1000ng pCMV-tag2 vector.After transfection for 24h,the cells were treated with 500ug/ml G418 for 10days and the medium were changed every 24h，then we picked monoclonal cells.

value: Embryonic stem cell

value: Zscan4 overexpression


title: MEFs, MT194, Cre, RNA-seq, biol rep1


title: H1_Day0_rep3


title: H1_Day0_rep2


title: MEFs, EV, GFP, RNA-seq, biol rep1

value: pLenti-EV; 7 days after Ad-GFP


title: M-2

value: mock treated at 12 hour post infection


title: Dunaliella salina Bardawil, 3 d, 0 µM Fe, rep1

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

data_processing:
Alignment to Dunaliella salina Bardawil genome with the STAR aligner (v2.4.0j) with --alignIntronMax 5000.
FPKMs were calculated with cuffdiff (v2.0.2)  with --multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand.
Assembly: Dunaliella salina Bardawil v1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: fasta file for genome assembly
Supplementary files format and content: gff3 file for annotations

organism: Dunaliella salina

source_name: liquid culture

growth_protocol: Three days growth in liquid cultures grown on shaking platforms at 140 rpm at 24°C under constant light (50 µE m^-2 sec^-1).

extract_protocol:
TRI Reagent RNA exptraction plus TURBO DNase digestion.
Standard Illumina poly(A)-selected

treatment_protocol: Media supplemented with 1.5 µM iron or 0 µM iron.

value: liquid culture

value: UTEX LB 2538

value: vegetative cells

value: WT

value: 3 d

value: 0 uM Fe

tag: variety

value: Bardawil


title: Dunaliella salina Bardawil, 3 d, 0 µM Fe, rep3

tag: cell line


title: Dunaliella salina Bardawil, 3 d, 1.5 µM Fe, rep3

tag: genotype

value: 1.5 uM Fe


title: MEFs, EV, Cre, RNA-seq, biol rep2

value: Embryo

value: Mouse Embryonic Fibroblasts (MEFs)

value: Nelfb flox/-

tag: treatment

value: pLenti-EV; 7 days after Ad-Cre-GFP


title: Rx2

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Yan_Scleroderma_Featurecount_STAR_DESeq_exp_log2_normalized.xlsx

data_processing:
Reads were filtered based on a mean base quality score of > 20, and adapters were trimmed by “trim_galore” (version 0.4).
Trimmed reads were mapped to mm10 and hg19 using STAR aligner (version 2.6) separately.
Ambiguous reads which mapping to both mm10 and hg19 reference genomes were assigned to mm10, hg19 or discarded using tool –“ Disambiguate" (Ahdesmäki MJ, 2016)
Subread featureCounts (version 1.4.6) was applied for gene quantification based on GENCODE annotation release (GRCh37,V19) . PCA analysis was carried out to detect any potential sample outliers. The Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability, was performed to identify the differential expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: skin

growth_protocol: Lesional skin tissues were obtained from three treatment-naïve SSc patients whose mRSS (modified Rodnan skin score) >10. Skin biopsies (1 cm2) were divided into two pieces and transplanted subcutaneously into irradiated nude mice.

extract_protocol:
Total RNA from  xenografts were extracted by TRIzol reagent. The RNA quality and integrity were analyzed by Nanodrop (Thermo Fisher Scientific USA) and 1% agarose electrophoresis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10mg/L iguratimod suspended in 10% DMSO normal saline or only 10% DMSO normal saline was injected around the skin graft daily at 100µL each time in different group.  Five weeks later, the grafts were collected and analyzed.

tag: tissue

value: skin

tag: dignosis

value: systemis sclerosis

tag: gender

value: female

value: iguratimod


title: Dunaliella salina Bardawil, 3 d, 1.5µM Fe, rep1


title: Dunaliella salina Bardawil, 3 d, 1.5 µM Fe, rep2


title: Wildtype ESC IP of H3K9me3

tag: strain

value: Embryonic stem cell

value: Wildytpe

tag: chip antibody


title: Rx1

value: male


title: MEFs, EV, GFP, RNA-seq, biol rep2

value: pLenti-EV; 7 days after Ad-GFP


title: H1_Day0_rep1

value: human embryonic stem cells (hESCs)

tag: genotype/variation

value: Wild type

tag: differentiation time


title: MEFs, Δ-C60-Cre, RNA-seq, biol rep 3

value: pBabe-delta-C60; Ad-Cre; single clone isolation


title: Wildtype ESC input of H3K9me3


title: NC2

value: vehicle


title: S38

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Reads were mapped to 202,272 Ensembl transcript IDs using the Smallseq data analysis pipeline (Hagemann-Jensen et al., 2018), and to 4,121 transfer RNA fragments (tRF) using the MINTmap pipeline (Loher et al., 2017).
Only small RNA with read counts higher than 1 in more than 20% of samples were kept, resulting in a list of 4,767 small RNA.
Counts were rounded and data normalization and differential expression analysis was performed with the DESeq2 package (version 1.26.0) (Love et al. 2014). Small RNA levels were used as the dependent variable and chronological age as the explanatory variable. A local fit was used for estimating dispersions. Size factor normalized small RNA counts were obtained using the counts functions with arguments normalized = T.
After DESeq2 analysis, small RNA with unclear transcripts biotypes were removed from all analysis since they indicate potential degradation products (i.e. protein coding, lncRNA, processed transcript, retained intron, …). Transcript biotypes were defined using the biomaRt package (version 2.42.0) (Durinck et al. 2005). A total of 587 small RNA were kept after this filtering step, of which 276 were significantly associated with age at an FDR threshold of 0.2.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts_Smallseq_Ensembl.txt (raw counts)
Supplementary_files_format_and_content: raw_counts_MINTmap_tRF.txt (raw counts)
Supplementary_files_format_and_content: DESeq2_normalized_counts.xlsx (normalized counts)
Supplementary_files_format_and_content: DESeq2_small_RNA_association_with_age.xlsx (significance table)

source_name: plasma

extract_protocol:
Total RNA was extracted from plasma samples using the Qiagen miRNeasy Serum/Plasma Kit. Briefly, frozen plasma samples were thawed, vortexed and centrifuged for 16000 x g in 10 minutes and 50 µl was used for RNA extraction following the manufacturer’s protocol. Purified RNA was eluted in 50µl H2O and saved at -80C.
4 µl of purified RNA was used in a Small-seq protocol to construct the libraries (Hagemann-Jensen et al., 2018). Small RNA libraries were pooled and sequenced using an Illumina HiSeq 3000 platform for 100 bp single read.

value: plasma

tag: disease state

value: healthy


title: M-1

value: mock treated at 12 hour post infection


title: Dunaliella salina Bardawil, 3 d, 0 µM Fe, rep2

city: Berkeley

institute: UC Berkeley

value: liquid culture

value: UTEX LB 2538

value: vegetative cells

value: WT

tag: time

value: 3 d

value: 0 uM Fe

value: Bardawil


title: S37


title: Zscan4 OE ESC input of H3K9me3

tag: cell type

value: Embryonic stem cell

value: Zscan4 overexpression


title: Rx3

value: skin

value: systemis sclerosis

value: female

value: iguratimod


title: S34

value: male


title: S33

value: plasma


title: MEFs, EV, Cre, RNA-seq, biol rep1

value: Embryo

value: Mouse Embryonic Fibroblasts (MEFs)

value: Nelfb flox/-

value: pLenti-EV; 7 days after Ad-Cre-GFP


title: S36

value: healthy


title: NC3

value: vehicle


title: NC1


title: MEFs, WT(N48)-Cre, RNA-seq, biol rep 1

value: pBabe-WT-ATG-NELFB; Ad-Cre; single clone isolation


title: MEFs, Δ-C60-Cre, RNA-seq, biol rep 1

value: pBabe-delta-C60; Ad-Cre; single clone isolation


title: S35


title: MEFs, Δ-C60-Cre, RNA-seq, biol rep 2


title: S30


title: d2192n_HER2

first: Jong Hoon

last: Park

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

institute: Sookmyung Women's university

description: The methylated fraction from HER2

data_processing:
Paired-end 100bp sequence reads were aligned to the hg19 genome reference using bowtie.
The methylation abundance within region of interest (ROI) was estimated by MEDIPS R package with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed_Merged_Samples_averaged_read_counts_ROI_CDS.txt is a tab-delimited text file that contains the read counts of gene symbols located in CDS regions and processed_Merged_Samples_averaged_read_counts_ROI_PROMOTER.txt is a tab-delimited text file that contains the read counts of gene symbols located in promoter regions.

source_name: human breast cancer adjacent normal tissue

extract_protocol:
Genomic DNA was isolated from normal breast and breast cancer samples with a Qiagen Puregene kit following the manufacturer's protocol. Approximately 1 µg genomic DNA was sheared to 200- to 400-bp fragments using a Covaris LE220 sonicator. The sonicated genomic DNA was immunoprecipitated with human MBD2 protein coupled with paramagnetic Dynabeads M-280 Streptavidin via a biotin linker using a MethylMiner Methylated DNA Enrichment Kit.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: methylated fraction


title: MEFs, MT486-Cre, RNA-seq, biol rep 3

value: pLenti-MT486; Ad-Cre; single clone isolation


title: S32


title: MEFs, MT486-Cre, RNA-seq, biol rep 2


title: MEFs, WT(N48)-Cre, RNA-seq, biol rep 2


title: IR only N1

city: Solna Stockholm

first: Christina

last: Neofytou

address: Tomtebodavägen 16, 32B

department: Neuroscience

institute: Karolinska Institutet

hyb_protocol: Human Clariom S chips were hybridized with 2.5 µg of fragmented biotin-labeled cDNA in 100 µl hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000 using Command Console Software (Thermo Fisher Scientific, Waltham, MA).

data_processing: Analysis Software: TAC, Method: SST-RMA, Transformation: log2

label: biotin

source_name: iPSC-derived hNSPCs, 2D cultured, 4GY irradiated

label_protocol: 100 ng of RNA was used from each sample to prepare fragmented biotin-labeled cDNA by GeneChip WT PLUS reagent kit

growth_protocol: Human induced pluripotent stem cell (iPSC)-derived hNSPCs were provided by the iPS Core Facility at Karolinska Institutet. Dermal fibroblasts procured from skin biopsies were reprogrammed into iPSCs using virus free synthetic mRNA (Stemgent, StemRNA 3rd Generation Reprogramming Kit Cat#00–0076) and pushed to hNSPC fate development following the Dual-SMAD inhibition protocol45. Neural rosettes were extracted and cultured in medium enriched with epidermal growth factor (EGF) and fibroblast growth factor-2 (FGF2). hNSPC cultures were grown in T12.5, T25 and T75 sterile flasks, coated with 10% Poly-L-Ornithine (Sigma-Aldrich, Cat#P4957) and 0.2% Laminin (Sigma-Aldrich, Cat#L2020), at 37°C in a 5% CO2-humidified incubator. Cells were cultured in Dulbecco’s Modified Eagle Medium: Nutrient mixture F-12 (DMEM/F12), GlutaMAX (Thermo Fisher Scientific, Cat# 10565018) supplemented with 1% Penicillin – Streptomycin (Pen/Strep) (10000 U, Life technologies, Cat# 15140-122), 1% N2 (100x, Life Technologies, Cat# 17502001), 0.1% B27 (50x, Life Technologies, Cat# 12587-010), 0.1% EGF (10ng/ml, R&D Systems, Cat# 236-EG), and 0.1% FGF2 (10ng/ul, R&D Systems, Cat# 233-FB). Growth factor supplementation maintained proliferative activity without differentiation. Half of the medium volume was changed daily, and cultures were split at 60-80% confluence every 3-4 days.

extract_protocol: RNA isolation was performed using the RNasy Easy Mini Kit (Qiagen), per manufacturer instructions.

treatment_protocol: Cells were seeded at 250,000 cells/well on pre-coated 12-well cell culture plates and expanded in medium overnight to approximately 60% confluence. Subsequently, cells were irradiated in an CIX2 Xstrahl X-Ray Irradiator with Aluminum filter at a focus-to-skin distance (FSD) of 40 cm and with an energy of 195kV, 10 mA for 2 minutes and 58 seconds, for a received dose of 4 Gray (4 GY). To allow for assessment of irradiation damage, cells remained in the incubator for 1 hour. Pre-warmed DMEM/F-12 was mixed with the appropriate amount of LiCl powder (Sigma-Aldrich, Cat# L9650-100G), passed through a 0.22 μm filter, and supplemented with 1% Penicillin-Streptomycin, 1% N2, 0.1% B27, 0.1% EGF, and 0.1% FGF2 to produce 3mM Lithium Chloride (LiCl) hNSPC medium.

value: iPSC-derived hNSPCs


title: S28


title: IR+LiCl N2

source_name: iPSC-derived hNSPCs, 2D cultured, 4GY irradiated + 3mM LiCl trated


title: d2202c

city: Seoul

description: The methylated fraction from HER2

source_name: human breast cancer tissue


title: LiCl only N1

source_name: iPSC-derived hNSPCs, 2D cultured, 3mM LiCl trated


title: IR only N2


title: S31


title: S27


title: Control N2

source_name: iPSC-derived hNSPCs, 2D cultured, control


title: S29


title: MEFs, WT(N48)-Cre, RNA-seq, biol rep 3


title: LiCl only N2


title: IR+LiCl N1


title: MEFs, MT194-Cre, RNA-seq, biol rep 2

value: pLenti-MT194; Ad-Cre; single clone isolation


title: d2192c

description: The methylated fraction from HER2


title: d2234c_1

description: The methylated fraction from luminalA

value: luminalA


title: S25


title: MEFs, MT194-Cre, RNA-seq, biol rep 1


title: MEFs, WT-Cre, RNA-seq, biol rep 3

value: pLenti-WT-NELFB; Ad-Cre; single clone isolation


title: MEFs, MT486-Cre, RNA-seq, biol rep 1


title: d2234n

description: The methylated fraction from luminalA

value: female


title: d2083n

description: The methylated fraction from luminalB

value: luminalB


title: MEFs, MT194-Cre, RNA-seq, biol rep 3


title: Control N1


title: d2370c

description: The methylated fraction from luminalA


title: S26

value: male


title: d2202n

description: The methylated fraction from HER2


title: d2317c

description: The methylated fraction from luminalB


title: MEFs, WT-Cre, RNA-seq, biol rep 2


title: S23

value: plasma


title: d2370n_1

description: The methylated fraction from luminalA


title: N50R2_4 lowN

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

country: Germany

institute: University Hospital Schleswig-Holstein, Campus Kiel

description: Gene expression data from K-562 cells, resistant to 0.05 µM nilotinib, biological replicate 2.

hyb_protocol: 3.5 µg fragmented and labeled ssDNA were hybridized on HuGene 2.0 arrays for 16 h at 45 °C using the Affymetrix Hybridization Oven 640. The arrays were washed using the Fluidics Station 450 using the protocol FS450_0002.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were processed using the Transcriptome Analysis Console 4.0 (Thermo Fisher Scientific).

label_protocol: 100 ng RNA was used for each sample with the GeneChip WT PLUS Reagent Kit according to the manufacturer's recommendations.

growth_protocol: Cells were grown in RPMI 1640 + 10% v/v FCS + 1 % v/v Pen/Strep w/o imatinib or nilotinib.

extract_protocol: RNA was isolated using miRVana microRNA isolation Kit (Thermo Fisher Scientific) according to the manufacturer's recommendation from 3 million cells.

treatment_protocol: Resistant cells were generated by step-wise increase of imatinib concentration to 0.5 and 2 µM imatinib or 0.05 µM nilotinib.

tag: tki resistance

value: lowN

value: resistant to 0.05 µM nilotinib


title: S22

tag: age


title: N50R2_1 lowN


title: d2083c_1

description: The methylated fraction from luminalB


title: S24


title: d2123c_1

description: The methylated fraction from TNBC

value: TNBC


title: MEFs, WT-Cre, RNA-seq, biol rep 1

value: Embryo

value: Mouse Embryonic Fibroblasts (MEFs)

value: Nelfb flox/-


title: d2317n

description: The methylated fraction from luminalB


title: S20

value: healthy


title: S21


title: N50R2_2 lowN


title: N50R2_3 lowN


title: S19


title: d2123n

description: The methylated fraction from TNBC


title: N50R1_3 lowN

description: Gene expression data from K-562 cells, resistant to 0.05 µM nilotinib, biological replicate 1.


title: d2129c

description: The methylated fraction from TNBC


title: N50R1_4 lowN


title: S17


title: 2R4_D highIM

description: Gene expression data from K-562 cells, resistant to 2 µM imatinib, biological replicate 4.

value: highIM

value: resistant to 2 µM imatinib


title: S18