title: SE1457-1

value: bacteria

value: WT

value: antibiotic


title: Nup1-AID, SDC 16h 3-IAA, Replicate 2

status: Public on Mar 24 2025

type: SRA

city: Evanston

first: Tiffany

last: Ge

state: IL

address: 2205 Tech Drive

country: USA

institute: Northwestern University

description: Library name: B56-TG20

library_source: transcriptomic

data_processing:
single-end sequencing reads were processed using the slamdunk all program from SLAM-DUNK (v0.4.3) with default parameters and reference genome SacCer3 v64.4.1 and a BED-file containing coordinates for 3’ UTRs. This bed file was generated using standard genomic coordinates with a 325bp 3’UTR.
For differential gene expression analysis, we used DESeq2 (v1.46.0) with reads that contain more than one T>C conversions (nascent RNA reads). Size factors were calculated using respective total RNA reads for normalization.
Assembly: SacCer3 v64.4.1
Supplementary files format and content: tab-delimited text files containing raw read counts (total read counts and T>C conversion read counts) at 3' UTR of genes

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in SDC overnight, diluted to ~0.1 OD and placed at 30°C shaking at 200 rpm for > 4 hours.

extract_protocol:
Cells were spun down and snap frozen. Total RNA was extracted using Phenol:Chloroform:IAA (25:24:1) extraction. 5 ug total RNA was treated with 10 mM iodoacetamide (Sigma-Aldrich, cat# I1149), for 15 min at 50˚C. RNA was isolated using phenol-chloroform extraction.
Alkylated RNA was used for 3' mRNA-seq libraries prepared using the QuantSeq 3'mRNA-seq Library Prep Kit for Illumina (FWD; Lexogen) following manufacturer's recommendations

treatment_protocol: Crm1 was inhibited by treating the cultures with 185 nM Leptomycin B (LMB; Cayman Chemical Company, cat#10004976) in ethanol for 30 min at 30˚C. Nup1 or Nup2 was degraded by treating cultures with 500 µM Indole-3-Acetic Acid (3-IAA; Gold Biotechnology, cat#I-110-100) in ethanol for 16 hours at 30˚C. Following treatment with 3-IAA or LMB, cultures were treated with 0.2 mM 4- thiouracil (4sU; Fisher Scientific, cat#AAH6191903), for 6 min at 30˚C.

tag: treatment

value: 500 uM 3-IAA for 16h

tag: cell line

tag: genotype

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 URA3:Tir1-3XMyc NUP1:AID-Myc-HygR


title: LTP15 gene silenced strain, Biological replicate 2

city: Tokyo

first: Sota

middle: ミズカミソウタ

last: Mizukami

country: Japan

institute: The university of Tokyo

description: Library name: SAMPLE 5

data_processing:
Illumina NovaSeq 6000
Sequence reads were trimmed, mapped, and assembled to the reference genome assembly (JCVI-ESG2-1.0).
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: JCVI-ESG2-1.0
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Entamoeba histolytica

source_name: strain

growth_protocol: Trophozoites of the E. histolytica clonal strain HM1: IMSS  G3 strain were maintained axenically in Diamond’s BI-S-33 medium at 35.5°C

extract_protocol:
Total RNA was purified using TRIZOL reagent (Thermo Fisher, Waltham, MA, USA) according to manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The trophozoites of G3 strain were transformed with either empty vector or silencing plasmid by liposome-mediated transfection. Transformants were initially selected in the presence of 1 μg/ml geneticin, and the geneticin concentrations were gradually increased during next two weeks prior to subjecting the transformants to analyses.

tag: tissue

value: strain

tag: cell type

value: trophozoite

value: EhLTP15 gene silenced


title: Nup1-AID, SDC 16h, Replicate 3

description: Library name: B56-TG19

value: ethanol for 16h


title: LTP15 gene silenced strain, Biological replicate 1

description: Library name: SAMPLE 4


title: RT (biol 2)

city: Zürich

first: Hakan

last: Köksal

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: irradiated

library_source: transcriptomic single cell

data_processing:
read alignment, cell barcode demultiplexing, deduplication of reads, generation of expression matrices and quality report were done using the Rhapsody Sequence Analysis Pipeline v2.0 (https://www.bdbiosciences.com/en-us/products/software/rhapsody-sequence-analysis-pipeline)
Assembly: mm39
Supplementary files format and content: Tab-separated value files and matrix files

organism: Mus musculus

source_name: tumor

extract_protocol:
Tumors were collected in RPMI with 10% FCS and digested with 1 mg/ml collagenase IV (Thermo Fisher Scientific) and 50 µg/ml DNase I (Roche) for 45 minutes at 37°C using a rotating device. The cells were then washed in PBS with 2 mM EDTA and passed through a 70-µm filter (Biologix). Red blood cells were lysed with a buffer (17 mM Tris pH 7.2, 144 mM NH4Cl) for 2 minutes, followed by a PBS wash.
Library amplification was carried out following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119 (02))

value: tumor

tag: Sex

value: female

tag: age

value: 12 weeks old

value: CD8+ T-cells

value: RT


title: BS1-liver.RNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

country: China

institute: Yunnan Agricultural University

data_processing:
IsoSeq (v4.1.1) was used to perform primer removal, polyA tail removal, chimeric reads removal, and reads clustering on the long reads (LRs).
The clustered LRs were aligned to the susScr11 reference genome using pbmm2 (version 1.13.1, parameters --preset ISOSEQ --sort). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The short reads (SRs) were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.10.1), and TPM values were summaized in the processed data table.
Assembly: susScr11.1
Supplementary files format and content: Long reads numbers mapped to each transcript have been summarized into eachSample.FLcount.txt.gz. Genes TPM values were summarized into Genes.exp.TPM.txt.gz. Transcript TPM values were summarized into Transcripts.exp.TPM.txt.gz.
Supplementary files format and content: PacBio's assembly GTF file was tab-delimited. PacBio's assembly sequences were fasta format.

organism: Sus scrofa

source_name: liver

growth_protocol: All samples were acquired from 12-month adult male pigs.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina paired-end sequencing uses standard RNAseq library construction protocol.

value: liver


title: Nup1-AID, SDC 16h 3-IAA, Replicate 1

description: Library name: B56-TG18


title: pSAP mock control strain, Biological replicate 3

description: Library name: SAMPLE 3


title: Hpc No AD NORACE Surveillant 015

city: Los Angeles

first: Warren

last: Tourtellotte

state: California

address: 8700 Beverly Blvd

department: Pathology and Laboratory Medicine

institute: Cedars-Sinai

description: Library name: 015

data_processing:
Illumina NextSeq 500
GeoMx_NGS_Pipeline_2.2.0.2
Assembly: mm10
Supplementary files format and content: Segments.jpg: images of segments on each tissue that correspond to the sequencing data
Supplementary files format and content: .dcc- contain raw read counts and probe barcodes
Library strategy: Spatial Transcriptomics

source_name: Hippocampus

extract_protocol:
FFPE tissues were cut at 4um with a cryostat
Spatial Transcriptome sequencing libraries were prepared using Nanostring GeoMx WTA (Ms) according to the manufacturers protocol

value: Hippocampus

value: Iba1+ microglia

value: No AD NORACE


title: Nup1-AID, SDC 16h, Replicate 2

description: Library name: B56-TG17


title: Hpc No AD NORACE Surveillant 014

description: Library name: 014


title: RT (biol1)

description: irradiated


title: Nup1-AID, SDC 16h, Replicate 1

description: Library name: B56-TG15


title: pSAP mock control strain, Biological replicate 2

description: Library name: SAMPLE 2

value: WT


title: pSAP mock control strain, Biological replicate 1

description: Library name: SAMPLE 1


title: Hpc No AD NORACE Surveillant 013

description: Library name: 013


title: Hpc No AD NORACE Surveillant 012

description: Library name: 012


title: Nup1-AID, SDC 3-IAA, Replicate 7

description: Library name: B56-TG14

value: 506 uM 3-IAA for 1h


title: UNTR (biol 2)

description: control

value: Untreated


title: xenograft tumors M78, bpAb-B/C 30mg/kg, Day 52

city: Cambridge

first: William

last: Sellers

state: Massachusetts

address: 415 Main street

institute: Broad Insititute

data_processing:
A combined human-mouse genome reference was constructed and RNA-seq reads from samples were aligned to this integrated genome using STAR aligner.
Feature Counts was used to quantify reads mapped specifically to mouse-derived genes, providing gene-level counts
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text files include raw counts for each samples
Supplementary files format and content: tab-delimited text files include meta data for each samples
Supplementary files format and content: tab-delimited text files include gene symbol and its ensembl IDs

organism: Homo sapiens/Mus musculus xenograft

source_name: xenograft tumors

extract_protocol:
RNA samples were quantified using Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA)
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: xenograft tumors

value: ICC13-7 and mouse stroma and immune cells

tag: samplename

value: Gal/N10 30mg/kg

tag: timepoint

tag: drugid

tag: conc.


title: TRAP1_KO_Rep2

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq reads were trimmed with TrimGalore (v0.4.0) and mapped to Gencode release 19 and annotated with TopHat2 (Kim et al, 2013) (v2.0.13). RNA-seq reads that mapped uniquely to the human genome, build hg38, were counted using featureCounts2 (Liao et al, 2014). DESeq2 was used for differential gene expression analysis of all replicates in each condition (Love et al, 2014). Genes with an adjusted P-value < 0.05 and absolute Log2 fold change > 1 were defined as significantly affected. Gene ontology (GO) analysis, Z-scores, and P-values for network enrichment in the RNA-seq data were provided by Enrichr (Chen et al, 2013).
Genome_build: hg38
Supplementary_files_format_and_content: Excel table with RPKM values in WT and TRAP1 KO cells.

organism: Homo sapiens

source_name: HeLa

growth_protocol: DMEM, 37 degrees Celsius, 5% CO2

extract_protocol: Total RNA was extracted and purified using the RNA Clean & Concentrator kit (Zymo Research, R1013) according the manufacturer’s protocol. On-column DNAse I treatment was performed to eliminate genomic DNA contamination. RNA-seq libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina, RS-122-2101) and analyzed by paired-end poly(A) RNA sequencing with an illumina HiSeq system.

treatment_protocol: CRISPR-generated KO

tag: condition

value: TRAP1 KO


title: Hpc No AD NORACE Surveillant 016

description: Library name: 016


title: Hpc No AD NORACE Surveillant 011

description: Library name: 011


title: Nup1-AID, SDC, Replicate 7

description: Library name: B56-TG13

value: ethanol for 1h

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 URA3:Tir1-3XMyc NUP1:AID-Myc-HygR


title: TRAP1_KO_Rep1


title: Nup1-AID, SDC 3-IAA, Replicate 6

description: Library name: B56-TG12

value: 505 uM 3-IAA for 1h


title: xenograft tumors M77, bpAb-B/C 30mg/kg, Day 52


title: Nup1-AID, SDC, Replicate 6

description: Library name: B56-TG11


title: UNTR (biol 1)

description: control

value: tumor

value: female

value: 12 weeks old


title: Hpc No AD NORACE Surveillant 010

description: Library name: 010


title: WT_Rep2

value: Control


title: xenograft tumors M58, bpAb-B/D 30mg/kg, Day 52

value: Gal/GE 30mg/kg


title: WT_Rep1


title: Hpc No AD NORACE Surveillant 009

description: Library name: 009

value: Hippocampus

value: Iba1+ microglia


title: WT_Rep3


title: Hpc No AD NORACE Surveillant 008

description: Library name: 008

value: No AD NORACE


title: xenograft tumors M67, bpAb-B/C 10mg/kg, Day 52

value: Gal/N10 10mg/kg


title: xenograft tumors M57, bpAb-B/D 30mg/kg, Day 52


title: Nup1-AID, SDC, Replicate 5

description: Library name: B56-TG09


title: Nup1-AID, SDC 3-IAA, Replicate 4

description: Library name: B56-TG08

value: 503 uM 3-IAA for 1h


title: Hpc No AD NORACE Surveillant 007

description: Library name: 007


title: xenograft tumors M48, bpAb-B/D 10mg/kg, Day 52

value: xenograft tumors

value: Gal/GE 10mg/kg


title: Hpc No AD NORACE Surveillant 006

description: Library name: 006


title: Prp20-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 4

description: Library name: B53-TG34

library_source: genomic

data_processing:
ChEC-seq2 mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn). Repetitive regions are masked.
Assembly: S288C, R64.3.1
Supplementary files format and content: bigwig files contain CPMn normalized coverage counts that are not trimmed. Trimming the bams to the first bp of each read as described in VanBelzen et al. 2024 is recommended for processing samples.
Library strategy: ChEC-seq

molecule: genomic DNA

extract_protocol:
ChEC was performed as described by Zentner et al., 2015 with modifications according to VanBelzen et al., 2024. SDC was removed from the cells after pelleting and replaced with BufferA. Cells were washed twice more with BufferA, then added to tubes containing 5 ul digitonin for a final concentration of 0.1% digitonin. Tubes were incubated at 30°C for 5' before 10 ul 20mM calcium was added. After cleaving for the factor-specific cleavage time at 30°C, 2x Stop Buffer and 8 ul proteinase K (20 ug/ul) was added. gDNA was isolated using phenol-chloroform extraction.
Libraries were made using partial MNase digestion optimized for each fusion protein, tagmentation with Tn5 loaded with  Illumina Nextera XT index adapters, and amplifying with the KAPA library amplification kit

treatment_protocol: Indole-3-Acetic Acid (3-IAA; Gold Biotechnology, cat#I-110-100) and estradiol (Sigma Aldrich, cat#E8875) were solubilized in ethanol. 5-Phenyl-1H-indole-3-acetic acid (5-Ph-IAA; Fisher Scientific, cat#NC1957890) was solubilized in DMSO. Nup2-AID and OsTIR1 only strains were treated with 500 µM 3-IAA for 1h at 30C, Leptomycin B (LMB; Cayman Chemical Company, cat#10004976)-sensitive strains (which have the crm1-T539C mutation) were treated with 185 nM LMB for 30 min at 30C, and Crm1-grAID strains were treated with 1 µM estradiol for 30 min at 30C followed by 1 µM 5-Ph-IAA for 2h. After treatments, cells were harvested for ChEC-seq2.

value: MATa can1-100 trp1-1 ura3-1 ADE2:OsTIR1(F74G) Crm1-GFP:His3MX6 LEU2:csGBP-mAID Prp20-MN:KanMX


title: Nup1-AID, SDC 3-IAA, Replicate 5

description: Library name: B56-TG10

value: 504 uM 3-IAA for 1h


title: TRAP1_KO_Rep3

value: TRAP1 KO


title: Prp20-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 2

description: Library name: B53-TG27


title: Hpc AD RACE PAM 018

description: Library name: 018

value: AD RACE


title: Prp20-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 3

description: Library name: B53-TG31


title: xenograft tumors M68, bpAb-B/C 10mg/kg, Day 52

value: ICC13-7 and mouse stroma and immune cells


title: Prp20-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 1

description: Library name: B53-TG23


title: Nup1-AID, SDC, Replicate 4

description: Library name: B56-TG07

value: ethanol for 1h

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 URA3:Tir1-3XMyc NUP1:AID-Myc-HygR


title: Nup1-AID, SDC 3-IAA, Replicate 3

description: Library name: B56-TG06

value: 502 uM 3-IAA for 1h


title: xenograft tumors M47, bpAb-B/D 10mg/kg, Day 52


title: xenograft tumors M8, Control, Day 52

value: Control


title: Hpc No AD NORACE Surveillant 003

description: Library name: 003


title: Hpc No AD NORACE Surveillant 004

description: Library name: 004


title: Nup1-AID, SDC, Replicate 3

description: Library name: B56-TG05


title: xenograft tumors M7, Control, Day 52


title: Nup1-AID, SDC 3-IAA, Replicate 2

description: Library name: B56-TG04

value: 501 uM 3-IAA for 1h


title: Prp20-MNase, Crm1-grAID, SDC, Replicate 3

description: Library name: B53-TG33


title: Hpc No AD NORACE Surveillant 002

description: Library name: 002

value: Hippocampus


title: Prp20-MNase, Crm1-grAID, SDC, Replicate 4

description: Library name: B53-TG36


title: xenograft tumors M73, bpAb-B/C 30mg/kg, Day 41

value: Gal/N10 30mg/kg


title: Prp20-MNase, Crm1-grAID, SDC, Replicate 2

description: Library name: B53-TG29


title: RNA-KO_rep6

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

data_processing:
TrimGalore v0.6.7 was used for quality and adatper trimming with parameters --quality 20 --illumina --stringency 5 --length 20 --paired.
Reads were mapped to the mm10 reference genome via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Read counts per gene were calculated by featureCounts (Subread v1.5.0-p1) with parameters "-s2 -Sfr -p".
Signal tracks were generated by STAR v2.5 with parameters "--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM", then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: Counts per gene per sample in tab-delimited text format.
Supplementary files format and content: Normalized signal tracks in bigWig format; one file per strand per sample.

source_name: Testis

extract_protocol:
PicoPure™ RNA Isolation Kit was used to isolate the RNA from 3 pooled testis per replicate
Two hundred and fifty ng of RNA were diluted to 50 uL in nuclease-free water and RNA libraries were prepared according to the TruSeq Stranded mRNA Library Prep protocol (Illumina, #20020594). HighPrep PCR beads were used for cleanup steps (MagBio Genomics, #AC-60050). SuperScript II Reverse Transcriptase was used for second strand synthesis (Invitrogen #100004925). cDNA was amplified with 14 PCR cycles.

value: Testis

value: Wt1 CreER x Nr2f2 f/f


title: RNA-KO_rep4


title: Nup1-AID, SDC, Replicate 2

description: Library name: B56-TG03


title: Nup1-AID, SDC, Replicate 1

description: Library name: B56-TG01


title: RNA-KO_rep3


title: Prp20-MNase, Crm1-grAID, SDC, Replicate 1

description: Library name: B53-TG25


title: xenograft tumors M71, bpAb-B/C 30mg/kg, Day 41


title: Nup1-AID, SDC 3-IAA, Replicate 1

description: Library name: B56-TG02

value: 500 uM 3-IAA for 1h


title: Nup2-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 2

description: Library name: B53-TG04

value: MATa can1-100 trp1-1 ura3-1 ADE2:OsTIR1(F74G) Crm1-GFP:His3MX6 LEU2:csGBP-mAID Nup2-MN:KanMX


title: xenograft tumors M54, bpAb-B/D 30mg/kg, Day 41

value: xenograft tumors

value: Gal/GE 30mg/kg


title: RNA-KO_rep5


title: Hpc No AD NORACE Surveillant 005

description: Library name: 005

value: Iba1+ microglia

value: No AD NORACE


title: Nup2-AID, SDC, Replicate 3

description: Library name: B44-TG39

value: ethanol for 16h

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 URA3:Tir1-3XMyc NUP2-AID-Myc:HygR


title: xenograft tumors M52, bpAb-B/D 30mg/kg, Day 41

value: ICC13-7 and mouse stroma and immune cells


title: xenograft tumors M61, bpAb-B/C 10mg/kg, Day 41

value: Gal/N10 10mg/kg


title: RNA-KO_rep2


title: Nup2-AID, SDC, Replicate 2

description: Library name: B44-TG37


title: Nup2-AID, SDC, Replicate 1

description: Library name: B44-TG35


title: Nup2-MNase, Crm1-grAID, SDC, Replicate 3

description: Library name: B53-TG21


title: xenograft tumors M46, bpAb-B/D 10mg/kg, Day 41

value: Gal/GE 10mg/kg


title: RNA-control_rep6

value: Nr2f2 f/f


title: Nup2-AID, SDC 3-IAA, Replicate 3

description: Library name: B44-TG38

value: 500 uM 3-IAA for 16h


title: xenograft tumors M65, bpAb-B/C 10mg/kg, Day 41


title: Nup2-MNase, Crm1-grAID, SDC, Replicate 2

description: Library name: B53-TG06


title: Nup2-AID, SDC 3-IAA, Replicate 2

description: Library name: B44-TG36


title: xenograft tumors M42, bpAb-B/D 10mg/kg, Day 41


title: Nup2-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 3

description: Library name: B53-TG22


title: xenograft tumors M4, Control, Day 41

value: Control


title: RNA-control_rep4


title: Nup2-MNase, Crm1-grAID, SDC, Replicate 1

description: Library name: B53-TG03


title: xenograft tumors M3, Control, Day 41


title: Nup2-MNase, Crm1(T539C), SDC LMB, Replicate 3

description: Library name: B36-DB42

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1delta::LEU2 [pCRM1-T539C] NUP2-Mnase:KanMx


title: Crm1(T539C), SDC, Replicate 3

description: Library name: B29-NM24

value: ethanol for 30 min

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1delta::LEU2 [pCRM1-T539C]


title: Nup2-AID, SDC 3-IAA, Replicate 1

description: Library name: B44-TG19


title: RNA-control_rep2

value: Testis


title: Nup2-MNase, Crm1-grAID, SDC 5-Ph-IAA E2, Replicate 1

description: Library name: B53-TG01

value: MATa can1-100 trp1-1 ura3-1 ADE2:OsTIR1(F74G) Crm1-GFP:His3MX6 LEU2:csGBP-mAID Nup2-MN:KanMX


title: RNA-KO_rep1

value: Wt1 CreER x Nr2f2 f/f


title: Crm1(T539C), SDC, Replicate 2

description: Library name: B29-NM23


title: Crm1(T539C), SDC, Replicate 1

description: Library name: B29-NM22


title: Nup2-MNase, Crm1(T539C), SDC LMB, Replicate 1

description: Library name: B36-DB40


title: RNA-control_rep3


title: Nup2-MNase, Crm1(T539C), SDC LMB, Replicate 2

description: Library name: B36-DB41


title: Nup2-MNase, Crm1(T539C), SDC, Replicate 3

description: Library name: B36-DB39


title: RNA-control_rep1


title: Mouse embryonic stem cells (mESCs) in 2iLIF ground state: E14_2iLIF

city: Singapore

first: Shiying

last: LIU

state: Singapore

address: 61 Biopolis Dr, Proteos, Singapore 138673

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description: Library name: Sample1

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Structure variation detection The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V4.1.2) were used to detect fusion genes and differential splicing genes (DSGs), respectively
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.12) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq （v1.48.0）or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: .xls file inlcuding fpkm, tpm, read_count of each sample

source_name: embryo

growth_protocol: Ground state mESC were cultured in 2iLIF medium, which consists of serum-free N2B27 with 1 μM PD0325901 (an FGF and ERK inhibitor), 3 μM CHIR99021 (GSK3 inhibitor) and LIF (100 units/ml).

extract_protocol:
Total RNAwas extracted from mESCs in 2iLIF and cEpiSC after conversion by RNeasy® Plus Mini Kit (Qiagen) following the manufacturer’s protocol
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then first-strand cDNA is generated using random hexamer-primed reverse transcription with the fragmented RNA as template. To synthesize the second-strand cDNA, the synthesis reaction system is prepared and dUTP is used to replace dTTP. After obtaining the double strand cDNA product, it is converted to blunt end with end repair reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the library adapters are ligated to the two ends of the cDNA with ligation reaction. Finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and sequencing reads with PE 100/150 bases length are generated on G400 platform (BGI-Shenzhen, China).

treatment_protocol: To induce conversion from mESCs to mEpiSC in vitro, mESCs in 2iLIF culture were plated on fibronectin-coated six-well plates at a density of 2×104 cells/cm2 with 2iLIF medium initially. After 24 h, the medium was replaced by N2B27 medium supplemented with 20 ng/ml activin A and 12 ng/ml FGF2 (RnD Systems). Cells were maintained in the induction medium for 2 days.

value: embryo

value: embryonic stem cells

value: WT

value: naïve pluripotent state


title: In vitro converted epiblast stem cells (cEpiSCs) from mESCs in 2iLIF: cEpiSCf2iLIF

description: Library name: Sample2

value: cEpiSCs converted in vitro

value: epiblast stem cells

value: prime pluripotent state after conversion in vitro


title: ChIP-NR2F2_rep2

data_processing:
TrimGalore v0.6.7 was used for quality and adatper trimming with parameters --quality 20 --illumina --stringency 5 --length 30.
Reads were mapped to the mm10 reference genome by Bowtie2 with the --local setting.
Alignments were filtered to require minimum MAPQ of 5, then duplicates were removed with Picard tools v1.110 MarkDuplicates.jar.
The two replicate ChIP samples were combined for peak calling by HOMER v4.11.1 with parameters -style -factor -fdr 1e-5; called peaks were redefined as 300mers centered on the HOMER peak midpoint.  Peaks overlapping blacklist regions were excluded from analysis.
Count per peak were collected via bedtools coverage using the -counts option, after aligned reads had been extended to the estimated fragment length via bedtools 'slop' function (slop -s -r 125 -l 0).
Signal tracks were generated by extending mapped reads to the estimated fragment size (bedtools slop -s -r 125 -l 0), converting to bedGraph (bedtools genomecov -bg), scaled to 10 million fragments per sample, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: Counts per peak in tab-delimited text format; one file per sample.
Supplementary files format and content: Normalized signal tracks in bigWig format; one file per sample.

source_name: testis

extract_protocol: Performed by ActiveMotif

value: testis

tag: chip antibody

value: NR2F2 - ActiveMotif #61213


title: Crm1(T539C), SDC LMB, Replicate 3

description: Library name: B29-NM21

value: 185 nM LMB for 30 min


title: RNA-control_rep5

value: Nr2f2 f/f


title: kidney, Ramipril/Empagliflozin/1,3-butanediol, 2

city: Munich

first: Linus

middle: Paul

last: Schreier

address: Goethestraße 31

institute: Ludwig-Maximilians-Universität

description: Library name: L2

data_processing:
The bioinformatics workflow, which included data filtering, mapped transcript prediction, analysis of differential gene expression and gene ontology, was carried out in accordance with the protocols of HISAT2, SAMtools, featureCounts, eisaR, and clusterProfiler.
Assembly: mm39
Supplementary files format and content: counts_BHB* = counts
Supplementary files format and content: Col4a3_KO_Ram_Empa_BHB* = tpm

source_name: kidney

extract_protocol:
Total RNA was isolated using an RNA extraction kit (Life Technologies, Darmstadt, Germany) according to the manufacturer´s instructions, and RNA quality was assessed using nano drop technology.
The library construction method and sequencing process are carried out according to thefollowing steps: 1.Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNAwith poly A tail;2. mRNA molecules were fragmented into small pieces;3. The fragmented mRNA was synthesized into first strand cDNA using random primers;4. The second strand cDNA was synthesized with dUTP instead of dTTP;5.The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors wereligated to the ends of these 3' adenylated cDNA fragments;6.Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) andperform PCR amplification;7. Library quality control;8. Library circularization;9. The library was amplified to make DNA nanoball (DNB);10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Mice were fed a food admix of either a) vehicle or b) 10 μg/g ramipril plus 30 μg/g empagliflozin or c) 10 μg/g ramipril plus 30 μg/g empagliflozin plus 0.04g/g 1,3-butanediol (the drug concentration is given per gram of bodyweight). The different types of food preparations were marked by different food colors. Treatment started at 6 weeks of age for 8 weeks.

value: kidney


title: Nup2-MNase, Crm1(T539C), SDC, Replicate 2

description: Library name: B36-DB38

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1delta::LEU2 [pCRM1-T539C] NUP2-Mnase:KanMx


title: Nup2-MNase, Crm1(T539C), SDC, Replicate 1

description: Library name: B36-DB37


title: Crm1(T539C), SDC LMB, Replicate 2

description: Library name: B29-NM20

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1delta::LEU2 [pCRM1-T539C]


title: ChIP-NR2F2_rep1


title: ChIP-input


title: Crm1(T539C), SDC LMB, Replicate 1

description: Library name: B29-NM19


title: Soluble MNase, OsTIR1 only, SDC 3-IAA, Replicate 3

description: Library name: B51-TG44

value: MATa leu2delta0 ura3delta0 met15delta0 HIS3:CYC1pro-SolubleMNase:TEFpro-KanMX-TEFterm TEFpro-OsTir1-ADH1term:LEU2


title: Male, saline, LL, rep4

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

data_processing:
Nextseq500-- 1 Flowcell High Output (400 M fragments) -- 75 cycles Single-End read (maximum 1x85 nt)
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequences were aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a.
Gene expressions were obtained from STAR both as readcounts and computed using RSEM in order to obtain normalized gene and transcript level expression, in FPKM and TPM values, for these stranded RNA libraries.
DESeq2 version 1.18.1 was then used to normalize gene readcounts.
Assembly: Assembly - De novo (contigs)
Supplementary files format and content: .xlsx file includes raw counts for each sample

molecule: polyA RNA

source_name: dorsal hippocampus

extract_protocol:
RNA was extracted using trizol/chloroform.
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hypreprep Kit and were further amplified for sequencing.

value: dorsal hippocampus

tag: strain

value: Saline, LL


title: Heads_TOT_3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

data_processing:
RNA-seq reads' quality control was assessed through FastQC and multiQC. An average of 50 million reads were sequenced per sample. Both adapters and low quality bases (QV < 20) were trimmed from reads’ extremities using Trimmomatic (v 0.33) with a minimum read length of 25 bp. All libraries were mapped against the Ensembl Drosophila_melanogaster.BDGP6.32 release-109 reference genome through STAR aligner (v 2.7.10a) with default parameters. STAR-generated sorted BAM files were used for assigning read counts to either gene or transcript features with featureCounts (v 2.0.1) with the following parameters: -T 24 -s 2 -M -O --fraction (plus the addition of '-g transcript_id' for the transcript-level execution). We relied on Ensembl Drosophila_melanogaster.BDGP6.32.109.gtf annotation file.
Read counts’ table generated by featureCounts was then used as input for differential expression (DE) analyses relying on the DeSeq2 negative binomial distribution model through a local fitting type and a 0.01 FDR threshold. DE pairwise comparisons beteen sample groups were performed either at gene- or transcript-level.
Assembly: Ensembl Drosophila_melanogaster.BDGP6.32.109
Supplementary files format and content: tab-delimited files containing raw read counts for each sample at either gene-level (readCounts_FBgn.tsv) or transcript-level (readCounts_FBtr.tsv)

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
Sample lysis, ribosome purification (sucrose gradient fractionation), DNase digestion (Ambion TURBO DNase), RNA purification (Zymo Quick-RNA kit), rRNA depletion (QIAGEN QIAseq FastSelect –rRNA Fly Kit)
TruSeq Stranded mRNA kit

value: Head

value: Wild type Dahomey


title: kidney, Ramipril/Empagliflozin/1,3-butanediol, 1

description: Library name: L1


title: Male, saline, LL, rep3


title: kidney, Ramipril/Empagliflozin/1,3-butanediol, 4

description: Library name: L4


title: PGF_luteal_steroidogenic_cells_4

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

data_processing:
All data processing was performed according to the standard BGI Bioinformatics pipeline. Filtering was performed using SOAPnuke v 1.5.2 software
Clean reads were aligned using the HISAT2 v2.0.4  and mapped using Bowtie v2.2.5
Mapped reads were counted using RSEM v1.2.8
DEseq2 was used for all analysis of differential expression. All fold changes are reported as log2 fold changes. Padj values are reported; multiple testing correction used was the Benjamini Hochberg correction. For the interaction analysis of the cell culture experiment, the LST model in DEseq2 was used to determine the statistical significance of the main effects of IFNT and PGF2A and the interaction. For all other analyses, pairwise comparisons were made, which is the default analysis method in DEseq2. A Padj < 0.05 was considered significant.
Assembly: NCBI GCF_000003205.7_Btau_5.0.1
Supplementary files format and content: Excel sheets of results of differential expression analyses in DEseq2

organism: Bos taurus

source_name: Corpus luteum

growth_protocol: Cattle were observed for natural estrus and the day of standing estrus was designated day 0. Corpora lutea (CL) were collected via transvaginal surgery on days 10-12 of the estrous cycle. This time was selected because these CL are fully developed and functional, but have not yet been exposed to even the earliest pulses of PGF2A. CL were dissociated and luteal cells were seeded in 12-well plates and cultured in Ham's F12 with Gentamycin and ITS, as previously described. Pate JL 1993 Isolation and culture of fully differentiated bovine luteal cells. Methods in Toxicology 3B 360–370.

extract_protocol:
Total RNA was isolated from cultured cells using the mirVANA miRNA isolation kit.
Libraries were constructed according to standard BGI protocols, using the DNBSEQ platform for library preparation and sequencing. Sequencing was performed with paired end 100 bp reads (PE100). Approximately 30-35 million read pairs were generated per sample.

treatment_protocol: Cells were allowed to adhere overnight. The next day, media was changed and treatments were added. Media composition was as above  and contained LH at 10 ng/mL. Cells were collected 24 hours after treatment. Triplicate wells were treated and were pooled prior to RNA isolation. Treatments were IFNT (1ng/mL; kindly supplied by Dr. Fuller Bazer, Texas A&M University), PGF2A (10 ng/mL), and PGF+IFNT.

value: Corpus luteum

value: Primary mixed luteal steroidogenic cells

value: PGF2A (10 ng/mL)


title: Soluble MNase, OsTIR1 only, SDC 3-IAA, Replicate 1

description: Library name: B51-TG40


title: Soluble MNase, OsTIR1 only, SDC, Replicate 3

description: Library name: B51-TG43


title: Soluble MNase, OsTIR1 only, SDC, Replicate 2

description: Library name: B51-TG41


title: Male, poly IC, LL, rep4

value: Poly IC, LL


title: kidney, Ramipril/Empagliflozin/1,3-butanediol, 3

description: Library name: L3


title: Heads_TOT_2


title: Male, saline, LL, rep2


title: CON_luteal_steroidogenic_cells_4

value: control (no treatment)


title: Soluble MNase, OsTIR1 only, SDC 3-IAA, Replicate 2

description: Library name: B51-TG42


title: Heads_TOT_1


title: IFNTPGF_luteal_steroidogenic_cells_4

value: IFNT (1ng/mL) and PGF2A (10 ng/mL)


title: IFNT_luteal_steroidogenic_cells_4

value: IFNT (1ng/mL)


title: Male, saline, LL, rep1


title: Heads_POLY_2


title: Heads_POLY_3


title: IFNT_luteal_steroidogenic_cells_3


title: PGF_luteal_steroidogenic_cells_3


title: Soluble MNase, OsTIR1 only, SDC, Replicate 1

description: Library name: B51-TG39


title: Male, poly IC, LL, rep3


title: Heads_POLY_1


title: Crm1-MNase, Nup2-AID, SDC auxin, Replicate 3

description: Library name: B43-JV72

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 Tir1-3xMYC:URA3 NUP2-AID-Myc:Hygromycin Crm1-3xFLAG-MNase:KanMX


title: Male, poly IC, LL, rep2


title: IFNTPGF_luteal_steroidogenic_cells_3


title: CON_luteal_steroidogenic_cells_3


title: Male, poly IC, LL, rep1


title: Crm1-MNase, Nup2-AID, SDC auxin, Replicate 2

description: Library name: B43-JV71


title: Heads_80S_1


title: Crm1-MNase, Nup2-AID, SDC auxin, Replicate 1

description: Library name: B43-JV70


title: Crm1-MNase, Nup2-AID, SDC, Replicate 3

description: Library name: B43-JV69


title: IFNTPGF_luteal_steroidogenic_cells_2


title: Male, saline, LD, rep2

value: Saline, LD


title: Heads_80S_3


title: Heads_80S_2


title: Crm1-MNase, Nup2-AID, SDC, Replicate 1

description: Library name: B43-JV67


title: PGF_luteal_steroidogenic_cells_2


title: Male, saline, LD, rep3


title: Male, saline, LD, rep1


title: IFNT_luteal_steroidogenic_cells_2


title: Crm1-MNase, Nup2-AID, SDC, Replicate 2

description: Library name: B43-JV68


title: CON_luteal_steroidogenic_cells_2


title: PGF_luteal_steroidogenic_cells_1


title: Male, poly IC, LD, rep4

value: Poly IC, LD


title: Rpb1-MNase, SDC, Replicate 2

description: Library name: B27-DB14

value: yeast cell

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RPB1-3FLAG-Mnase:KanMX


title: Male, poly IC, LD, rep3


title: Rpb1-MNase, SDC, Replicate 3

description: Library name: B27-DB15


title: GSC 1206-sample

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

data_processing:
HiC-Pro pipeline (version 3.1.0) was used for processing paired-end files with default setting. Aligned filtered reads were assigned to ARIMA-enzyme restriction fragments and valid read pairs (interactions) were used  for generating binned interaction matrices with Juicer-tools at 5,10,25,50,100,250,500 and 1000kb resolutions.
Assembly: hg38
Supplementary files format and content: JuicerTools version 2.20.00 was used to generate normalized (VC, VC_SQRT,KR) .hic matrices.
Supplementary files format and content: HiC: .hic files displaying interaction matrices at 5,10,25,50,100,250,500 & 1000KB resolution

source_name: glioma-stem cell

growth_protocol: GSCs were cultured in Neurobasal medium A (NBE medium, Thermo Fisher Scientific) supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), human recombinant bFGF and EGF (25 ng/mL each, R&D Systems), heparin (2ng/ml, Sigma), Penicilin-Streptomycin solution (LifeTech), and L-glutamine (200 mM/100X. LifeTech). lt-NSCs were cultured in poly-L-ornithine and laminin coated plates with DMEM/F12 w/o HEPES supplemented with N2 (Gibco), insulin (SIgma),glucose (Sigma), human recombinant bFGF and EGF ( R&D Systems) and CHIR99021 (R&DSystems).

extract_protocol:
10M cells were collected by trypsinization and fixed with 2% formaldehyde.
Hi-C samples were prepared using the Arima-HiC+ kit (Arima, A510008) according to the manufacturer’s instructions, with a few modifications.
Libraries were generated with the KAPA Hyper Prep Kit (Roche, KK8502) and SeqCap Adapter (Roche, 07141530001), following the respective protocols, and underwent 8 to 9 cycles of PCR amplification. The libraries were quantified with Qubit, and quality and final library size were assessed via Tapestation.

value: glioma-stem cell

value: patient-derived glioma stem cells


title: Male, saline, LD, rep4

value: dorsal hippocampus


title: WTΔtrpP_vs_WT 3

type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 7 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 7). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum

source_name: WTΔtrpP

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: A first preculture was prepared in BHI medium by inoculating with a single colony from a BHI plate and cultivated at 30 °C and 900 rpm for 8 h. Sedimented cells (4000g, 10 min) from this culture were used to inoculate a second preculture in CGXII medium with 2 % (w/v) glucose  and cultivated over night at 30 °C and 900 rpm. Main cultures were inoculated to a starting-OD600 of 0.8 in 500 ml baffled shake flasks with 50 ml CGXII medium with 2 % (w/v) glucose. Main cultures were incubated at 30 °C and 130 rpm in a Minitron shaker (Infors HT, Einsbach, Germany). For analysis of the gene expression profile, Corynebacterium glutamicum cells were grown in main cultures to an OD600 of 5 and then harvested.

extract_protocol: Cells were harvested and used for RNA isolation with the RNeasy MiniKit (QIAGEN, Hilden, Germany) as described elsewhere (Zuchowski, Schito et al. 2023). The concentration of the resulting RNA was determined at 260 nm with a Colibri Microvolume Spectrometer (Titertek-Berthold, Germany). Afterwards, 15 µg RNA were employed for random hexamer-primed cDNA synthesis using SuperScript III reverse transcriptase (Life Technologies, Darmstadt, Germany) for usage in the microarrays as described before (Vogt, Haas et al. 2014, Kranz, Polen et al. 2022).

treatment_protocol: see growth protocol

value: WTΔtrpP

source_name: WT

value: WT


title: IFNT_luteal_steroidogenic_cells_1

value: Corpus luteum


title: Rpb1-MNase, SDC, Replicate 1

description: Library name: B27-DB13


title: IFNTPGF_luteal_steroidogenic_cells_1

value: Primary mixed luteal steroidogenic cells


title: GSC 810-sample


title: Male, poly IC, LD, rep2


title: Soluble MNase, SDC, Replicate 3

description: Library name: B24-DB15

value: MATa leu2delta0 met15delta0 ura3delta0 HIS3:solubleMNase


title: WTΔtrpP_vs_WT 4


title: WTΔtrpP_vs_WT 1


title: Female, saline, LL, rep4

value: Saline, LL


title: Male, poly IC, LD, rep1


title: WTΔtrpP_vs_WT 2


title: IFNTPAG_lutealtissue_4

growth_protocol: Postpubertal Holstein heifers (N=30; 12-17 months of age) were estrous synchronized with an  intramuscular injection of a PGF2A analog (Estroplan, 500 μg of cloprostenol sodium, Parnell) and were monitored for estrus behavior (day 0).

extract_protocol:
Total RNA was isolated from luteal tissue using the mirVana RNA Isolation Kit
Libraries were constructed according to standard BGI protocols, using the DNBSEQ platform for library preparation and sequencing. Sequencing was performed with paired end 100 bp reads (PE100). Approximately 30-35 million read pairs were generated per sample.

treatment_protocol: Briefly, intrauterine catheters were placed on day 14 of the cycle in cyclic heifers. Four total treatments groups were included, with n=4 per group. Control heifers received 20 mL of PBS containing bovine serum albumin (BSA; 200 mg/mL) two times per day on days 14-16 (BSA). Two groups of heifers received IFNT alone. One group received IFNT (10 mg/mL which is 200 mg per infusion) in the control solution 2X per day from day 14-16 (3-day IFNT) and a second group received infusions of the same concentration of IFNT from day 14-19 of the cycle (6-day IFNT). A fourth group received the same IFNT infusions as the 6-day IFNT group, and on days 17-19, this group also received 5 mg/mL PAG (100 mg/infusion). Treatments were prepared using recombinant ovine IFNT, which was kindly supplied by Dr. Fuller Bazer, Texas A&M University, and PAG purified from first-trimester bovine placenta, which was kindly supplied by Josh Branen, Biotracking LLC Inc.

value: whole tissue

value: IFNT+PAG


title: CON_luteal_steroidogenic_cells_1

value: control (no treatment)


title: GSC 320-sample


title: Soluble MNase, SDC, Replicate 1

description: Library name: B24-DB13


title: Soluble MNase, SDC, Replicate 2

description: Library name: B24-DB14


title: IFNTPAG_lutealtissue_3


title: Crm1-MNase, SDC, Replicate 3

description: Library name: B24-DB27

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 CRM1-MNase:KanMx


title: DSE-spleen.PacBio

description: DSE-spleen

source_name: spleen

value: spleen


title: Female, saline, LL, rep3


title: Female, saline, LL, rep2


title: DSE-lung.PacBio

description: DSE-lung

source_name: lung

value: lung


title: IFNTPAG_lutealtissue_2


title: Crm1-MNase, SDC, Replicate 2

description: Library name: B24-DB26

value: yeast cell


title: Female, saline, LL, rep1


title: DSE-liver.PacBio

description: DSE-liver

value: liver


title: IFNTPAG_lutealtissue_1


title: Crm1-MNase, SDC, Replicate 1

description: Library name: B24-DB25


title: DSE-kidney.PacBio

description: DSE-kidney

value: kidney


title: IFNT6day_lutealtissue_4

value: IFNT 6 days


title: Nup157-MNase, SDC, Replicate 3

description: Library name: B48-DB43

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 NUP157-MNase:KanMx


title: DSE-heart.PacBio

description: DSE-heart

source_name: heart

value: heart


title: IFNT6day_lutealtissue_3


title: Female, poly IC, LL, rep2

value: dorsal hippocampus

value: Poly IC, LL


title: GSC 728-sample

value: glioma-stem cell

value: patient-derived glioma stem cells


title: IFNT6day_lutealtissue_2

value: Corpus luteum


title: Female, poly IC, LL, rep1


title: Female, poly IC, LL, rep3


title: Nup157-MNase, SDC, Replicate 2

description: Library name: B48-DB42


title: IFNT6day_lutealtissue_1

description: PCA identified this sample as an outlier. This is detailed in the manuscript.

value: whole tissue


title: DT-lung.PacBio

description: DT-lung


title: Nup157-MNase, SDC, Replicate 1

description: Library name: B48-DB41


title: Female, saline, LD, rep4

value: Saline, LD


title: Nup1-MNase, SDC, Replicate 3

description: Library name: B48-DB31

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 NUP1-MNase:KanMx


title: DT-liver.PacBio

description: DT-liver

source_name: liver


title: IFNT3day_lutealtissue_4

value: IFNT 3 days


title: Female, saline, LD, rep3


title: IFNT3day_lutealtissue_3


title: DT-kidney.PacBio

description: DT-kidney


title: Female, poly IC, LL, rep4


title: Nup1-MNase, SDC, Replicate 1

description: Library name: B48-DB29


title: DT-heart.PacBio

description: DT-heart


title: Female, saline, LD, rep1


title: Nup60-MNase, SDC, Replicate 3

description: Library name: B36-DB09

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 NUP60-MNase:KanMx


title: BS-spleen.PacBio

description: BS-spleen

value: spleen


title: DT-spleen.PacBio

description: DT-spleen


title: Female, poly IC, LD, rep4

value: Poly IC, LD


title: IFNT3day_lutealtissue_1


title: Nup60-MNase, SDC, Replicate 2

description: Library name: B36-DB08

value: yeast cell


title: BS-lung.PacBio

description: BS-lung

value: lung


title: BSA3day_lutealtissue_4

value: BSA


title: Nup60-MNase, SDC, Replicate 1

description: Library name: B36-DB07


title: BS-liver.PacBio

description: BS-liver

value: liver


title: Female, poly IC, LD, rep3


title: Female, poly IC, LD, rep2


title: Nup1-MNase, SDC, Replicate 2

description: Library name: B48-DB30


title: Nup2-MNase, SDC, Replicate 3

description: Library name: B24-DB03

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 NUP2-MNase:KanMx


title: BS-kidney.PacBio

description: BS-kidney

value: kidney


title: BSA3day_lutealtissue_2


title: Nup2-MNase, SDC, Replicate 2

description: Library name: B24-DB02


title: Female, poly IC, LD, rep1

value: dorsal hippocampus


title: BS-heart.PacBio

description: BS-heart

value: heart


title: MT947_NCC d5 HSTE rep3

status: Public on Mar 23 2025

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

description: Library name: MT947_NCC d5 HSTE rep3

data_processing:
Adaptors were removed using TrimGalore!, reads were mapped and quantified using Kallisto and differential gene expression was analysed using DESeq2.
ChIP-seq data were aligned to hg38 using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
ATAC-seq data were aligned to hg38 (5-day protocol) or hg19 (18-day protocol, supplementary figure) using BWA-mem. MACS2 was used to call peaks using default parameters and FDR <5%
Assembly: hg38 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq

growth_protocol: Human iPSCs were plated on Geltrex LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix and maintained in feeder-free, serum-free mTeSR Plus medium.

extract_protocol:
RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs, T2010).
RNA libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760). 300 ng of total RNA input was used for each library. Libraries were sequenced on Illumina NovaSeq X Plus, producing 150bp paired-end reads.
Barcoded libraries were made with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) using NEBNext Multiplex Oligos Dual Index Primers for Illumina (NEB, E7600S), and sequenced on Illumina NovaSeq X Plus, producing 150 bp paired-end reads.
ATAC-seq was performed using 100,000 cells per sample. Libraries were prepared using the ATAC-seq Kit (Active Motif, 53150) and sequenced on Illumina NovaSeq X Plus producing 150 bp paired-end reads.

value: hiPSC-derived cranial neural crest cells

value: plus gRNA

value: cranial neural crest cell specification


title: Nup2-MNase, SDC, Replicate 1

description: Library name: B24-DB01


title: Female, saline, LD, rep2

value: Saline, LD


title: IFNT3day_lutealtissue_2

value: Corpus luteum

value: whole tissue


title: MT944_NCC d5 NOG rep2

description: Library name: MT944_NCC d5 NOG rep2

value: minus gRNA


title: MT946_NCC d5 NOG rep3

description: Library name: MT946_NCC d5 NOG rep3


title: MT943_NCC d5 HSTE rep1

description: Library name: MT943_NCC d5 HSTE rep1


title: MT937_NCC d5 HSTE rep1

description: Library name: MT937_NCC d5 HSTE rep1

value: Histone H3 (tri methyl K9) antibody - ChIP Grade (Abcam #ab8898)


title: MT936_NCC d5 NOG rep1

description: Library name: MT936_NCC d5 NOG rep1


title: MT841_C2277 SVA gRNA D18 rep2

description: Library name: MT841_C2277 SVA gRNA D18 rep2


title: MT840_C2277 no gRNA D18 rep2

description: Library name: MT840_C2277 no gRNA D18 rep2


title: BSA3day_lutealtissue_3


title: MT941_NCC d5 HSTE rep6

description: Library name: MT941_NCC d5 HSTE rep6


title: MT940_NCC d5 NOG rep6

description: Library name: MT940_NCC d5 NOG rep6


title: MT939_NCC d5 HSTE rep5

description: Library name: MT939_NCC d5 HSTE rep5


title: MG6-4_day4_2_TDP43_3

city: Boston

first: Songlei

last: Liu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

description: Library name: Sample 12

data_processing:
Coutns were generated with STAR v2.5.2b using the following command: STAR --runThreadN $cores --genomeDir $genome --readFilesIn $R1 $R2 --outFileNamePrefix $align_out --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --quantMode GeneCounts
Assembly: GRCh38
Supplementary files format and content: csv files include raw STAR alignment counts for each sample

growth_protocol: TFiMGL’s were fully cultured in stem cell media, mTeSR Plus from day 0 until day 6.

extract_protocol:
Cultured cells were dissolved directly with TRIzol (Thermo Fisher Scientific, 15596018) for total RNA purification with Direct-zol RNA MiniPrep Kit (Zymo Research, R2050). RNA concentration was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Q32852). RNA integrity was confirmed by presence of 18S and 28S bands on a 2% E-Gel EX Agarose Gel (Thermo Fisher Scientific, G402002). Between 100 ng to 1000 ng total RNA was used as input for mRNA enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490), followed by library construction with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) following the manufacturer’s instructions.
Biopolymers Facility at Harvard Medical School performed library QC and sequencing.

treatment_protocol: TFiMGLs were treated in triplicates with each of the three molecules for 24 hours.

value: iPSC

value: 6 Transcription Factors + Dox + TDP43


title: MG6-4_day4_2_TDP43_1

description: Library name: Sample 10


title: MG6-4_day4_2_TDP43_2

description: Library name: Sample 11


title: MG6-4_day4_2_fAb_3

description: Library name: Sample 6

value: 6 Transcription Factors + Dox + fibrillary amyloid beta


title: MT938_NCC d5 NOG rep5

description: Library name: MT938_NCC d5 NOG rep5


title: MG6-4_day4_2_INFg_3

description: Library name: Sample 9

value: 6 Transcription Factors + Dox + Interferon gamma


title: MG6-4_day4_2_INFg_2

description: Library name: Sample 8


title: BSA3day_lutealtissue_1

value: BSA


title: MG6-4_day4_2_INFg_1

description: Library name: Sample 7


title: MG6-4_day4_2_fAb_2

description: Library name: Sample 5


title: MG6-4_day4_2_control_3

description: Library name: Sample 3

value: 6 Transcription Factors + Dox


title: MG6-4_day4_2_fAb_1

description: Library name: Sample 4


title: MT942_NCC d5 NOG rep1

description: Library name: MT942_NCC d5 NOG rep1


title: TFiMG64._Sample1_Seq1

description:
Library name: Sample 1
Parse Biosciences

data_processing:
Sequenced data was processed using Parse Batch Analysis (version 1.0.9) on the DNAnexus platform to demultiplex into library fastq files and count matrices.
Assembly: GRCh38
Supplementary files format and content: h5ad file with single-cell raw count matrices

growth_protocol: TF (pBAN-TF-BC) and Super PiggyBac (SPB) Transposase (System Biosciences, PB210PA-1) expression vectors were mixed at a mass ration of 4:1 and transfected into hiPSCs using P3 Primary Cell 4D-Nucleofector X Kit L (Lonza, V4XP-3024) on a 4D-Nucleofector X Unit (Lonza, AAF-1002X) following manufacturer’s instructions. For SCF-MCI vector, 600,000 cells were transfected with 5 µg of DNA and seeded into one well of a 6-well plate. Program CB150 was used for the nucleofections. 48 hours after nucleofection, 1 µg/mL of puromycin (Gibco, A1113803) or 50 µg/mL of zeocin (Gibco, R25001) was added to the culture for the selection of TF-integrated cells. Cells were passaged again when reaching 80% confluency.

extract_protocol:
Undifferentiated iPSCs and TFiMGLs at days 2-, 4-, and 6-post induction (both MT and MG media conditions for days 4 and 6) were harvested by first washing with PBS (- calcium, - magnesium) followed by dissociating cultures into single cell suspensions with Accutase (StemCell Technologies, 07920) for 10 minutes at 37°C, cultures were then quenched with DMEM/F12 (Gibco, 11320033) and subsequently centrifuged at 300g for 3 minutes. The cell pellet was rinsed with PBS (- calcium, - magnesium) and centrifuged again at 300g for 3 minutes prior to fixation. Single cell suspensions from each sample were processed using the Parse Biosciences Fixation Kit following manufacturer’s instructions (SB1001) and subsequently stored at -80°C until all samples of the time course were harvested.
Libraries for all samples were prepared using the Parse Whole Transcriptome Mini V1 kit following manufacturer’s instructions (EC-W01010) where an average of 450bp libraries were generated.

treatment_protocol: TFiMGL’s were fully cultured in either stem cell media, mTeSR Plus (MT), or switched to commercially available microglia media (MG) (Stemcell Technologies, 100-0020) from day 2 until day 6. All media was supplemented with 0.5 µg/mL doxycycline for the duration of the experiment.

value: TF induced microglia

value: 6 TFs + Dox


title: MG6.4_Dox_timeline_Day4_seq2

description: Library name: Sample 8

treatment_protocol: All media was supplemented with 0.5 µg/mL doxycycline for the duration of the experiment.


title: MG6.4_Dox_timeline_Day6_seq2

description: Library name: Sample 10


title: MG6-4_day4_2_control_1

description: Library name: Sample 1


title: MG6.4_Dox_timeline_Day6_seq1

description: Library name: Sample 9


title: MG6.4_Dox_timeline_Day3_seq1

description: Library name: Sample 5


title: MT839_C2277 SVA gRNA D18 rep1

description: Library name: MT839_C2277 SVA gRNA D18 rep1


title: MT838_C2277 no gRNA D18 rep1

description: Library name: MT838_C2277 no gRNA D18 rep1


title: MG6.4_Dox_timeline_Day3_seq2

description: Library name: Sample 6


title: MG6.4_Dox_timeline_Day2_seq2

description: Library name: Sample 4


title: MG6.4_Dox_timeline_Day1_seq1

description: Library name: Sample 1


title: MG6.4_Dox_timeline_Day1_seq2

description: Library name: Sample 2


title: MG3_1_2AC5_plus42TF_10X_scRNAseq_2

description:
Library name: Sample 4
10x Genomics

data_processing:
The demultiplexing, bacod processing, gene couting and aggregation were made using the cell Ranger software cellranger-6.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: TF (pBAN-TF-BC) and Super PiggyBac (SPB) Transposase (System Biosciences, PB210PA-1) expression vectors were mixed at a mass ration of 4:1 and transfected into hiPSCs using P3 Primary Cell 4D-Nucleofector X Kit L (Lonza, V4XP-3024) on a 4D-Nucleofector X Unit (Lonza, AAF-1002X) following manufacturer’s instructions. For the pooled TF screen, 600,000 cells were transfected with 5 µg of DNA and seeded into one well of a 6-well plate. Program CB150 was used for the nucleofections. 48 hours after nucleofection, 1 µg/mL of puromycin (Gibco, A1113803) or 50 µg/mL of zeocin (Gibco, R25001) was added to the culture for the selection of TF-integrated cells. Cells were passaged again when reaching 80% confluency.

extract_protocol:
Cells were harvested by first washing with PBS (- calcium, - magnesium) followed by dissociating cultures into single cell suspensions with Accutase (StemCell Technologies, 07920) for 10 minutes at 37°C, cultures were then quenched with DMEM/F12 (Gibco, 11320033) and subsequently centrifuged at 300g for 3 minutes. The cell pellet was rinsed with PBS (- calcium, - magnesium) and centrifuged again at 300g for 3 minutes prior to library prep and resuspended in PBS-/- supplemented with 0.04% w/v BSA.
scRNA-seq experiments were performed using 10x Genomics Chromium Single Cell 3' Reagent Kits v3 or v3.1 following the manufacturer’s instruction. 5000 single cells were calculated as targeted input for each sample. For the first iteration, 10% of stem cells were spiked in as undifferentiated control. For the second iteration, 5% stem cells and 5% MG3.1-SFC were spiked in as undifferentiated and initial differentiation control. The only modification made to the protocol was at the Sample Index PCR step, where 5 µL of the PCR mix was taken out and mixed with 0.5 µL 1000X SYBR Gold (Invitrogen, S11494) for a qPCR reaction. The optimal amplification cycle was determined as the cycle just before half maximum of the total signal. Final libraries were sequenced on NextSeq 500 or NovaSeq with a goal of at least 30,000 reads per cell.

treatment_protocol: For induction of TF expression, cells were seeded into mTeSR Plus media containing 0.5 µg/mL doxycycline (Sigma-Aldrich, D3072) and 10 µM Y-27632 ROCK inhibitor and were changed into media only containing doxycycline after 24 hours. Dox treatment was continued for 4 days.

value: 42 Transcription Factors + SCF + DOX


title: MG3_1_2AC5_plus42TF_10X_scRNAseq_1

description:
Library name: Sample 3
10x Genomics

value: 42 Transcription Factors + SCF + DOX + Tra1-60 negative


title: 40TF_PGP1_TRA160minus_40TF_PGP1_TRA160minus_Sample2_run1

description:
Library name: Sample 4
10x Genomics

data_processing:
The demultiplexing, bacod processing, gene couting and aggregation were made using the cell Ranger software v3.0.2
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

value: 40 Transcription Factors + DOX + Tra1-60 negative


title: 40TF_PGP1_TRA160minus_40TF_PGP1_TRA160minus_Sample1_run2

description:
Library name: Sample 5
10x Genomics


title: 40TF_PGP1_TRA160minus_40TF_PGP1_TRA160minus_Sample1_run1

description:
Library name: Sample 3
10x Genomics


title: 40TF_PGP1_TRA160minus_40TF_PGP1_TRA160minus_Sample2_run2

description:
Library name: Sample 6
10x Genomics


title: TSKb20_TCR-seq

city: Philadelphia

first: Molly

last: Bunkofske

state: Pennsylvania

address: 380 S University Ave

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were made using the CellRanger software 6.1.2
Assembly: mm10-2020 (refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0)
Supplementary files format and content: Tab-separated files, matrix files, and comma-separated value files
Library strategy: scTCR-seq

source_name: Skeletal muscle

extract_protocol:
T cells were isolated from skeletal muscle using an EDTA/Collagenase digest followed by a Percoll gradient to enrich for lymphocytes. Cells were stained for viability, CD8, and TSKb20 tetramer then sorted on a cell sorter. TSKb20-tetramer bound and Nur77-GFP+ T cell populations were each sorted out from 5 individual mice then pooled together.
Libraries for scRNA-seq were prepared according to the manufacturer's instructions, using Chromium Single Cell 5' Dual Index Library & Gel Bead Kit, Chromium Single Cell A Chip Kit, and Chromium Multiplex Kit (10x Genomics). Amplified cDNA was used to generate single-cell TCRαβ libraries using Chromium Single Cell V(D)J Enrichment kit for mouse T cells (10x Genomics).

value: Skeletal muscle

value: TSKb20 tetramer+ CD8 T cells


title: TSKb20_scRNA-seq

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were made using the CellRanger software 6.1.2
Assembly: mm10-2020 (refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0)
Supplementary files format and content: Tab-separated files, matrix files, and comma-separated value files


title: Nur77-GFP+_scRNA-seq

description: 10x Genomics

value: Nur77-GFP+ CD8 T cells


title: CITE-seq, PBMC, M34, week6, ADT

city: Toulouse

first: Anne

last: Montfort

address: 2 avenue Hubert Curien

country: France

institute: INSERM

description:
Library name: M34_S6_ADT
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
CITE-seq data were aligned to the human transcriptome using Cell Ranger version 7.1
Assembly: 2020-A
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.tsv.gz
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
Droplet-based single-cell libraries were generated using Chromium Instruments and Chromium Single Cell 3′ Library & Gel Bead Kit v3. 15 000 cells injected per sample
Chromium Single Cell 3′ Library & Gel Bead Kit v3 was used

treatment_protocol: PBMC from patients before and 6 weeks after nivolumab+ipilimumab therapy.

value: PBMC

value: Immune cells

value: nivolumab + ipilimumab

tag: library type

value: ADT

tag: adt

value: TotalSeq-A0154 anti-human CD27, TotalSeq-A0034 anti-human CD3, TotalSeq-A0080 anti-human CD8, TotalSeq-A0081 anti-human CD14, TotalSeq-A0083 anti-human CD16, TotalSeq-A0136 anti-human IgM, TotalSeq-A0045 anti-human CD4, TotalSeq-A0050 anti-human CD19, TotalSeq-A0063 anti-human CD45RA, TotalSeq-A0159 anti-human HLA-DR, TotalSeq-A0147 anti-human CD62L


title: CITE-seq, PBMC, M34, week6, GEX

description:
Library name: M34_S6_GEX
PolyA RNA

value: GEX


title: MG6-4_day4_2_control_2

description: Library name: Sample 2

value: iPSC


title: CITE-seq, PBMC, M34, week0, GEX

description:
Library name: M34_S1_GEX
PolyA RNA

value: Pre-treatment


title: MG6.4_Dox_timeline_Day4_seq1

description: Library name: Sample 7

value: 6 Transcription Factors + Dox


title: Nur77-GFP+_TCR-seq

description: 10x Genomics


title: CITE-seq, PBMC, M28, week6, ADT

description:
Library name: M28_S6_ADT
Antibody-derived oligonucleotide (ADT)


title: CITE-seq, PBMC, M28, week6, GEX

description:
Library name: M28_S6_GEX
PolyA RNA


title: CITE-seq, PBMC, M25, week6, GEX

description:
Library name: M25_S6_GEX
PolyA RNA


title: CITE-seq, PBMC, M28, week0, ADT

description:
Library name: M28_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: CITE-seq, PBMC, M28, week0, GEX

description:
Library name: M28_S1_GEX
PolyA RNA


title: CITE-seq, PBMC, M13, week6, ADT

description:
Library name: M13_S6_ADT
Antibody-derived oligonucleotide (ADT)


title: MG6.4_Dox_timeline_Day2_seq1

description: Library name: Sample 3


title: CITE-seq, PBMC, M25, week0, ADT

description:
Library name: M25_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: CITE-seq, PBMC, M25, week0, GEX

description:
Library name: M25_S1_GEX
PolyA RNA


title: CITE-seq, PBMC, M13, week6, GEX

description:
Library name: M13_S6_GEX
PolyA RNA


title: CITE-seq, PBMC, M13, week0, ADT

description:
Library name: M13_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: Bladder tumor Tri58MJ

city: West Lafayette

first: Deborah

last: Knapp

address: 625 Harrison Street

institute: Purdue University

data_processing:
Strand NGS (v4.0, Strand Life Sciences Pvt Ltd, Bangalore, India) was used to align the data to ENSEMBL (CanFam3.1).  After quantification, data were normalized using TMM.
Assembly: CanFam3.1
Supplementary files format and content: Tab delimited text file with raw counts.

organism: Canis lupus familiaris

source_name: Invasive urothelial carcinoma

extract_protocol:
Bladder tumors were collected via cystoscope. Tissues were stored directly in trizol and flash frozen. RNA was extracted and purified using RNAeasy (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: organ

value: Bladder

tag: disease

value: Invasive urothelial carcinoma


title: Bladder tumor Dex34


title: CITE-seq, PBMC, M13, week0, GEX

description:
Library name: M13_S1_GEX
PolyA RNA

tag: treatment


title: Bladder tumor 04RH


title: CITE-seq, PBMC, M34, week0, ADT

description:
Library name: M34_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: Bladder tumor 66PG


title: Bladder tumor 65ZB


title: Bladder tumor T62MJ


title: Bladder tumor RN49CW


title: SUM149_sh17_shKDM4C_5_RNAseq

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Briefly, fastq files were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out. The gene-level counts from all studies were then normalized using TMM with edgeR  (Robinson et al., 2010). Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)] were used for analysis. For samples sequenced on different days, batch correction was applied using removeBatchEffect function from limma package (Smyth, 2005).
Assembly: hg19
Supplementary files format and content: Matrix table (in .csv format) with raw gene counts for every gene and every sample

source_name: Breast Cancer

growth_protocol: HCC1954 and HCC1806 cells were cultured in RPMI-1640 medium with 10% FBS and 100U/ml Penicillin-Streptomycin. SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin.  HDQP1 cells were cultured in DME with 10% FBS and 100U/ml Penicillin-Streptomycin.

extract_protocol:
Total RNA were extracted following manufacturer's protocol pf Qiagen Rneasy Mini Kit. (Qiagen, #74106)
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

treatment_protocol: Cells were seeded in six well plates and treatment of 0.1% DMSO, 0.1μg/ml doxycycline, 10 μM ML324 or 1 μM QC6352 were added the next day. Cells were treated for 5 days until RNA collection.

value: Breast Cancer

tag: cell line

value: Human breast cancer epithelial cell

tag: genotype

value: Dox-inducible shKDM4C

value: 0.1 ug/ml doxycycline


title: SUM149_sh20_shKDM4C_2_RNAseq

tag: tissue

tag: cell type


title: CITE-seq, PBMC, M25, week6, ADT

description:
Library name: M25_S6_ADT
Antibody-derived oligonucleotide (ADT)


title: SUM149_sh17_ML324_5_RNAseq


title: SUM149_sh17_ML324_6_RNAseq


title: A549_M11-5-1

city: Yokohama

first: Takeshi

last: Furuhashi

state: Kanagawa

address: 5th Floor Technocising Building, 2-6-3, Chojyamachi, Naka Ward

institute: ASM

description:
A549_35
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

data_processing:
Raw fastq were trimmed using Trim Galore.
Pseudoalignment using trimmed reads and quantifying abundance of gene expression with Kalisto.
Assembly: GRCh38 (Human genome) downloaded from Ensembl v106.
Supplementary files format and content: *.tsv: Tab-separated text files include counts and TPMs.

source_name: Lung

growth_protocol: 2x10^6 cells (HPF, HLB and A549) in DMEM culture, star T75 flask at Day 3.

extract_protocol:
RNeasy plus mini kit 250 (QIAGEN, 74136).
NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat#E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat#E7770L).

treatment_protocol: Glucose (high/low), O2 (Normoxia/Hypoxia), Lactate (0, 12.5μM, 125μM, 1.25mM).

value: Lung

value: Cancer cell

value: Low glucose with lactate (1.25mM), Hypoxia


title: A549_M11-6-1

description:
A549_36
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M11-4-1

description:
A549_34
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: SUM149_sh20_shKDM4C_1_RNAseq


title: A549_M11-3-1

description:
A549_33
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M11-1-1

description:
A549_31
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M10-6-1

description:
A549_30
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: Low glucose with lactate (125uM), Hypoxia


title: A549_M10-5-1

description:
A549_29
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M10-4-1

description:
A549_28
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M10-2-1

description:
A549_26
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M10-3-1

description:
A549_27
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: Bladder tumor Ros76


title: Bladder tumor 61ME


title: SUM149_sh17_shKDM4C_6_RNAseq


title: A549_M7-5-1

description:
A549_23
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: Low glucose with lactate (12.5uM), Hypoxia


title: A549_M7-6-1

description:
A549_24
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M7-3-1

description:
A549_21
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M7-4-1

description:
A549_22
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M7-2-1

description:
A549_20
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M7-1-1

description:
A549_19
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M5-6-1

description:
A549_18
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: High glucose, Hypoxia


title: A549_M5-5-1

description:
A549_17
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M5-1-1

description:
A549_13
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M11-2-1

description:
A549_32
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M4-6-1

description:
A549_12
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: Low glucose, Hypoxia


title: A549_M5-3-1

description:
A549_15
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M4-3-1

description:
A549_9
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M4-2-1

description:
A549_8
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M1-6-1

description:
A549_6
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: High glucose, Normoxia


title: A549_M4-1-1

description:
A549_7
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M5-4-1

description:
A549_16
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M4-5-1

description:
A549_11
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M4-4-1

description:
A549_10
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M1-5-1

description:
A549_5
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M10-1-1

description:
A549_25
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M1-4-1

description:
A549_4
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M1-3-1

description:
A549_3
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M1-1-1

description:
A549_1
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M11-4-2

description:
HPF_34
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: HPF

value: Primary cell


title: HPF_M11-6-1

description:
HPF_36
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M1-2-1

description:
A549_2
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M11-5-2

description:
HPF_35
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M11-1-1

description:
HPF_31
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: A549_M5-2-1

description:
A549_14
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M10-6-1

description:
HPF_30
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M11-2-1

description:
HPF_32
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M10-5-1

description:
HPF_29
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M11-3-1

description:
HPF_33
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M10-4-1

description:
HPF_28
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M10-2-1

description:
HPF_26
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M10-3-1

description:
HPF_27
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M10-1-1

description:
HPF_25
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M7-6-1

description:
HPF_24
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M7-4-1

description:
HPF_22
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M7-5-1

description:
HPF_23
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M7-2-1

description:
HPF_20
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M7-3-1

description:
HPF_21
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M7-1-2

description:
HPF_19
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M5-6-2

description:
HPF_18
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M5-3-1

description:
HPF_15
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M5-5-1

description:
HPF_17
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M5-1-1

description:
HPF_13
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M5-2-1

description:
HPF_14
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M4-4-1

description:
HPF_10
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M4-6-1

description:
HPF_12
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M4-5-1

description:
HPF_11
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M4-2-1

description:
HPF_8
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M4-3-1

description:
HPF_9
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M4-1-1

description:
HPF_7
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M1-4-1

description:
HPF_4
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M1-5-1

description:
HPF_5
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M1-3-1

description:
HPF_3
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M1-2-1

description:
HPF_2
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M1-1-1

description:
HPF_1
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M11-4-1

description:
HLB_34
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: HLB

value: Immortalized cell


title: HLB_M11-5-1

description:
HLB_35
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M11-3-1

description:
HLB_33
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M11-1-1

description:
HLB_31
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M5-4-1

description:
HPF_16
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M10-6-1

description:
HLB_30
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M10-4-1

description:
HLB_28
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M10-2-1

description:
HLB_26
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M10-3-1

description:
HLB_27
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M10-1-1

description:
HLB_25
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M7-6-1

description:
HLB_24
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M7-5-1

description:
HLB_23
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M7-4-1

description:
HLB_22
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M7-3-1

description:
HLB_21
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M7-1-1

description:
HLB_19
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M5-5-1

description:
HLB_17
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M5-6-1

description:
HLB_18
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M7-2-1

description:
HLB_20
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HPF_M1-6-1

description:
HPF_6
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M5-4-1

description:
HLB_16
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 2×105 low seeding density, Day 15, rep3

city: beijing

first: qian

last: dong

address: No. 27 Taiping Road ，Haidian Distric

institute: Beijing Institute of Radiation Medicine

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
We used Bowtie2 (Version：v2.2.5) to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM (Version：v1.3.1) to calculate the gene expression level of each sample.
Differential gene detection: The DEseq2 (v1.4.5) method is based on the principle of negative binomial distribution. Parameters: Qvalue (Adjusted Pvalue) <= 0.05
Cluster heatmap: According to the results of differential gene detection, the R package pheatmap (v1.0.8) was used to perform hierarchical clustering analysis on the union set differential genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts values and variance stabilizing transformation normalized values for each Sample

growth_protocol: hESCs-H1 were cultured on Matrigel-coated wells in mTeSR Plus.

extract_protocol:
Total RNA was extracted from 1x106 cells at indicated induction time using TRIzol reagent  (Invitrogen), qualified and quantified with DNF-471 Standard Sensitivity RNA Analysis Kit (Agilent). 200ng of total RNA was used for the construction of sequencing libries.
RNA libraries for RNA-seq were prepared using BGI Optimal Dual-mode mRNA library construction kit (BGI, China) following manufacturer's protocols.

treatment_protocol: For embryoid body-based erythroid induction, in stage 1 of differentiation (Days 0-2), cells were grown in Advanced DMEM/F-12 supplemented with AA2P, bFGF, BMP4,Activin A, CHIR99021, GlutaMAX, and Pen/Strep by 6×105/well or 2×105/well in 6-well-plate, embryoid bodies (EBs) were formed spontaneously at this stage. In stage 2 of differentiation (Days 2-6), cells were grown in Advanced DMEM/F-12 supplemented with AA2P, bFGF, VEGF165, GlutaMAX, and Pen/Strep. In stage 3 of differentiation (Days 6-15), cells were grown in BEL supplemented with SCF, TPO, Flt-3L, IL-3, VEGF165, SB431542, EPO, and human holo-transferrin. In stage 4 of differentiation (Days 15-18), EBs were filtered out with a 100 μm strainer, and the remaining suspended cells were adjusted to 5×106/3mL/well and grown in BEL, in which BSA was replaced with AB serum supplemented with EPO and heparin solution. Stages 1-3 used ultra-low attachment six-well plates, and stage 4 used normal six-well plates.

value: erythroid differentiation

value: 2×105 low seeding density

tag: time

value: Day 15


title: hESC-H1 derivatives, from 2×105 low seeding density, Day 15, rep2


title: HLB_M11-2-1

description:
HLB_32
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M11-6-1

description:
HLB_36
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M5-2-1

description:
HLB_14
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M5-3-1

description:
HLB_15
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 6×105 high seeding density, Day 15, rep2

value: 6×105 high seeding density


title: hESC-H1 derivatives, from 6×105 high seeding density, Day 15, rep1


title: HLB_M4-6-1

description:
HLB_12
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M10-5-1

description:
HLB_29
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 2×105 low seeding density, Day 15, rep1


title: HLB_M4-5-1

description:
HLB_11
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M4-4-1

description:
HLB_10
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 2×105 low seeding density, Day 6, rep3

value: Day 6


title: hESC-H1 derivatives, from 2×105 low seeding density, Day 6, rep1


title: HLB_M4-3-1

description:
HLB_9
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: Lung


title: hESC-H1 derivatives, from 2×105 low seeding density, Day 6, rep2


title: hESC-H1 derivatives, from 6×105 high seeding density, Day 6, rep3


title: HLB_M4-1-1

description:
HLB_7
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M4-2-1

description:
HLB_8
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 6×105 high seeding density, Day 6, rep2


title: HLB_M1-6-1

description:
HLB_6
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 6×105 high seeding density, Day 6, rep1


title: HLB_M1-4-1

description:
HLB_4
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: dCas9-activator MEF, induced, rep2

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
counts.tsv
Assembly: mm10
Supplementary files format and content: counts.tsv

source_name: MEF

growth_protocol: Cells were maintained in high glucose DMEM containing 10% tet-free FBS, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1x non-essential amino acids, 1 mM sodium pyruvate, and 400 mg/ml hygromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 10 ug of total RNA was further processed to remove the remaining DNA with TURBO DNase and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.
RNA-Seq, 150 bp paired-end

treatment_protocol: MEF dCas9-Activator cells were treated with 10 ng/ml doxycycline for 6 hrs, MEF dCas9-Repressor cells were treated with 100 ng/ml doxycycline for 24 hrs, and MEF dCas9-control cells were treated with 10 ng/ml doxycycline for 24 hrs.

value: MEF

value: mouse embryonic fibroblast

value: inducible expression of dCas9-VPR

value: 10 ng/ml doxycycline, 6 hr


title: dCas9-activator MEF, induced, rep3


title: dCas9-activator MEF, induced, rep1


title: HLB_M1-5-1

description:
HLB_5
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M1-3-1

description:
HLB_3
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: hESC-H1 derivatives, from 6×105 high seeding density, Day 15, rep3


title: HLB_M5-1-1

description:
HLB_13
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end

value: High glucose, Hypoxia


title: HLB_M1-2-1

description:
HLB_2
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: HLB_M1-1-1

description:
HLB_1
mRNA
NextSeq 500/550 High Output Kit v2.0 (Illumina)
36 bp paired-end


title: dCas9-activator MEF, uninduced, rep2

value: untreated


title: dCas9-activator MEF, uninduced, rep3


title: dCas9-activator MEF, uninduced, rep1