title: HD252_Weslaco(TX)_2019_S79

city: College station

first: Hisashi

last: Koiwa

state: Texas

address: 495 Horticulture Rd.

department: Department of Horticultural Sciences

institute: Texas A&M University

data_processing:
The raw RNA-seq expression data were pre-processed by filtering out the transcripts with count per million (CPM) below 1 (low expressed transcripts).
Then the data were normalized following the DESeq function implemented in the DESeq2 R package after adjusting for the known biological melon sample covariates of cultivar location, fruit type, and binary Tobacco ringspot virus (TRSV) contamination status.
The binary TRSV contamination status of samples was determined by checking for any unmapped TRSV sequences in melon fruit sample sequences.
Following the instructions from DESeq2 data processing pipeline, we then performed variance stabilizing transformation (VST) on the RNA-seq data by the vst function implemented in the DESeq2 package.
Assembly: CM3.6.1_pseudomol http://cucurbitgenomics.org/ftp/genome/melon/DHL92/v3.6.1/
Supplementary files format and content: Fruit_normalized_VST.csv (The geneIDs are available on Melon DB https://melonet-db.dna.affrc.go.jp/ap/top)
Supplementary files format and content: Location_normalized_VST.csv (The geneIDs are available on Melon DB https://melonet-db.dna.affrc.go.jp/ap/top)

organism: Cucumis melo

source_name: Fruit

growth_protocol: The plants were grown during the spring growing season (March–June 2019) in fields located at the Texas A&M AgriLife Research Center – Texas A&M University System in Weslaco, Texas (latitude 26° 9' N, longitude 97° 57' W; elevation 21 m). In addition, F39 and TTDV plants were grown in TX (Uvaldi, 2018 and 2019), GA, NC, CA, IN, and AZ in 2019. Fruits were harvested at maturity (approximately 45 days after flowering).

extract_protocol:
Approximately 0.25 g of the powdered, frozen tissues were mixed with 1 ml of Trizol reagent (ThermoFisher) and incubate for 5 minutes.  The solution was mixed with 0.5 ml of chloroform and centrifuged at 12,000g for 10 minutes after incubation for 5 minutes.  The aqueous phase was mixed with 350 µl of ethanol and loaded to an EconoSpin column (Epoch Life Science), and centrifuged at 8,000 g for 40 seconds.  The column was washed twice with 450 µl of 3M sodium acetate and with 320 µl of 70% ethanol.  RNA was eluted with 30 µl of RNase-free water.  Subsequently, RNA samples were treated with DNase and cleaned up with phenol-chloroform extraction and ethanol precipitation.
cDNA libraries were synthesized using Universal Plus mRNA-seq with NuQuant Kit (NuGen) according to the manufacturer's protocol

value: Fruit

tag: cultivar

tag: location

value: Weslaco(TX)

tag: year

value: WT


title: ICSI_Eq_41b, blastomere, scRNA-seq

status: Public on Mar 01 2024

type: SRA

city: Muenster

first: Wojciech

last: Makalowski

address: Niels Stensen Strasse 14

department: Faculty of Medicine

country: Germany

institute: University of Muenster

description:
Smart-Seq2
Plate1_I02-ICSI_Eq-41b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

library_source: transcriptomic single cell

data_processing:
Reads were trimmed and adapters were removed using Trimmomatic (V.039).
Read quality was checked for each cell using FastQC (v0.12.1).
Reads were mapped to mm10, and expression of genes were quntified using STAR (2.7.10b) pipeline
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-seperated values files (features and barcodes) plus matrix files

molecule: total RNA

organism: Mus musculus

source_name: preimplantation embryo Theiler stage 2

growth_protocol: In vitro culture of fertilized oocytes in KSOM medium supplemented with aminoacids, in pool (4-well plate) up to the 2-cell stage, then individually after bisection (one blastomere per well of 96-well plate), at 37 °C under 5% CO2 in air, as described (PMID 28811525).

extract_protocol:
Single blastomeres or single blastocysts were lysed in 10X Lysis Buffer from Takara (cat.no. 635013). Then the RNA was extracted by TaKaRa SMART-Seq Single Cell Kit (cat.no. 634470).
Total RNA was converted to cDNA using the TaKaRa SMART-Seq Single Cell Kit (cat.no. 634470) and sequencing libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit (cat.no. FC-131-1024). Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Sperm deposition by ICSI in three different ooplasmic locations (contralateral, isolateral or equatorial relative to meiotic spindle)

tag: tissue

value: preimplantation embryo Theiler stage 2

tag: cell type

value: blastomere

tag: genotype


title: Nexus-Pol2-GR-TAD

city: Melbourne

first: Charles

middle: C

last: Bell

state: VICTORIA

address: VCCC, Gate 1, 14 Flemington Road

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

library_source: genomic

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
eads that passed the Illumina quality filter were filtered for the presence of a fixed barcode. The fixed barcode was used to demultiplex the samples, before being filtered from the reads by Cutadapt70. The random barcode on each read was retained to enable UMI based quantification. Any remaining adapter sequences were trimmed, and reads were removed if they were less than 22bp in length.
Reads were then aligned using Bowtie271 to a human genome (GRCh38) that was modified to contain an additional chromosome with the relevant reporter construct sequence.
Duplicate reads were removed, and each sample was converted into two bigwig files, one with strand specific information and one that aggregates the reads from both strands. The sequence coverage across the reporter construct was then visualised using IGV.
Assembly: GRCh38
Supplementary files format and content: Bed files

molecule: genomic DNA

organism: Homo sapiens

source_name: Haematopoetic

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37C).

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody. Briefly, the immunoprecipitation and washes were performed using the same conditions as the ChIP protocol. Upon completion of these steps, the DNA was end-repaired, A-tailed, adaptors ligated, exonuclease treated, circularized on Dynabeads as described previously.
Constructed via PCR during ChIP-nexus protocol

treatment_protocol: Cells were treated with DMSO or CDK8i (Sennexin A, 10uM) for 1hrs prior to crosslinking with 1% formaldehyde for 15mins.

value: Haematopoetic

tag: cell line

tag: chip antibody

value: anti-RNA polymerase II Antibody clone CTD4H8


title: HD252_Weslaco(TX)_2019_S78

country: USA

library_source: transcriptomic


title: mESC_Firre_Rescue_firre_induced_5760min_dox_long_rep2

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

data_processing:
Quality control, read mapping, and quantification was performed using nf-core/rnaseq v1.4.2. Reads were mapped to mm10 and quantified with Salmon v1.5.2 using the Gencode M25 annotation.
Assembly: mm10
Supplementary files format and content: comma-separated text file contains TPM values for each Sample
Supplementary files format and content: comma-separated text file contains raw counts values for each Sample

molecule: polyA RNA

source_name: mESC

growth_protocol: Cells were maintained on 0.1% gelatin in KnockOut DMEM (Thermo Fisher, 10829018) supplemented with 12.5% FCS (MilliporeSigma, ES-009-B), 1X GlutaMAX supplement (Thermo Fisher, 35050061), 1X non-essential amino acids (Thermo Fisher, 11140050), 100 U/mL penicillin/streptomycin (Thermo Fisher, 15140122), 100 μM 2-mercaptoethanol (Thermo Fisher, 31350010), 1 μM PD0325901 (MilliporeSigma, PZ0162-5MG), 3 μM CHIR99021 (MilliporeSigma, SML1046-5MG), and 100 U/mL LIF (MilliporeSigma, ESG1107) at 37°C and 7.5% CO2. Cells were routinely tested for mycoplasma contamination by PCR.

extract_protocol:
Total RNA was extracted using TRIzol lysis reagent (Thermo Fisher) and purified using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was measured with a Qubit fluorometer (Invitrogen), and RNA quality was determined using a Bioanalyzer or TapeStation (Agilent Technologies).
RNA-seq libraries were prepared from 1 μg of total RNA using the TruSeq RNA Library Prep Kit v2 (Illumina) with poly(A) selection according to the manufacturer’s instructions. Multiples of 12 randomized samples were each multiplexed, pooled, and run in one HiSeq lane.

treatment_protocol: Cells were treated with 1 ng/μL dox (MilliporeSigma, D9891-5G) the day after they were seeded and one hour after medium was changed to reduce cell stress.

value: mESC

value: embryonic stem cells

value: Firre KO / Firre inducible transgene

tag: treatment

value: doxycycline

tag: time

value: 5760 minutes


title: ICSI_Eq_41a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I01-ICSI_Eq-41a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_1440min_dox_long_rep3

value: 1440 minutes


title: HD252_Weslaco(TX)_2019_S77


title: Nexus-Pol2-Gal4-KO-TAD


title: Patient 2

type: RNA

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 2

hyb_protocol: Standard nanostring nCounter miRNA Hybridization Protocol; The final hybridization reaction contained the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (555 fields of view).

data_processing: The miRNA data analysis was performed using nSolver Analysis (version 4·0) software. Each miRNA count data was subtracted from the geometric mean of the negative controls. Profiling data were then normalized by the geometric mean of the positive controls and the geometric mean of the top 100 most highly-expressed microRNAs.

source_name: grade 2-3

label_protocol: Standard nanostring miRNA protocols (nCounter Human v3 miRNA Expression Assays (NanoString Technologies,Seattle, USA))

extract_protocol: Total RNA was extracted from 400 mL of serum sample using miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s protocol.

tag: grade

value: grade 2-3 (CNS5 WHO)

tag: age

tag: gender

value: female

tag: ihd status

value: MT


title: ICSI_Eq_40b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H10-ICSI_Eq-40b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: HD150_Weslaco(TX)_2019_S76


title: mESC_Firre_Rescue_firre_induced_1440min_dox_long_rep2


title: mESC_Firre_Rescue_firre_induced_1440min_dox_long_rep1


title: ICSI_Eq_40a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H09-ICSI_Eq-40a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: HD150_Weslaco(TX)_2019_S75


title: mESC_Firre_Rescue_firre_induced_720min_dox_long_rep3

value: 720 minutes


title: Nexus-Pol2-Irf1-TAD


title: HD150_Weslaco(TX)_2019_S74

value: Fruit


title: ICSI_Eq_39b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H08-ICSI_Eq-39b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 1

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 1

value: male


title: Nexus-Pol2-p53-TAD


title: ICSI_Eq_39a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H07-ICSI_Eq-39a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Nexus-Pol2-NfKB-TAD


title: ICSI_Eq_38b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H06-ICSI_Eq-38b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_2880min_dox_long_rep1

value: 2880 minutes


title: mESC_Firre_Rescue_firre_induced_720min_dox_long_rep2


title: CRUSER_Weslaco(TX)_2019_S72

value: CRUSER

value: Weslaco(TX)

value: WT


title: mESC_Firre_Rescue_firre_induced_720min_dox_long_rep1


title: Nexus-Pol2-Notch-TAD

value: Haematopoetic

value: anti-RNA polymerase II Antibody clone CTD4H8


title: CRUSER_Weslaco(TX)_2019_S73


title: ICSI_Eq_38a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H05-ICSI_Eq-38a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: ICSI_Eq_37b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H04-ICSI_Eq-37b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Nexus-Pol2-EWS-TAD


title: Nexus-Pol2-Pu1-TAD


title: OC164_Weslaco(TX)_2019_S70


title: mESC_Firre_Rescue_firre_induced_0min_dox_long_rep2

value: mESC

value: embryonic stem cells

value: Firre KO / Firre inducible transgene

value: doxycycline

value: 0 minutes


title: ICSI_Eq_37a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H03-ICSI_Eq-37a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_0min_dox_long_rep3


title: Nexus-Pol2-VP64-TAD


title: D7-EF1a-screen

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
Assembly: Hg19
Supplementary files format and content: Guide Counts file

extract_protocol:
Genomic DNA was extracted using Monarch Genomic DNA purification kit
PCR was conducted to maintain guide representation, using Q5 High Fidelity DNA Polymerase

treatment_protocol: K562 cells containing Cas9 were infected with a sgRNA library. For the transcription screens, GFP negative, guide positive cells were sorted on D5, D6 and D7 after guide infection. For dropout screen, cells were grown until D14, before being isolated for sequencing.


title: ICSI_Eq_36b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H02-ICSI_Eq-36b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_0min_dox_long_rep1


title: OC164_Weslaco(TX)_2019_S69


title: mESC_Firre_Rescue_control_5760min_dox_long_rep3

value: Firre KO

value: 5760 minutes


title: D6-EF1a-screen


title: ICSI_Eq_36a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_H01-ICSI_Eq-36a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_5760min_dox_long_rep2


title: D5-EF1a-screen


title: PRIMO_Weslaco(TX)_2019_S67

value: Fruit

value: PRIMO


title: ICSI_Eq_35b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G10-ICSI_Eq-35b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_5760min_dox_long_rep1


title: PRIMO_Weslaco(TX)_2019_S66


title: ICSI_Eq_35a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G09-ICSI_Eq-35a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_2880min_dox_long_rep3

value: 2880 minutes


title: CRUSER_Weslaco(TX)_2019_S71

value: CRUSER


title: D7-EF1a-library-control


title: Nexus-Pol2-Myb-TAD


title: PRIMO_Weslaco(TX)_2019_S65

value: Weslaco(TX)


title: D6-EF1a-library-control


title: D5-EF1a-library-control


title: ICSI_Eq_34a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G07-ICSI_Eq-34a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_2880min_dox_long_rep1


title: ICSI_Eq_34b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G08-ICSI_Eq-34b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_1440min_dox_long_rep3

value: 1440 minutes


title: TH-6_Weslaco(TX)_2019_S58

value: WT


title: D7-RPL30-screen

value: Haematopoetic


title: ICSI_Eq_33b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G06-ICSI_Eq-33b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: D6-RPL30-screen


title: TH-6_Weslaco(TX)_2019_S56


title: TH-6_Weslaco(TX)_2019_S57


title: OC164_Weslaco(TX)_2019_S68


title: mESC_Firre_Rescue_control_1440min_dox_long_rep2


title: ICSI_Eq_32b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G04-ICSI_Eq-32b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: TH-5_Weslaco(TX)_2019_S55


title: D5-RPL30-screen


title: ICSI_Eq_33a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G05-ICSI_Eq-33a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D7-MYB-screen


title: mESC_Firre_Rescue_control_720min_dox_long_rep3

value: mESC

value: 720 minutes


title: mESC_Firre_Rescue_control_2880min_dox_long_rep2

value: embryonic stem cells


title: TH-5_Weslaco(TX)_2019_S53


title: D6-MYB-screen


title: ICSI_Eq_31b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G02-ICSI_Eq-31b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_720min_dox_long_rep2

value: doxycycline


title: TH-5_Weslaco(TX)_2019_S54


title: TTDV_Uvalde(TX)_2018_S52

value: TTDV

value: Uvalde(TX)


title: ICSI_Eq_32a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G03-ICSI_Eq-32a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_720min_dox_long_rep1

value: Firre KO


title: D5-MYB-screen


title: ICSI_Eq_31a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_G01-ICSI_Eq-31a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D7-HBB-screen


title: ICSI_Is_30b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F10-ICSI_Is-30b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: TTDV_Uvalde(TX)_2018_S50

value: Fruit


title: TTDV_Uvalde(TX)_2018_S51


title: D6-HBB-screen


title: mESC_Firre_Rescue_control_1440min_dox_long_rep1


title: ICSI_Is_30a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F09-ICSI_Is-30a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_0min_dox_long_rep3

value: 0 minutes


title: mESC_Firre_Rescue_control_0min_dox_long_rep2


title: D7-HSV-TK-screen


title: ICSI_Is_29b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F08-ICSI_Is-29b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D5-HBB-screen


title: mESC_Firre_Rescue_control_0min_dox_long_rep1


title: F39_Uvalde(TX)_2018_S48


title: F39_Uvalde(TX)_2018_S49


title: TTDV_Indiana(TX)_2019_S41

value: Indiana(TX)


title: ICSI_Is_28b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F06-ICSI_Is-28b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_330min_dox_short_rep2

value: Firre inducible transgene

value: 330 minutes


title: mESC_Firre_OE_firre_induced_300min_dox_short_rep2

value: 300 minutes


title: F39_Uvalde(TX)_2018_S47

value: WT


title: mESC_Firre_OE_firre_induced_330min_dox_short_rep1


title: D7-HSP1A1-screen

value: Haematopoetic


title: mESC_Firre_OE_firre_induced_300min_dox_short_rep1


title: D5-HSV-TK-screen


title: D6-HSV-TK-screen


title: ICSI_Is_28a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F05-ICSI_Is-28a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: ICSI_Is_27a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F03-ICSI_Is-27a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: TTDV_Indiana(TX)_2019_S40


title: mESC_Firre_OE_firre_induced_270min_dox_short_rep2

value: mESC

value: 270 minutes


title: TTDV_Uvalde(TX)_2019_S38


title: ICSI_Is_27b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F04-ICSI_Is-27b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: TTDV_Indiana(TX)_2019_S39


title: D7-MLP-screen


title: mESC_Firre_OE_firre_induced_270min_dox_short_rep1

value: embryonic stem cells


title: ICSI_Is_26a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F01-ICSI_Is-26a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D6-MLP-screen


title: D6-HSP1A1-screen


title: D5-HSP1A1-screen


title: ICSI_Is_29a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F07-ICSI_Is-29a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_26b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_F02-ICSI_Is-26b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: TTDV_Uvalde(TX)_2019_S37


title: ICSI_Is_25b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E10-ICSI_Is-25b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: TTDV_Uvalde(TX)_2019_S36


title: ICSI_Is_25a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E09-ICSI_Is-25a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_240min_dox_short_rep1

value: doxycycline

value: 240 minutes


title: mESC_Firre_OE_firre_induced_240min_dox_short_rep2


title: F39_Uvalde(TX)_2019_S34

value: Uvalde(TX)


title: D5-MLP-screen


title: D7-YB-TATA-screen


title: mESC_Firre_OE_firre_induced_180min_dox_short_rep2

value: 180 minutes


title: mESC_Firre_OE_firre_induced_210min_dox_short_rep2

value: 210 minutes


title: F39_Uvalde(TX)_2019_S33

value: Fruit


title: ICSI_Is_23b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E06-ICSI_Is-23b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: TTDV_North Carolina_2019_S32

value: TTDV

value: North Carolina


title: ICSI_Is_24a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E07-ICSI_Is-24a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_23a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E05-ICSI_Is-23a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D7-SCP-screen


title: mESC_Firre_OE_firre_induced_210min_dox_short_rep1

value: Firre inducible transgene


title: D6-YB-TATA-screen


title: mESC_Firre_OE_firre_induced_180min_dox_short_rep1


title: TTDV_North Carolina_2019_S31


title: D5-YB-TATA-screen


title: mESC_Firre_OE_firre_induced_150min_dox_short_rep1

value: 150 minutes


title: F39_North Carolina_2019_S29

value: WT


title: TTDV_North Carolina_2019_S30


title: F39_Uvalde(TX)_2019_S35


title: F39_North Carolina_2019_S28


title: ICSI_Is_22b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E04-ICSI_Is-22b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_120min_dox_short_rep1

value: 120 minutes


title: D6-SCP-screen

value: Haematopoetic


title: F39_North Carolina_2019_S27


title: mESC_Firre_OE_firre_induced_120min_dox_short_rep2


title: D6-CMV-screen


title: mESC_Firre_OE_firre_induced_90min_dox_short_rep2

value: 90 minutes


title: mESC_Firre_OE_firre_induced_150min_dox_short_rep2

value: mESC


title: ICSI_Is_24b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E08-ICSI_Is-24b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: ICSI_Is_21a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E01-ICSI_Is-21a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_22a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E03-ICSI_Is-22a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_21b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_E02-ICSI_Is-21b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D5-CMV-screen


title: ICSI_Is_20b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D10-ICSI_Is-20b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_20a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D09-ICSI_Is-20a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: TTDV_Georgia_2019_S26

value: Georgia


title: TTDV_Georgia_2019_S25


title: F39_Georgia_2019_S24


title: D5-SCP-screen


title: D7-CMV-screen


title: ICSI_Is_19a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D07-ICSI_Is-19a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D6-RPL30-library-control


title: F39_Georgia_2019_S22


title: ICSI_Is_18b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D06-ICSI_Is-18b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_60min_dox_short_rep1

value: embryonic stem cells

value: doxycycline

value: 60 minutes


title: mESC_Firre_OE_firre_induced_30min_dox_short_rep2

value: 30 minutes


title: mESC_Firre_OE_firre_induced_60min_dox_short_rep2


title: TTDV_California_2019_S94

value: Fruit

value: California


title: D5-RPL30-library-control


title: F39_Georgia_2019_S23


title: mESC_Firre_OE_firre_induced_0min_dox_short_rep2

value: 0 minutes


title: D5-MYB-library-control


title: mESC_Firre_OE_firre_induced_30min_dox_short_rep1

value: Firre inducible transgene


title: mESC_Firre_OE_firre_induced_90min_dox_short_rep1


title: ICSI_Is_17b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D04-ICSI_Is-17b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_0min_dox_short_rep1


title: TTDV_California_2019_S93

value: TTDV


title: TTDV_California_2019_S92

value: WT


title: D7-MYB-library-control


title: D7-RPL30-library-control


title: mESC_Firre_OE_control_330min_dox_short_rep2

value: 330 minutes


title: D6-HBB-library-control

value: Haematopoetic


title: ICSI_Is_19b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D08-ICSI_Is-19b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_17a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D03-ICSI_Is-17a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_16b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D02-ICSI_Is-16b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D7-HBB-library-control


title: F39_California_2019_S91


title: D6-MYB-library-control


title: mESC_Firre_OE_control_330min_dox_short_rep1


title: ICSI_Is_16a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D01-ICSI_Is-16a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_300min_dox_short_rep2

value: 300 minutes


title: D5-HBB-library-control


title: ICSI_Is_18a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_D05-ICSI_Is-18a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: F39_California_2019_S90


title: F39_California_2019_S89


title: ICSI_Co_15b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C10-ICSI_Co-15b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_300min_dox_short_rep1

value: mESC


title: D7-HSV-TK-library-control


title: TTDV_Arizona_2019_S87

value: Arizona


title: ICSI_Co_15a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C09-ICSI_Co-15a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: TTDV_Arizona_2019_S86


title: ICSI_Co_14b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C08-ICSI_Co-14b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D5-HSV-TK-library-control


title: D6-HSV-TK-library-control


title: D7-HSP1A1-library-control


title: mESC_Firre_OE_control_270min_dox_short_rep1

value: embryonic stem cells

value: 270 minutes


title: ICSI_Co_14a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C07-ICSI_Co-14a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_240min_dox_short_rep2

value: doxycycline

value: 240 minutes


title: D6-HSP1A1-library-control


title: ICSI_Co_13b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C06-ICSI_Co-13b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_240min_dox_short_rep1


title: F39_Arizona_2019_S84

value: Fruit


title: F39_Arizona_2019_S85


title: D5-HSP1A1-library-control


title: mESC_Firre_OE_control_210min_dox_short_rep2

value: 210 minutes


title: TTDV_Arizona_2019_S88


title: F39_Arizona_2019_S83


title: D7-MLP-library-control


title: ICSI_Co_12b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C04-ICSI_Co-12b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_210min_dox_short_rep1


title: D6-MLP-library-control


title: ICSI_Co_12a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C03-ICSI_Co-12a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_270min_dox_short_rep2


title: Infinite Gold_Weslaco(TX)_2019_S81

value: Infinite Gold

value: Weslaco(TX)


title: Infinite Gold_Weslaco(TX)_2019_S82


title: D5-MLP-library-control


title: mESC_Firre_OE_control_180min_dox_short_rep2

value: 180 minutes


title: ICSI_Co_11b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C02-ICSI_Co-11b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Co_11a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C01-ICSI_Co-11a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Infinite Gold_Weslaco(TX)_2019_S80

value: WT


title: mESC_Firre_OE_control_180min_dox_short_rep1


title: D6-YB-TATA-library-control


title: D7-YB-TATA-library-control


title: ICSI_Co_13a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_C05-ICSI_Co-13a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_150min_dox_short_rep2

value: 150 minutes


title: D5-YB-TATA-library-control

value: Haematopoetic


title: ICSI_Co_10a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B09-ICSI_Co-10a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_150min_dox_short_rep1


title: ICSI_Co_9b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B08-ICSI_Co-9b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_120min_dox_short_rep2

value: 120 minutes


title: mESC_Firre_OE_control_90min_dox_short_rep2

value: mESC

value: 90 minutes


title: mESC_Firre_OE_control_120min_dox_short_rep1


title: D7-SCP-library-control


title: D6-SCP-library-control


title: ICSI_Co_8b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B06-ICSI_Co-8b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: D5-SCP-library-control


title: D7-CMV-library-control


title: ICSI_Co_10b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B10-ICSI_Co-10b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: ICSI_Co_8a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B05-ICSI_Co-8a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_60min_dox_short_rep2

value: embryonic stem cells

value: 60 minutes


title: ICSI_Co_7a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B03-ICSI_Co-7a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Arabidopsis mutant with depleted NAA50 steady-state level, replicate 4

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of AraGene-1_0-st from Thermo Fischer Scientific. A Custom CDF Version 22 with TAIR based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis mutant with depleted NAA50 rosette leave

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Arabidopsis plants were grown for seven weeks on soil under short day conditions.

extract_protocol: The material was ground to a fine powder an mRNA was extracted with the Universal RNA Kit (Roboclon) according to the manufacturer´s instructions

treatment_protocol: Leaf material was harvested two hours after onset of light and snap frozen in liquid nitrogen.

value: leaf

tag: ecotype


title: mESC_Firre_OE_control_30min_dox_short_rep2

value: doxycycline

value: 30 minutes


title: Arabidopsis mutant with depleted NAA50 steady-state level, replicate 2


title: Arabidopsis mutant with depleted NAA50 steady-state level, replicate 3


title: Wild type control replicate 4

source_name: Arabidopsis rosette leaves from wild type


title: Wild type control replicate 3


title: ICSI_Co_7b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B04-ICSI_Co-7b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: D6-CMV-library-control


title: Arabidopsis mutant with depleted NAA50 steady-state level, replicate 1


title: mESC_Firre_OE_control_60min_dox_short_rep1


title: ASH-5

city: Oklahoma City

first: Xinxing

last: Zhang

state: Oklahoma

address: 940 Stanton L. Young Blvd, BMSB Rm538

department: Department of Cell Biology

institute: University of Oklahoma Health Sciences Center

description: FACS sorted

data_processing:
The reads were firstly concatenated into a single .fastq file for each sample.
Then, the quality of the raw reads data was checked using FastQC (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low-quality scores, over-represented sequences, inappropriate GC content).
ASH-5 (Sample_85108) was excluded for further analysis. Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics.
Briefly, reads were aligned to the reference genome including both mRNAs (Wormbase WB220/WBS235) using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
Differential gene expression (DEG) analysis was done using both Cufflinks/CuffDiff and HTseq/DESeq2
Assembly: WB220
Supplementary files format and content: excel file with DEG
Supplementary files format and content: excel file with DEG

organism: Caenorhabditis elegans

source_name: Neurons

growth_protocol: Normal C. elegans NGM plate

extract_protocol:
FACS sorted cells were extracted using Trizol LS, then RNase-Free DNase Kit, and further cleaned with RNeasy MinElute Cleanup Kit (Qiagen)
Strand-specific mRNA libraries were made using polyA-selection with a 125 nt fragment length

treatment_protocol: No-treatment

value: Neurons

value: Wild type


title: mESC_Firre_OE_control_90min_dox_short_rep1


title: D5-CMV-library-control


title: mESC_Firre_OE_control_30min_dox_short_rep1


title: ASH-4

description: FACS sorted


title: ICSI_Co_6b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B02-ICSI_Co-6b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: CRSwNP Donor 4 TCR

city: Boston

first: Patrick

last: Brennan

state: MA

address: 75 Francis St

institute: Brigham & Women's Hospital

data_processing:
Raw sequencing data was demultiplexed and aligned to the reference genome (GrCh38) and then processed according to the 10X Cell Ranger pipeline.
scRNA-seq reads were processed with Cell Ranger and quantification was performed using STAR aligner against the GRCh38 transcriptome.
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids), features.tsv: (gene ids)

source_name: Nasal Mucosa

extract_protocol:
Single cell suspensions from human nasal polyp biopsies were generated, and cells were then FACS sorted as described below. Cells were then immediately processed for scRNA-seq with the Chromium Single Cell Controller following the manufacturer’s instructions.
Single Cell 5′ kit, 10X Genomics

value: Nasal Mucosa

value: Lymphocyte


title: ICSI_Co_9a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B07-ICSI_Co-9a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: CRSwNP Donor 3 TCR


title: CRSwNP Donor 1 TCR


title: ASH-3

description: FACS sorted


title: ICSI_Co_6a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_B01-ICSI_Co-6a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_0min_dox_short_rep2

value: WT

value: 0 minutes


title: Wild type control replicate 2


title: Wild type control replicate 1


title: mESC_Firre_OE_control_0min_dox_short_rep1


title: ASH-2

description: FACS sorted


title: ICSI_Co_5a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A09-ICSI_Co-5a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_5760min_dox_long_rep3

value: Firre inducible transgene

value: 5760 minutes


title: ICSI_Co_4b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A08-ICSI_Co-4b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_5760min_dox_long_rep2

value: mESC


title: ASH-1

description: FACS sorted


title: CRSwNP Donors 4-7


title: Non-ASHControl-4

description: FACS sorted

source_name: not specified

value: not specified


title: Non-ASHControl-5

description: FACS sorted


title: mESC_Firre_OE_firre_induced_5760min_dox_long_rep1


title: CRSwNP Donor 3


title: mESC_Firre_OE_firre_induced_2880min_dox_long_rep3

value: 2880 minutes


title: Non-ASHControl-3

description: FACS sorted


title: ICSI_Co_5b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A10-ICSI_Co-5b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: ICSI_Co_3b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A06-ICSI_Co-3b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Co_4a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A07-ICSI_Co-4a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_2880min_dox_long_rep2

value: embryonic stem cells


title: Non-ASHControl-2

description: FACS sorted


title: ICSI_Co_3a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A05-ICSI_Co-3a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: CRSwNP Donor 2


title: CRSwNP Donor 2 TCR


title: ICSI_Co_2b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A04-ICSI_Co-2b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_firre_induced_2880min_dox_long_rep1


title: HUVEC, invading, replicate 2, scRNAseq

city: Bryan

first: Colette

middle: Ann

last: Abbey

state: TX

address: 8447 Riverside Pkwy

department: Medical Physiology

institute: Texas A&M Health

description:
10x Genomics
28B_28C_38B_38C.CLOUPE

data_processing:
The scRNA-Seq analyses were performed with the 10X Genomics Cell Ranger (v4.0) pipeline using the default settings.
The raw Illumina NextSeq 500 base call file outputs were demultiplexed into FASTQ files by cellranger mkfastq.
For the final analysis, libraries of non-invading and invading populations were aggregated and read depth was normalized using cellranger aggr.
Assembly: Cellranger count was used to align reads to the human genome GRCh38 and generate single-cell feature counts.
Supplementary files format and content: cloupe files with upregulated genes in the invading population of Ecs compared with the non-invading.

source_name: HUVEC

extract_protocol:
HUVEC were collected 6 hrs after seeding onto a collagen matrix and allowed to invade in the presence of S1P, VEGF and bFGF.  Total samples were processed by removing growth media and plucking gels into a M199/Collagenase (1mg/ml) buffer at 37°C for 5 min to obtain a mix containing non-invading and invading cells.   Non-invading samples were collected by removing growth media, rinsinsing with 1X Hepes-Saline +5 mM EDTA and collecting cells on the surface of the collagen (but not invading) with 0.25 %trypsin. Plates were tapped to dislodge cells and the trypsin was neutralized with an equal amoun of serum. Liberated cells were collected and wells were rinsed again with 1X Hepes-Saline +5 mM EDTA to collect remaining non-invading cells. After collection of the non-invading cells, invading cells were collected from the same gels by placing them in a M199/Collagenase (1mg/ml) buffer at 37°C for 5 minfor digestion. All samples were centrifuged at 500 x g for 5 min, supernatant was aspirated,and cell pellets were resuspended in 0.1%BSA in 1X PBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GEMs were generated with a Chromium Chip by combining barcoded gel beads, cell suspensions in a master mix, and partitioning oil. To make barcoded, full-length cDNA from poly-A-RNA, GEMs, containing single cells, were  reverse transcribed with an Ilumina TruSeq Read 1 primer, 16 nt 10X barcode, 12 nt UMI and 30 nt poly(dT) sequence. cDNA was purified, amplified and size selected before library construction. Using End Repair, A-tailing, Adaptor Ligation and PCR, libraries were generated with paired-end consructs containing the P5 and P7 Illumina primers.

value: HUVEC

value: Umbilical vein endothelial cell

value: 6 hr invsion


title: mESC_Firre_OE_firre_induced_1440min_dox_long_rep3

value: doxycycline

value: 1440 minutes


title: Non-ASHControl-1

description: FACS sorted

value: Wild type


title: ICSI_Co_2a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A03-ICSI_Co-2a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: 86-1 melon Control 24d, replicate 3

city: Urumqi

first: Bai

middle: Yu

last: jia

address: Nong Da Dong Lu No. 311, Urumqi, Xinjiang，China

country: China

institute: Xinjiang Agricultural University, College of Food Science and Pharmacy

description:
fpkm.txt
XW24P_3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cucumis_melo_L_CM3_6_1_MeloV4 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters  -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Cucumis_melo_L_CM3_6_1_MeloV4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: melon fruit(pulp)

extract_protocol:
In total, approximately 1 μg total RNA was initially used for BGISEQ-500 library construction. In general, DNase I was initially used to degrade double-stranded and single-stranded DNA contaminant in RNA samples. The mRNA molecules were then purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The cDNA thus synthesized was subjected to end-repair and 3′ adenylation. Subsequently, adaptors were ligated to the ends of these 3′ adenylated cDNA fragments. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single stranded circular DNAs were formatted as the final library for Agilent Technologies 2100 bioanalyzer validation and subsequent SE50 sequencing.
RNA libraries were prepared for sequencing using BGISEQ-500 platform

value: Control treatment


title: HUVEC, non-invading, replicate 2, scRNAseq

description:
10x Genomics
28B_28C_38B_38C.CLOUPE


title: ICSI_Co_1b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A02-ICSI_Co-1b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: 86-1 melon Control 24d, replicate 2

description:
fpkm.txt
XW24P_2


title: HUVEC, non-invading, replicate 1, scRNAseq

description:
10x Genomics
28B_28C_38B_38C.CLOUPE


title: ICSI_Co_1a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_A01-ICSI_Co-1a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: CRSwNP Donor 1

value: Nasal Mucosa

value: Lymphocyte


title: HUVEC, total, replicate 2, scRNAseq

description:
10x Genomics
28A38A.CLOUPE

value: total:non-invading and invading


title: mESC_Firre_OE_firre_induced_1440min_dox_long_rep1

value: Firre inducible transgene


title: KO_CDAHFD_3

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

data_processing:
The quality of the raw sequencing reads was evaluated using FastQC (v0.11.5)
Alignment to genome reference consortium mouse build 38 (GRCm38) was performed with the STAR (v.2.7.3a) tool
Differential gene expression and pathway analysis were performed using DESeq2 R package software41 and the Omics Playground tool (v2.8.12) platform
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was extracted from the livers of the mice after tissue disruption with the TissueRuptor (Qiagen) with the RNeasy kit (Qiagen, 75162), according to the manufacturer’s protocol
The non-directoinaly librabry protocol of Novogene was performed on site. Briefly, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The cDNA was ready for sequencing after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: liver

value: PPAR(alpha) KO

value: CDAHFD


title: 86-1 melon Control 18d, replicate 3

description:
fpkm.txt
XW18P_3


title: 86-1 melon Control 24d, replicate 1

description:
fpkm.txt
XW24P_1


title: mESC_Firre_OE_firre_induced_720min_dox_long_rep3

value: mESC

value: 720 minutes


title: HUVEC, total, replicate 1, scRNAseq

description:
10x Genomics
28A38A.CLOUPE


title: mESC_Firre_OE_firre_induced_720min_dox_long_rep2

value: embryonic stem cells


title: BRG1KD_d3NPC_K27ac

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

data_processing:
*library strategy: Cut&Tag
Paired-end reads were trimmed with cutadapt, aligned to hg19 with bowtie2, and deduplicated with picardtools. Coverage files and meta-profiles were generated with Deeptools
genome build/assembly: hg19
processed data files format and content: coverage bigwig files

source_name: H1 human embryonic stem cells

growth_protocol: ESCs were cultured as described and collected as single cell suspensions using the TrypLE Express reagent. Cells were then cultured according to the STEMCELL Technologies instructions for the STEMDiff Dual Neural Induction System for the generation of neural progenitor cells (NPC) using dual SMAD inhibition. Briefly, ESCs were plated as single cells at a density of 2.0E05cells/cm2 in STEMDiff Neural Induction Media with SMADi, and 10uM Y-27632, on Matrigel coated plates, and incubated in a 5% CO2 atmosphere at 37°C. Media was changed daily with STEMDiff Neural Induction Media with SMADi.

extract_protocol:
ESCs and NPCs were collected using TrypLE. Nuclei were isolated, fixed for 2 minutes with 0.1% Formaldehyde at room temperature, and cryopreserved prior to all Cut&Tag experiments. For each experiment, nuclei were thawed and 100,000 nuclei were used per reaction. Nuclei were bound to activated Concanavalin A beads and 0.5ug of primary antibody was bound overnight at 4C. Secondary antibody was bound for 30 minutes at room temperature, pAG-Tn5 was bound for 1 hour at room temperature, and the  tagmentation reaction was incubated at 37C for 1 hour.
Libraries were amplified with NEBNext high-fidelity PCR mix, cleaned-up with AMPure XP beads, and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory.

treatment_protocol: Doxycycline treatment for induction of shRNA expression was performed using 1ug/ml doxycycline in TeSR-E8 media for 3 days and maintained in NPC differentiation media until collection. PROTAC treatment for BRG1 degradation was performed using 0.5uM PROTAC in TeSR-E8 media for 1 day and maintained in NPC differentiation media until collection.

value: H1 human embryonic stem cells

value: Doxycycline

value: NPC differentiation media


title: 86-1 melon Control 18d, replicate 2

description:
fpkm.txt
XW18P_2


title: HUVEC, invading, replicate 1, scRNAseq

description:
10x Genomics
28B_28C_38B_38C.CLOUPE

value: HUVEC

value: Umbilical vein endothelial cell

value: 6 hr invsion


title: KO_CDAHFD_2


title: mESC_Firre_OE_firre_induced_720min_dox_long_rep1

value: doxycycline


title: KO_CHW_2

value: chow


title: KO_CDAHFD_1


title: PROTAC_d3NPC_K27ac

value: PROTAC


title: KO_CHW_1


title: mESC_Firre_OE_firre_induced_1440min_dox_long_rep2

value: 1440 minutes


title: mESC_Firre_OE_firre_induced_0min_dox_long_rep3

value: Firre inducible transgene

value: 0 minutes


title: 86-1 melon Control 12d, replicate 2

description:
fpkm.txt
XW12P_2

value: Control treatment


title: 86-1 melon Control 12d, replicate 3

description:
fpkm.txt
XW12P_3


title: mESC_Firre_OE_firre_induced_0min_dox_long_rep2


title: WT_CDAHFD_3

value: liver

value: WT

value: CDAHFD


title: 86-1 melon Control 12d, replicate 1

description:
fpkm.txt
XW12P_1


title: WT_CDAHFD_2


title: Control_ESC_K27ac

value: Untreated


title: mESC_Firre_OE_control_5760min_dox_long_rep3

value: mESC

value: embryonic stem cells

value: 5760 minutes


title: mESC_Firre_OE_control_5760min_dox_long_rep2


title: 86-1 melon Control 6d, replicate 2

description:
fpkm.txt
XW06P_2


title: WT_CDAHFD_1


title: U266, untreated, p52 ChIP, biorep3

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Reads aligned to hg38 using bwa mem and filtered for duplicates, poor quality and blacklisted regions
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

source_name: Haematopoietic and Lymphoid

growth_protocol: Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).

extract_protocol:
Cells were fixed in 1% formaldehyde for 12 minutes, swelled in 0.5% SDS buffer then lysed in 0.5% SDS + 5% Triton buffer (2:1). Genomic DNA was sheared to 100-500bp by sonication.
ChIP libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Cells were transduced with TLCV2-containing virus and selected with 0.5 µg/ml puromycin for 72H. Transduced cells were subjected to 1 µg/ml Doxycycline to induce Cas9 expression before GFP sorting.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

tag: Sex

value: Male

value: untreated

value: NFKB2 antibody (A300-BL7039; Bethyl Laboratories)


title: U266, untreated, p52 ChIP, biorep2


title: 86-1 melon Control 6d, replicate 3

description:
fpkm.txt
XW06P_3


title: 86-1 melon Control 18d, replicate 1

description:
fpkm.txt
XW18P_1


title: mESC_Firre_OE_control_5760min_dox_long_rep1

value: doxycycline


title: 86-1 melon Control 6d, replicate 1

description:
fpkm.txt
XW06P_1


title: U266, untreated, p52 ChIP, biorep1


title: Control_d3NPC_K27ac

value: H1 human embryonic stem cells

value: NPC differentiation media


title: WT_CHOW_3

value: chow


title: WT_CHOW_2


title: MM1S, untreated, p52 ChIP, biorep3

value: Female


title: WT_CHOW_4

value: liver


title: mESC_Firre_OE_firre_induced_0min_dox_long_rep1

value: Firre inducible transgene

value: 0 minutes


title: 86-1 melon Control 0d, replicate 2

description:
fpkm.txt
XW00P_2

value: Control treatment


title: WT_CHOW_1

value: WT


title: mESC_Firre_OE_control_2880min_dox_long_rep1

value: mESC

value: embryonic stem cells

value: 2880 minutes


title: 86-1 melon Control 0d, replicate 1

description:
fpkm.txt
XW00P_1


title: PROTAC_ESC_K27ac

value: PROTAC

value: Untreated


title: MM1S, untreated, p52 ChIP, biorep1

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: untreated


title: MM1S, untreated, p52 ChIP, biorep2

value: NFKB2 antibody (A300-BL7039; Bethyl Laboratories)


title: mESC_Firre_OE_control_1440min_dox_long_rep3

value: doxycycline

value: 1440 minutes


title: 86-1 melon Infection by Alternaria alternata 24d, replicate 3

description:
fpkm.txt
XA24P_3

value: Infection by Alternaria alternata


title: mESC_Firre_OE_control_1440min_dox_long_rep2


title: KMS11, untreated, p52 ChIP, biorep3

value: Female


title: KMS11, untreated, p52 ChIP, biorep2


title: 86-1 melon Control 0d, replicate 3

description:
fpkm.txt
XW00P_3


title: 86-1 melon Infection by Alternaria alternata 24d, replicate 1

description:
fpkm.txt
XA24P_1


title: mESC_Firre_OE_control_2880min_dox_long_rep2


title: 86-1 melon Infection by Alternaria alternata 18d, replicate 3

description:
fpkm.txt
XA18P_3


title: KMS11, untreated, p52 ChIP, biorep1


title: 86-1 melon Infection by Alternaria alternata 24d, replicate 2

description:
fpkm.txt
XA24P_2


title: U266, untreated, input ChIP, biorep1

value: Male

value: no antibody


title: mESC_Firre_OE_control_720min_dox_long_rep2

value: 720 minutes


title: mESC_Firre_OE_control_720min_dox_long_rep3

value: WT


title: 86-1 melon Infection by Alternaria alternata 18d, replicate 2

description:
fpkm.txt
XA18P_2


title: MM1S, untreated, input ChIP, biorep1


title: 86-1 melon Infection by Alternaria alternata 18d, replicate 1

description:
fpkm.txt
XA18P_1


title: KMS11, untreated, input ChIP, biorep1


title: 86-1 melon Infection by Alternaria alternata 12d, replicate 3

description:
fpkm.txt
XA12P_3


title: mESC_Firre_OE_control_720min_dox_long_rep1

value: mESC


title: U266, untreated, H3K27ac ChIP, biorep3

value: H3K27ac antibody (07-360; Merck)


title: Hi-TrAC_GATA3_WT_Naive_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. DIFF files for RNA-seq differential gene expression were provided. BEDPE files for Hi-TrAC or Hi-C data with high quality uniquely mapped paired-end tags (PETs) were provided.
Library strategy: Hi-TrAC

source_name: CD4+ T cells

extract_protocol:
Detailed procedures for ChIP-Seq: 1. Three plates (15-cm) of HeLa or SW-13 cells cultured in 20 ml of DMEM containing 10% FCS and antibiotics were stimulated with 500 units/ml of IFN-α for 2 hrs. 2. Add HCHO to 1% of each plate and incubate at 37°C for 10 min; Stop the crosslinking by aspirating the medium. Wash the cells twice with 10 ml of 1xPBS. 3. Aspirate the buffer (keep 0.5 ml in the plate). Harvest cells by scraping. Wash the plate once with 0.5% BSA/PBS. Combine the cells from the three plates. 4. Spin down the cells at 3000rpm, 3 min, 4oC. 5. Remove supernatant and resuspend the cells in 2.5 ml of 1 x TE + 1 mM PMSF + 1 x proteinase inhibitor cocktail. For anti-AcH3 or anti-AcH4 CHIP, add sodium butyrate to 5 mM. Sonicate 20 x 20 seconds in ice-water bath with power setting at 5 with an Ultrasonic Processor XL (HEAT System) to break chromatin to about 0.3-05 kb. 6. Adjust to RIPA buffer + 200 mM NaCl by adding 0.28 ml of 10% TX100, 28 μl of 10% Na-Deoxycholate, 28 μl of 10% SDS, 110 μl of 5M NaCl. Mix well. Incubate for 5 min on ice. Spin in a microfuge, 13K rpm, 10 min, 4oC. 7. Collect supernatant. 8. Add 4 μg of the antibodies to 40 μl of Dynabeads protein A beads. Incubate at 4°C 4- 6hrs with rotation. Wash away antibody by 1xPBS. 9. Add 500 μl of the chromatin ( sup.) to the beads+antibody. Incubate at at 4°C overnight with rotation. 10. Wash the beads twice with RIPA buffer; twice with RIPA buffer (+0.3M NaCl); twice with LiCl buffer (1xTE, 0.25M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate); and twice with 1xTE. 11. Resuspend the beads in 100 μl of 1xTE, 2.5 μl of 10% SDS, 5 μl of 10 mg/ml proteinase K, mix well, incubate at 65oC, overnight. Also treat 100 μl of the input chromatin in the same way. 12. Collect sup. Wash the beads once with 100 μl of 1xTE. Combine the supernatants. Extract 1 x with Phenol-CHCl3. 13. Precipitate DNA with 2 μl of 20mg/ml glycogen, 20 μl of 3M NaOAc pH5.2, 500 μl of ethanol. Incubate 10 min on dry ice. Spin 20 min at 4 °C in a microfuge. Remove sup, wash pellet 1 x with 70% ethanol, air dry, resuspend in 30 μl of 1 x TE. Use 3 μl for one PCR reaction. 14. The concentration of the input DNA is determined by spectrophotometer. RIPA buffer: 1X In 1X TE 0.1% SDS 0.1% Na deoxycholate 1% Triton X100.                                                                                For RNA-Seq, five thousand cells were sorted into 700μl of QIAzol Lysis Reagent (miRNAeasy Micro Kit (QIAGEN, Cat#217084). Total RNA was extracted and on-column digestion with DNase (QIAGEN, Cat#79254) was performed, followed by elution with 10μl of RNase-free water. Total RNA from 1K cells was reverse transcribed by SuperScript II (Invitrogen, Cat#18064-014) with oligo-dT and LNA-containing TSO primers in a final reaction volume of 10μl using the condition: 42°C for 90min, 10 cycles of 50°C 2min to 42°C 2min, 70°C for 15min and hold at 4°C. cDNA was pre-amplified by PCR using KAPA HiFi HotStart ReadyMix (KAPABIOSYSTEMS Cat#KK2602) with IS PCR for 12 cycles in 25μl. PCR products were purified by Ampure XP beads (Beckman Coulter, Cat#A63881) and eluted with 17.5μl Nuclease-free water as described for Smart-seq2 method (Picelli et al., 2014). PCR pre-amplified cDNA (40μl) was sonicated to 200~400bps by Bioruptor Pico (Diagenode) for 15 cycles (30″ on and 30″ off). Sonicted cDNA was blunt-ended by End-It DNA-Repair kit (Epicentre, Cat#ER81050), ligated to “Y” adaptor and PCR-amplified for 12 cycles and sequenced as described for the scDNase-seq libraries. For Hi-TrAC, cells were fixed with 1% Formaldehyde at room temperature for 10 minutes, and then incubated with the transposase complex to bridge interacting chromatin at 37 °C for 2 hours. Genomic DNA was purified after reverse cross-linking.
1. Repair DNA ends using the Epicentre DNA END-Repair kit (Cat. No. ER0720, Epicentre Biotechnologies, Tel 800-284-8474) This step generates blunt-ended DNA. 1-34 ul DNA (0.1 to 5 ug) 5 ul 10x End repair buffer (330 mM Tris-acetate, pH7.8, 660 mM potassium acetate, 100 mM magnesium acetate, 5 mM DTT) 5 ul 2.5 mM each dNTPs 5 ul 10 mM ATP x ul H2O to adjust the reaction volume to 49 ul 1 ul End-Repair Enzyme mix (T4 DNA Pol + T4 PNK) Incubate 45 min at room temperature. Purify the DNA using MinElute Reaction Cleanup Kit and protocol, eluting in 32 ul of EB. 2. Add “A” to 3’ ends 32 ul DNA from above 5 ul 10x Klenow buffer 10 ul 1 mM dATP 3 ul 5 U/ ul Klenow Exo- Incubate for 30 min at 37°C. Purify the DNA as before. Eluting in 22 ul of 1x EB. 3. Linker ligation (two mixed linkers). The oligo mix should contain 10x molar excess of the DNA templates. 23 ul DNA (300ng) 3 ul 10x T4 DNA ligase buffer 1 ul Index PE Adapter Oligo Mix (1:10 diluted) 3 ul T4 DNA ligase (400 units/ul) 2 Incubate for 30 min at room temperature. Purify the DNA as before. Eluting in 20 ul of 1x EB. 4. Size selection-2% E-Gel Load 20 ul linker ligated DNA onto a 2% E-Gel (Invitrogen). Cut the gel around 200-400 bp region (DNA will not be visible). Extract the DNA using MinElute gel extraction kit (every 900ul of QG Buffer add 400ul of 2-Propanol). Elute in 22 ul EB. (Note: (1) Dissolve gel slices at room temperature with frequent mixing, but not at elevated temperature. This helps to reserve AT-rich DNA that can be easily denatured at higher temperature and gets lost at column binding step. (2) NEVER run PCR-amplified samples of Step 7 with the linker-ligated products of Step 5 together on the same gel because the latter can be contaminated!). 5. Amplify the DNA using Solexa primers and enzyme mix (using half amount of the reagents and run a 25 ul reaction). 18 ul of DNA 20 ul of master mix 1 ul of PCR primer InPE1.0 (2x diluted) 1 ul of PCR Primer Index<#> (2x diluted) Total volume: 50 ul Denature at 98°C for 30 sec. 98°C, 10”; 65°C, 30”; 72°C, 30”. Try 18 cycles first, check 2.5 ul of product on 1.8% gel. If the band is not clearly visible, do 3 more cycles. Check again. 6. Purify the amplified products on 2.5% agarose gel. Excise the band near 220 bp and purify the DNA using QIAquick gel extraction kit. Measure the DNA concentration using Qubit fluorometer. (Note: Dissolve gel slices at room temperature with frequent mixing, but not at elevated temperature. This helps to reserve AT-rich DNA that can be easily denatured at higher temperature and gets lost at column binding step). For Hi-TrAC libraries, gaps in purified genomic DNA was repaired with T4 DNA polymerase. Genomic DNA was digested with MluCI and NlaIII restriction enzymes, and biotin labeled DNA fragments was enriched by streptavidin beads. Perform adapter ligation with T7 ligase on beads, and then run PCR to amplify and add index to libraries.

tag: strain

value: mixed C57BL/6 and 129

value: Naive CD4+ T cells

value: lymph nodes

value: GATA3 WT(CD4+CD8-CD62L+CD44-)


title: Hi-TrAC_GATA3_WT_Naive_rep3


title: Hi-TrAC_GATA3_WT_Th2_72h_rep1

value: Th2 CD4+ T cells

value: Cell culture

value: GATA3 WT(DAPI-)


title: Hi-TrAC_GATA3_KO_Th2_72h_rep2

value: GATA3 KO(DAPI-)


title: Hi-TrAC_GATA3_WT_Naive_rep4


title: Hi-TrAC_GATA3_WT_Th2_72h_rep2


title: Hi-TrAC_GATA3_KO_Th2_72h_rep1


title: Hi-TrAC_GATA3_WT_Naive_rep1


title: mESC_Firre_OE_control_0min_dox_long_rep2

value: embryonic stem cells

value: doxycycline

value: 0 minutes


title: mESC_Firre_OE_control_1440min_dox_long_rep1

value: 1440 minutes


title: 86-1 melon Infection by Alternaria alternata 12d, replicate 2

description:
fpkm.txt
XA12P_2

value: Infection by Alternaria alternata


title: U266, untreated, H3K27ac ChIP, biorep2

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: Male

value: untreated


title: Hi-TrAC_GATA3_KO_Naive_rep4

value: mixed C57BL/6 and 129

value: GATA3 KO(CD4+CD8-CD62L+CD44-)


title: 86-1 melon Infection by Alternaria alternata 12d, replicate 1

description:
fpkm.txt
XA12A_1


title: Hi-TrAC_GATA3_KO_Naive_rep3

value: Naive CD4+ T cells

value: lymph nodes


title: mESC_Firre_OE_firre_induced_150min_ATACseq

data_processing:
Quality control, read mapping, and peak calling were carried out using nf-core/atacseq v1.2.0. Reads were mapped to mm10 and the mm10 v2 blacklist from ENCODE was used.
Within the nf-core/atacseq pipeline MACS2 v2.2.7.1 (Feng et al. 2012; Zhang et al. 2008) was used to call peaks in each experiment separately.
Consensus peaks were called using the peak regions present in any single experiment. Reads within peaks were calculated using featureCounts.
Assembly: mm10
Supplementary files format and content: comma-separated text file with the consensus peak coordinates
Supplementary files format and content: comma-separated text file containing the peak counts in each Sample

extract_protocol:
Genomic DNA was isolated using the Tagment DNA Enzyme and Buffer Kit (Illumina).
ATAC-seq libraries were prepared from 25,000 cells following the Omni-ATAC protocol (Corces et al., 2017) and using the Tagment DNA Enzyme and Buffer Kit (Illumina).

value: mESC

value: Firre inducible transgene

value: 150 minutes


title: mESC_Firre_OE_control_0min_dox_long_rep1

value: WT


title: 86-1 melon Infection by Alternaria alternata 6d, replicate 3

description:
fpkm.txt
XA06P_3


title: U266, untreated, H3K27ac ChIP, biorep1

value: H3K27ac antibody (07-360; Merck)


title: Hi-TrAC_GATA3_KO_Naive_rep2


title: 86-1 melon Infection by Alternaria alternata 6d, replicate 2

description:
fpkm.txt
XA06P_2


title: MM1S, untreated, H3K27ac ChIP, biorep2

value: Female


title: mESC_Firre_OE_control_0min_dox_long_rep3

value: embryonic stem cells

value: doxycycline

value: 0 minutes


title: mESC_Firre_OE_firre_induced_90min_ATACseq

value: 90 minutes


title: mESC_Firre_OE_firre_induced_120min_ATACseq

value: 120 minutes


title: Hi-TrAC_GATA3_KO_Naive_rep1


title: MM1S, untreated, H3K27ac ChIP, biorep3

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma


title: 86-1 melon Infection by Alternaria alternata 6d, replicate 1

description:
fpkm.txt
XA06P_1

value: Infection by Alternaria alternata


title: mESC_Firre_OE_firre_induced_60min_ATACseq

value: 60 minutes


title: 86-1 melon Infection by Alternaria alternata 0d, replicate 2

description:
fpkm.txt
XA00P_2


title: RNA-seq_GATA3_WT_Th2_72h_rep1

description: RNA-seq_GATA3_WTvsKO_Th2_72h_gene_exp.diff

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. DIFF files for RNA-seq differential gene expression were provided. BEDPE files for Hi-TrAC or Hi-C data with high quality uniquely mapped paired-end tags (PETs) were provided.

value: mixed C57BL/6 and 129

value: Th2 CD4+ T cells

value: Cell culture

value: GATA3 WT(DAPI-)


title: RNA-seq_GATA3_WT_Naive_rep4

description: RNA-seq_GATA3_WTvsKO_Naive_gene_exp.diff

value: Naive CD4+ T cells

value: lymph nodes

value: GATA3 WT(CD4+CD8-CD62L+CD44-)


title: 86-1 melon Infection by Alternaria alternata 0d, replicate 3

description:
fpkm.txt
XA00P_3


title: RNA-seq_GATA3_WT_Th2_72h_rep2


title: MM1S, untreated, H3K27ac ChIP, biorep1

value: WT

value: Female

value: untreated

value: H3K27ac antibody (07-360; Merck)


title: mESC_Firre_OE_firre_induced_30min_ATACseq

value: mESC

value: embryonic stem cells

value: Firre inducible transgene

value: doxycycline

value: 30 minutes


title: KMS11, untreated, H3K27ac ChIP, biorep3

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma


title: KMS11, untreated, H3K27ac ChIP, biorep2


title: 86-1 melon Infection by Alternaria alternata 0d, replicate 1

description:
fpkm.txt
XA00P_1

value: Infection by Alternaria alternata


title: mESC_Firre_OE_firre_induced_0min_ATACseq

value: 0 minutes


title: KMS11, untreated, H3K27ac ChIP, biorep1


title: RNA-seq_GATA3_WT_Naive_rep2

value: mixed C57BL/6 and 129


title: mESC_Firre_OE_control_150min_ATACseq

value: 150 minutes


title: Jiashi melon Control 24d, replicate 3

description:
fpkm.txt
JW24P_3

value: Control treatment


title: mESC_Firre_OE_control_120min_ATACseq

value: 120 minutes


title: Jiashi melon Control 24d, replicate 2

description:
fpkm.txt
JW24P_2


title: RNA-seq_GATA3_WT_Naive_rep3

value: Naive CD4+ T cells

value: lymph nodes

value: GATA3 WT(CD4+CD8-CD62L+CD44-)


title: HUVEC_VEGF-18h_FOXO1_ChIP-seq_abcam

city: Kumamoto

first: Shunsuke

last: Kamei

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using BWA.
ChIP-seq peaks were called using MACS2 (Model-Based Analysis of ChIP-seq) with p=1X10-4.
ENCODE blacklisted regions were removed.
Assembly: hg19
Supplementary files format and content: Peak files are BED files and BigWig files for each sample.

growth_protocol: HUVECs were maintained in EGM-2 medium supplemented with 5% (v/v) fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
HUVECs were fixed with 1% formaldehyde for 10 min and neutralized with 0.2 M glycine. After cell corecting, ChIP was performed with the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer's instructions. Chromatin was sonicated using a Bioruptor UCD-300 (5 cycles; 30 sec on /30 sec off; Tosyodenki).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illimina (New England Biolabs) according to the manufacturer's instructions.

treatment_protocol: HUVECs ware starved in EBM-2 basal medium with 0.5% (v/v) fetal bovine serum for 10h, treated with 20 ng/mL human recombinant VEGF-A165 for 18h.

value: HUVEC

value: Vascular endothelial cell

value: FOXO1A (abcam, ab39670)


title: mESC_Firre_OE_control_90min_ATACseq

value: mESC

value: embryonic stem cells

value: WT

value: 90 minutes


title: HUVEC_VEGF-18h_FOXO1_ChIP-seq_CST


title: Jiashi melon Control 24d, replicate 1

description:
fpkm.txt
JW24P_1


title: HUVEC_VEGF-18h_input_ChIP-seq


title: RNA-seq_GATA3_KO_Th2_72h_rep2

value: Th2 CD4+ T cells

value: Cell culture

value: GATA3 KO(DAPI-)


title: RNA-seq_GATA3_WT_Naive_rep1

value: mixed C57BL/6 and 129


title: RNA-seq_GATA3_KO_Th2_72h_rep1


title: Jiashi melon Control 18d, replicate 2

description:
fpkm.txt
JW18P_2


title: RNA-seq_GATA3_KO_Naive_rep4

value: GATA3 KO(CD4+CD8-CD62L+CD44-)


title: mESC_Firre_OE_control_30min_ATACseq

value: doxycycline

value: 30 minutes


title: RNA-seq_GATA3_KO_Naive_rep3

value: Naive CD4+ T cells


title: Jiashi melon Control 18d, replicate 3

description:
fpkm.txt
JW18P_3

value: Control treatment


title: mESC_Firre_Rescue_firre_induced_150min_ATACseq

value: Firre KO / Firre inducible transgene

value: 150 minutes


title: Jiashi melon Control 18d, replicate 1

description:
fpkm.txt
JW18P_1


title: RNA-seq_GATA3_KO_Naive_rep2

value: lymph nodes


title: Safe NoTNF and Safe TNF

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
STARsolo was used to generate a STAR index for the human  (hg19) genome
STARsolo is used to map the reads to the STAR reference genome. R1 sample contains the sample barcode and the UMI. R2 contains the cDNA sequence.
Seurat is used to extract raw count tables from the STAR solo output folder.
DESeq2 is used to do differential analyses.
Assembly: hg19
Supplementary files format and content: Raw count matrices and sample info sheets

source_name: K562 cells

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using a plate based in-house library prep method based on DRUG-seq (Ye et al., 2018).
The method results in 3’ RNA-seq libraries containing a UMI and a well ID on read 1, and the unique transcript information on read 2. Libraries were sequenced on the NextSeq500 using the 75bp single end chemistry, run with paired-end settings. 25bps was allocated for the Read1 and 50bps for Read

treatment_protocol: Cells were infected with relevant sgRNAs for 4 days prior to harvest. TNF treatment was performed for 6hrs at 25ng/ml.

tag: condition

value: Safe

value: Day 4 after infection with relevant sgRNA


title: mESC_Firre_OE_control_2880min_dox_long_rep3

value: mESC

value: embryonic stem cells

value: 2880 minutes


title: mESC_Firre_OE_control_60min_ATACseq

value: WT

value: 60 minutes


title: Safe_p65

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with cutadapt.
K562 ChIP-seq reads were aligned to the GRCh37.73 ensembl genome assembly using BWA.
Sam files were converted into Bam files using samtools. Tdf files were generated using igvtools.
Peak calling was performed using MACS2.
Assembly: hg19
Supplementary files format and content: Bed files

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: Cells were infected with relevant sgRNAs for 4 days prior to crosslinking with 1% formaldehyde for 15mins.

value: anti-Nf-KB p65 antibody clone D14E12


title: Jiashi melon Control 12d, replicate 3

description:
fpkm.txt
JW12P_3


title: RNA-seq_GATA3_KO_Naive_rep1

value: mixed C57BL/6 and 129


title: Jiashi melon Control 12d, replicate 2

description:
fpkm.txt
JW12P_2


title: Jiashi melon Control 12d, replicate 1

description:
fpkm.txt
JW12P_1


title: Ints5__KO_TNF_RNApol2

value: anti-RNA polymerase II Antibody clone CTD4H8

value: 6hrs after TNF additon - 25ng/ml


title: Safe_TNF_RNApol2


title: mESC_Firre_Rescue_firre_induced_90min_ATACseq

value: doxycycline

value: 90 minutes


title: Ints5_KO_RNApol2


title: ChIP-seq_GATA3_WT_Th2_72h_H3K4me3_rep2

value: Th2 CD4+ T cells

value: Cell culture

value: GATA3 WT(DAPI-)


title: mESC_Firre_Rescue_firre_induced_60min_ATACseq

value: Firre KO / Firre inducible transgene


title: Jiashi melon Control 6d, replicate 3

description:
fpkm.txt
JW06P_3

value: Control treatment


title: CyclinC_KO_RNApol2

value: Day 4 after infection with relevant sgRNA


title: ChIP-seq_GATA3_WT_Th2_72h_H3K4me3_rep1


title: mESC_Firre_OE_control_0min_ATACseq

value: mESC

value: 0 minutes


title: Safe_TNF_p65


title: mESC_Firre_Rescue_firre_induced_30min_ATACseq

value: embryonic stem cells

value: 30 minutes


title: ChIP-seq_GATA3_WT_Th2_72h_H3K4me1_rep2


title: Jiashi melon Control 6d, replicate 1

description:
fpkm.txt
JW06P_1


title: ChIP-seq_GATA3_WT_Th2_72h_H3K4me1_rep1


title: mESC_Firre_Rescue_control_150min_ATACseq

value: Firre KO

value: 150 minutes


title: Med25_KO_RNApol2


title: Med24_KO_RNApol2


title: mESC_Firre_Rescue_control_120min_ATACseq

value: 120 minutes


title: ChIP-seq_GATA3_WT_Th2_72h_H3K27ac_rep2

value: mixed C57BL/6 and 129


title: ChIP-seq_GATA3_WT_Th2_72h_H3K27ac_rep1


title: mESC_Firre_Rescue_control_60min_ATACseq

value: 60 minutes


title: Jiashi melon Control 0d, replicate 1

description:
fpkm.txt
JW00P_1


title: mESC_Firre_Rescue_control_90min_ATACseq

value: doxycycline


title: Med14_KO_RNApol2

value: anti-RNA polymerase II Antibody clone CTD4H8


title: Jiashi melon Infection by Alternaria alternata 24d, replicate 3

description:
fpkm.txt
JA24P_3

value: Infection by Alternaria alternata


title: Med12_KO_RNApol2


title: Med16_KO_RNApol2


title: ChIP-seq_GATA3_WT_Naive_H3K4me3_rep1

value: Naive CD4+ T cells

value: lymph nodes

value: GATA3 WT(CD4+CD8-CD62L+CD44-)


title: Jiashi melon Infection by Alternaria alternata 24d, replicate 2

description:
fpkm.txt
JA24P_2


title: Jiashi melon Control 6d, replicate 2

description:
fpkm.txt
JW06P_2

value: Control treatment


title: mESC_Firre_Rescue_control_30min_ATACseq


title: mESC_Firre_Rescue_control_0min_ATACseq


title: Safe_RNApol2

value: Safe

value: Day 4 after infection with relevant sgRNA


title: mESC_Firre_Rescue_firre_induced_0min_ATACseq

value: mESC

value: Firre KO / Firre inducible transgene

value: 0 minutes


title: CDK8_KO_RNApol2


title: Jiashi melon Infection by Alternaria alternata 24d, replicate 1

description:
fpkm.txt
JA24P_1


title: ChIP-seq_GATA3_WT_Naive_H3K4me1_rep2


title: D14-Myb-library-control

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
Supplementary files format and content: Guide Counts file


title: iLIN28AGFP_clone A3_b_dox_6hrs

city: London

first: Jernej

last: Ule

address: 10-12 Russell sq

department: Neuromuscular Diseases

country: United Kingdom

institute: UCL Institute of Neurology

description:
iLIN28AGFP inducible overexpression, More details in the methods section listed in doi: https://doi.org/10.1101/2021.03.15.433780
A3_b_dox_6

data_processing:
To calculate mRNA T>C conversion the pipeline was enclosed in Snakemake5.3.0 (Koster and Rahmann, 2012). For analysis of mRNA 3’ end sequencing data, reads were demultiplexed with Cutadapt 1.18 prohibiting mismatches in the barcode (Martin, 2011).
Then, sequencing reads quality was assessed (-q 20), barcode trimmed (--cut 12) discarding short reads (--length 16). Poly-adenylated stretches (>4) at the 3’ end were removed up to 20 tandems without indels nor mismatches. Trimmed reads were aligned with Slamdunk map0.3.3 (Neumann et al., 2019) to reference mouse genome (mm10) using local alignment and allowing up to 100 multi-mapping reads (-n 100). Aligned reads were subject to a filtering step retaining only alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped. Reads ambiguously mapping to more than one 3’UTR were discarded (https://github.com/AmeresLab/UTRannotation).
SNPs were called using VarScan 2.4.1with default parameter and establishing 10 fold coverage cut off and a variant fraction cut off 0.8 (-c 10 -f 0.8). SNPs overlapping T> C conversions need to present at least >26 base quality Phred score. T> C conversions were counted with rolling windows and normalised by T content, coverage of each position and average per possible transcript 3’UTR. Finally, the T> C conversion quality was assessed by Slamdunk alleyoop0.3.3 (Neumann et al., 2019).
To calculate half-life, T> C conversion were background-subtracted and normalised to the chase S4U treatment. T> C conversions were fit to exponential decay non-linear function using the R minpack.lm 1.2 (Bates and Chambers, 2017). Only 3’UTR half-life that correlated to the model R2 > 0.6 in all the experimental conditions were retrained.
Genome_build: mm10
Supplementary_files_format_and_content: T>C S4U Conversions

source_name: ESC

growth_protocol: All mouse ESC lines e.g., J1 IDG3.2 and V6.5, were maintained in 1:1 Neurobasal (21103049) DMEM (11320033) medium containing N2 (17502048) and B27 (17504044) supplements, 1% Glutamax (35050), 1% nonessential amino acids (1140050), 0.1 mM 2-mercaptoethanol (31350-010) (all Thermo Fisher Scientific), 1 mM MEK inhibitor PD0325901 (1408, Axon Medchem), 3 mM GSK3 inhibitor CHIR99021 (4953/50 Tocris), and 1,000 U/ml LIF (ESGRO ESG1107, Merck), a condition named 2iLIF. Cells were passaged using Stempro-Accutase (A1110501, Thermo Fisher Scientific). Cells were grown on gelatin coated plates which were prepared by first incubating the wells 0.1% gelatin (EmbryoMax® ES-006-B, Merck) with 1% FBS (EmbryoMax® ES Cell Qualified FBS, ES-009-B, Merck) for 1 h at 37 °C followed by a rinse with PBS. To transit from naive ESC to priming ESC cells, accutased naive ESCs were seeded onto gelatine and FBS-coated plates in N2B27 medium supplemented with recombinant 20 ng ml–1activin A (338-AC-050, R&D Systems) and 12 ng ml–1 bFGF (100-18B, Peprotech) for 12 hours.

extract_protocol:
The cells were lysed directly in Qiazol (Qiagen, 79306), followed by RNA preparation using miRNeasy Micro Kit (Qiagen, 217084) according to the manufacturer’s instructions.
0.5 μg of totalRNA was used per library prepared using Lexogen QuantSeq-FWD kit (Lexogen GmbH, 0.15) according to manufacturer’s instructions.
3'end mRNAseq (QuantSeqFWD)

treatment_protocol: Thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAMseq) has been generated according to the published protocol (Ameres et al., 2017). Naïve or priming ESC were treated with 100 μM 4-thiouridine (s4U) (Sigma, T4509-25MG) for 24hours of pulse labeling. During the last 15hours of pulse labeling, fresh s4U-containing media has been exchanged every 3hours to enhance s4U incorporation in RNA species. Prior to initiation of the chase labeling with 10mM Uridine-containing (Sigma, U3750-25G) growth medium (100X excess of uridine compared to initial s4U concentrations), the media from the cells have been removed and washed twice with chase-labeling medium. The chase-labeling was initiated upon washing off pulse-labeling medium and upon indicated time-points, the media was taken off and cells were lysed directly in Qiazol (Qiagen, 79306), followed by RNA preparation.

value: mESC V6.5.

tag: developmental stage

value: naive embryonic stem cells

value: Naive ESCs were treated with 100 μM 4-thiouridine for 24hours of pulse labeling.Chase labeling was initiated for 6hour with 10mM Uridine-containing (Sigma, U3750-25G) growth medium

tag: genotype,

value: dooxycyclin treated

tag: 4su treatment hours


title: ChIP-seq_GATA3_WT_Naive_H3K4me1_rep1

value: mixed C57BL/6 and 129

tag: cell type

tag: tissue


title: Jiashi melon Infection by Alternaria alternata 18d, replicate 3

description:
fpkm.txt
JA18P_3


title: Jiashi melon Control 0d, replicate 2

description:
fpkm.txt
JW00P_2


title: Jiashi melon Control 0d, replicate 3

description:
fpkm.txt
JW00P_3


title: ChIP-seq_GATA3_WT_Naive_H3K27ac_rep2

tag: genotype