title: Icam-rep2-Truseq

description:
HBCs were isolated with antimouse CD54 (Icam1) conjugated to phycoerythrin (Biolegend).
tetO-Mex_experiment_count_matrix.txt

value: Cd54+ (Horizontal Basal Cells)


title: Pollen 42, MuActive Plant ND67-42

status: Public on May 09 2025

type: SRA

city: Athens

first: Brad

last: Nelms

state: Georgia

address: 120 East Green St

department: Genetics

country: USA

institute: University of Georgia, Athens

description:
MuSeq2 Pollen sample from MuActive plant ND67-42
Library name: P42

library_source: genomic

data_processing:
Processed file "MuSeq2 data for maize tissues.csv.gz" was generated by mapping the Mu sequencing reads to the W22 V2 genome using Bowtie2 and bam files were converted to txt files which were then imported into R. Sample txt files were filtered and combined into a large matrix, containing unique molecules detected per sample per genome location across all MuSeq2 samples in the dataset.
Processed file "'MuSeq2 data for maize tissues _ separated Left and Right transposon borders.tar'" was generated from "MuSeq2 data for maize tissues.csv.gz" by separating the molecules based on transposon border. Each row represents the chromosome, position, and direction for each molecule detected.
Assembly: W22 Version 2
Supplementary files format and content: To generate processed file "MuSeq2 data for maize tissues.csv.gz", Sequencing reads were mapped to the W22 V2 genome with Bowtie2. Reads were then converted to molecule counts using both the adapter ligation position and a unique molecular identifier (UMI) incorporated during adapter ligation. Molecule counts mapping to both sides of the transposon border were combined. The rownames in this file are listed as chromosome:position1,position2 where positions 1 and 2 are the first genomic coordinate immediately adjacent to the the left and right side of the transposon insertion (respectively).
Supplementary files format and content: Processed file "MuSeq2 data for maize tissues separated Left and Right transposon borders.tar” data was generated as an intermediate in calculating "MuSeq2 data for maize tissues.csv.gz". This contains two csv files with the molecule counts separated for left and right side of the transposon. The rownames are given as chromosome:position where the position is the genomic coordinate immediately adjacent to the transposon border.

molecule: genomic DNA

organism: Zea mays

source_name: Pollen

growth_protocol: All Mu-Active plants were first grown in vermiculite and transplanted 10-13 days after sowing to soil, where they were grown in maturity in a greenhouse. Mu-Inactive samples were grown in soil and grown for 10-13 days until the V2 stage before being harvested.

extract_protocol:
Leaf and root samples were extracted using a Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Pollen and Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution.
Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details
A universal adapter was ligated onto the sheared DNA, then DNA fragments spanning the genome-transposon junction were amplified by PCR and sequenced using the MuSeq2 protocol.

tag: tissue

value: Pollen

tag: genotype

value: W22 MuActive


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 3, lane2

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

data_processing:
.fastq.gz: sequence reads of sgRNA expression cassette integrated into RKO genome
custom amplicon-seq on the PCR product consist of sgRNA expression cassette.
the raw sequencing data were transformed into a table of the absolute amount of sgRNA read detected from each sample using MAGeCK package
differential gene expression was called from the normalized and log-transformed sgRNA counts from each sample using LIMMA package.
Assembly: custom sgRNA library
Library strategy: Amplicon-seq

organism: Homo sapiens

source_name: colorectal cancer

growth_protocol: RKO colorectal cancer cells were cultured in RPMI 1640 supplemented with 10 % FCS, 2 mM L-glutamine, 1 % Penicillin/Streptomycin, and 1x Glutamax.

extract_protocol:
gDNA from RKO was isolated using QIAGEN Blood & Cell Culture DNA Maxi Kit. PCR was performed on the purified gDNA to amplify the sgRNA expression cassette.
as previously described in Henkel, L., Rauscher, B., Schmitt, B., Winter, J., & Boutros, M. (2020). Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library. BMC biology, 18, 1-21.

treatment_protocol: After sgRNA library transduction and puromycin selection, the RKO cells were expanded for a period of time before FACS-sorted into 3 subpopulation according different level of CPY-CA/EGFP signal ratio.

value: colorectal cancer

tag: cell line

value: RKO

tag: cell type

value: adherent

value: WT

tag: phenotype

value: basal CPY-CA/EGFP signal ratio


title: Pollen 107, MuActive Plant ND58-107

description:
MuSeq2 Pollen sample from MuActive plant ND58-107
Library name: P107


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 3, lane1


title: Icam-rep1-Truseq

city: New York

first: Rachel

last: Duffié

state: NY

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

institute: Columbia University

library_source: transcriptomic

data_processing:
libraries were quality checked with fastqc, then cutadapt was used to remove adapter sequences
lirbaries were aligned with STAR with a .bam file as output
.bam files were loaded into R studio and analyzed with DESeq2
Assembly: mm10
Supplementary files format and content: TE_RNASeq_Measurements_Raw.tsv (raw and normalized counts as well as translation efficiency score): Cells from this experiment were divided - one part for ribosome profiling,   one part for RNA-Seq. The RNA-Seq is an internal control for the ribosome   profiling, and as such is all part of the same experiment. The processed   data file is intended to be easy for any user to compare translation   efficiency and RNA abundance in the same sample.

molecule: total RNA

organism: Mus musculus

source_name: Main olfactory epithelium

growth_protocol: mice had access to food and water ad libitum

extract_protocol:
RNA was extracted using TRIzol reagent, followed by standard 1-Bromo-3-chloropropane/isopropanol methods, or with a DirectZol kit from Zymo (ribosome profiling RNA control libraries)
libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara), except for TetO-Mex3a experiment samples, which were prepared with the TruSeq Stranded Total RNA (Illumina) kit

treatment_protocol: cells were isolated using papain enzymatic treatment (Worthington)

value: Main olfactory epithelium

tag: treatment


title: JL195, DSB, , biol rep 1

city: Boston

first: Kaifu

last: Chen

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: JL195 biol rep 1

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

organism: Saccharomyces cerevisiae

source_name: mutant isogenic to JKM139

extract_protocol:
All colonies on YP-galactose plates were collected, combined, and mixed vigorously. Approximately 80 μL cells were spun down for isolating genomic DNA. Standard glass beads-phenol/chloroform/isoamyl alcohol (25:24:1) method. The DNA was dissolved in water and adjusted to a concentration of 10 ng/μL. The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850)
The DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min

value: mutant isogenic to JKM139


title: YY530, DSB, , biol rep 3

description: Library name: YY530 biol rep 3


title: Pollen 106, MuActive Plant ND58-106

description:
MuSeq2 Pollen sample from MuActive plant ND58-106
Library name: P106


title: RKO cells day0 control, replicate 2, lane4

value: control


title: OMP_rep2_clonetech

description:
OMP-ires-GFP (Shykind et al 2004) marks mature OSNs with GFP
Developmental_timecourse_experiment_count_matrix.txt

value: OMP-GFP+ cells (mature OSNs)

value: OMP-ires-GFP


title: Pollen 105, MuActive Plant ND58-105

description:
MuSeq2 Pollen sample from MuActive plant ND58-105
Library name: P105


title: MuInactive Leaf 3 Technical Replicate, Plant ND59-3

description:
MuSeq2 Leaf sample Technical Replicate split after DNA shearing from MuInactive plant ND59-3
Library name: MI3T

source_name: MuInactive Leaf

value: MuInactive Leaf

value: W22 Mu-Inactive


title: OMP_rep1_clonetech


title: RKO cells day0 control, replicate 2, lane3


title: MuInactive Leaf 3, Plant ND59-3

description:
MuSeq2 Leaf sample from MuInactive plan5 ND59-3
Library name: MI3


title: YY530, DSB, , biol rep 1

description: Library name: YY530 biol rep 1


title: RKO cells day0 control, replicate 2, lane2


title: Atf5_rep1_clonetech

description:
Cells fluoresce iRFP+ when the nuclear form of Atf5 would be translated (under UPR conditions) (Shayya et al 2022). This reporter marks cells that are actively undergoing UPR. Because the iRFP does not switch off, an OMP-ires-GFP allele was bred in (Shykind et al 2004). Only iRFP+ cells (and not double positive with GFP) were used for this experiment
Developmental_timecourse_experiment_count_matrix.txt

value: Atf5 translating cells (immature OSN)

value: Atf5 iRFP-Cre; OMP-GFP


title: YY531, DSB, , biol rep 3

description: Library name: YY531 biol rep 3


title: Atf5_rep2_clonetech

description:
Cells fluoresce iRFP+ when the nuclear form of Atf5 would be translated (under UPR conditions) (Shayya et al 2022). This reporter marks cells that are actively undergoing UPR. Because the iRFP does not switch off, an OMP-GFP allele was bred in. Only iRFP+ cells (and not double positive with GFP) were used for this experiment
Developmental_timecourse_experiment_count_matrix.txt


title: Mash1-rep1-Truseq

description:
Ascl1CreERT2*/+ (Kim et al. 2011); Ai14 tdTomato*/+ (Madisen et al 2010) mice were injected with Tamoxifen between the ages of PN2 and PN4, and red cells were sorted 48 hours later
tetO-Mex_experiment_count_matrix.txt

value: Ascl1/Mash1+ (Globose Basal Cells)

value: Ascl1CreERT2; Ai14 tdTomato


title: MuInactive Leaf 2, Plant ND59-2

description:
MuSeq2 Leaf sample from MuInactive plan5 ND59-2
Library name: MI2


title: RKO cells day0 control, replicate 2, lane1


title: Ngn_rep2_clonetech

description:
Mice were bred to be heterozygous for all three alleles, Ascl1CreERT2 (Kim et al. 2011); Ngn1-GFP (Magklara et al. 2011); Ai14 tdTomato (Madisen et al 2010) then entire litters aged P2-P4 were injected with tamoxifen and sorted 48 hours after. Red cells are Ascl1+ (GBCs), yellow cells are Ascl+/Ngn1+ INPs, and green cells are Ngn+ late INP/iOSN.
Developmental_timecourse_experiment_count_matrix.txt

value: Ngn-GFP+((/Ascl1 Negative) (late Immediate Neuronal Progenitor/ immature OSN)

value: Ascl1CreERT2; Ai14 tdTomato; Ngn1-GFP

value: Tamoxifen injection when pups were P2 to P4, FAC sorted 48 hours later


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 2, lane4

value: colorectal cancer

value: RKO

value: adherent

value: low CPY-CA/EGFP signal ratio


title: YY531, DSB, , biol rep 2

description: Library name: YY531 biol rep 2

value: mutant isogenic to JKM139


title: MuInactive Leaf 1, Plant ND59-1

description:
MuSeq2 Leaf sample from MuInactive plan5 ND59-1
Library name: MI1


title: Ngn_rep1_clonetech

value: Main olfactory epithelium


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 2, lane3

value: WT


title: Ascl1_Ngn_rep2_clonetech

value: Ascl1/Ngn-GFP double positive (Immediate Neuronal Progenitor Cells)


title: YY530, DSB, , biol rep 2

description: Library name: YY530 biol rep 2


title: JL29, DSB, , biol rep 1

description: Library name: JL29 biol rep 1


title: Leaf 79, MuActive Plant ND58-79

description:
MuSeq2 Leaf sample from MuActive plant ND58-79
Library name: L79

source_name: Primary Leaf

value: Primary Leaf

value: W22 MuActive


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 2, lane2


title: Ascl1_Ngn_rep1_clonetech


title: Leaf 78, MuActive Plant ND58-78

description:
MuSeq2 Leaf sample from MuActive plant ND58-78
Library name: L78


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 2, lane1


title: Ascl1-rep2_clonetech


title: JL210, DSB, 3mM Fe 6hr, biol rep 2

description: Library name: JL210 biol rep 2

value: 3mM Fe 6hr


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 2, lane4

value: high CPY-CA/EGFP signal ratio


title: Leaf 76, MuActive Plant ND58-76

description:
MuSeq2 Leaf sample from MuActive plant ND58-76
Library name: L76


title: JL210, DSB, , biol rep 1

description: Library name: JL210 biol rep 1 exp1


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 2, lane3


title: Icam_rep2_clonetech

description:
HBCs were isolated with antimouse CD54 (Icam1) conjugated to phycoerythrin (Biolegend).
Developmental_timecourse_experiment_count_matrix.txt

value: Cd54+ (Horizontal Basal Cells)


title: JL115B, DSB, , biol rep 1

description: Library name: JL115B biol rep 1

value: mrs3 (respiration competent)


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 2, lane2


title: Leaf 75, MuActive Plant ND58-75

description:
MuSeq2 Leaf sample from MuActive plant ND58-75
Library name: L75


title: Icam_rep1_clonetech


title: JL115A, DSB, , biol rep 2

description: Library name: JL115A biol rep 2

value: mrs3 (respiration deficient)


title: Leaf 83, MuActive plant ND58-83

description:
MuSeq2 Leaf sample from MuActive plant ND58-83
Library name: L83


title: Leaf 74 Technical Replicate, MuActive Plant ND58-74

description:
MuSeq2 Leaf sample Technical Replicate, split after DNA shearing from MuActive plant ND58-74
Library name: L74T


title: YY531, DSB, , biol rep 1

description: Library name: YY531 biol rep 1


title: Riboseq-Mex3aKO_OMP_rep2

description:
RNA from ribosome footprints
Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016); OMP-ires-GFP (Shykind et al. 2004) - OMP GFP+ cells

data_processing:
libraries were quality checked with fastqc, then cutadapt was used to remove adapter sequences
lirbaries were aligned with STAR with a .bam file as output
.bam was analyzed using custom code
Assembly: mm10
Supplementary files format and content: TE_RNASeq_Measurements_Raw.tsv (raw and normalized counts as well as translation efficiency score): Cells from this experiment were divided - one part for ribosome profiling,   one part for RNA-Seq. The RNA-Seq is an internal control for the ribosome   profiling, and as such is all part of the same experiment. The processed   data file is intended to be easy for any user to compare translation   efficiency and RNA abundance in the same sample.
Library strategy: Ribo-Seq

source_name: Main olfactory epithelium (MOE)

extract_protocol:
cells were isolated using papain enzymatic treatment (Worthington), RNA was extracted using TRIzol reagent, followed by standard 1-Bromo-3-chloropropane/isopropanol methods, or with a DirectZol kit from Zymo (ribosome profiling RNA control libraries)
libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara)

value: Main olfactory epithelium (MOE)

value: OMP-GFP positive mature OSNs

value: Mex3a fl/fl; Foxg1iresCre; OMP-ires-Cre


title: JL115A, DSB, , biol rep 1

description: Library name: JL115A biol rep 1


title: Riboseq-Mex3aKO_OMP_rep1


title: Leaf 74, MuActive plant ND58-74

description:
MuSeq2 Leaf sample from MuActive plant ND58-74
Library name: L74


title: JL98, DSB, , biol rep 1

description: Library name: JL98 biol rep 1


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 2, lane3

value: colorectal cancer

value: RKO

value: basal CPY-CA/EGFP signal ratio


title: Endosperm 99, MuActive plant ND58-99

description:
MuSeq2 Endosperm chip from MuActive plant ND58-99
Library name: E99

source_name: Endosperm

value: Endosperm


title: Endosperm 85, MuActive plant ND58-85

description:
MuSeq2 Endosperm chip from MuActive plant ND58-85
Library name: E85


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 2, lane2

value: adherent


title: Riboseq-Mex3aWT_OMP_rep2

description:
RNA from ribosome footprints
Mex3a flox/flox or Mex3a flox/+  (Alvarez-Varela et al. 2022) (no Cre driver); OMP-ires-GFP (Shykind et al 2004) - OMP GFP+ cells

value: Mex3a fl/fl; OMP-ires-GFP


title: JL114, DSB, , biol rep 1

description: Library name: JL114 biol rep 1

value: mutant isogenic to JKM139


title: JL210, DSB, 3mM Fe 6hr, biol rep 1

description: Library name: JL210 biol rep 1 exp2


title: JL96, DSB, , biol rep 1

description: Library name: JL96 biol rep 1


title: Leaf 75 Technical Replicate, MuActive Plant ND58-76

description:
MuSeq2 Leaf sample Technical Replicate, split after DNA shearing from MuActive plant ND58-75
Library name: L75T

value: Primary Leaf


title: Ascl1-rep1_clonetech

value: Main olfactory epithelium

value: Ascl1/Mash1+ (Globose Basal Cells)

value: Ascl1CreERT2; Ai14 tdTomato; Ngn1-GFP

value: Tamoxifen injection when pups were P2 to P4, FAC sorted 48 hours later


title: Endosperm 83, MuActive plant ND58-83

description:
MuSeq2 Endosperm chip from MuActive plant ND58-83
Library name: E83

value: W22 MuActive


title: Riboseq-Mex3aKO_Ngn_rep2

description:
RNA from ribosome footprints
Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016) Ngn1-GFP (Magklara et al. 2011) - Ngn1 GFP+ cells

value: Ngn1-GFP+ immediate neuronal progenitors/immature olfactory sensory neurons (INP/iOSN)

value: Mex3a fl/fl; Foxg1iresCre; Ngn1-GFP


title: JL97, DSB, , biol rep 1

description: Library name: JL97 biol rep 1


title: WT_2h_B

first: Bastian

last: Linder

address: Meyerhofstraße 1

department: Genome Biology Unit

institute: European Molecular Biology Laboratory (EMBL)

data_processing:
library strategy: SLAMseq (thiol (SH)-Linked Alkylation for the Metabolic Sequencing of RNA
SLAM-Seq reads were processed using GRAND-SLAM pipeline
Assembly: hg38
Supplementary files format and content: GRAND-SLAM output

source_name: Human embryonic kidney cells

growth_protocol: HEK 293T cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37C.

extract_protocol:
Total RNA was extracted using phenol:chloroform method.
Wild-type, ELP1-KO and CTU1-KO HEK 293T cells were grown in 100 μM 4-thiouridine (Tocris) for 1h or 2h and harvested by adding 300 μl Trizol (Invitrogen) directly to the dishes. RNA was isolated, treated with iodoacetamide (Merk) and sequencing libraries generated using QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (Lexogen) according to the manufacturer’s instructions.

value: HEK 293T

value: WT

value: s4U treated


title: Endosperm 79, MuActive plant ND58-79

description:
MuSeq2 Endosperm chip from MuActive plant ND58-79
Library name: E79


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 2, lane1

value: colorectal cancer

value: RKO

value: high CPY-CA/EGFP signal ratio


title: WT_2h_A


title: Endosperm 78, MuActive plant ND58-78

description:
MuSeq2 Endosperm chip from MuActive plant ND58-78
Library name: E78

value: Endosperm


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 2, lane4

value: adherent

value: basal CPY-CA/EGFP signal ratio


title: JL117, DSB, , biol rep 1

description: Library name: JL117 biol rep 1

value: mutant isogenic to JKM139


title: Riboseq-Mex3aWT_Ngn_rep2

description:
RNA from ribosome footprints
Mex3a flox/flox or Mex3a flox/+  (Alvarez-Varela et al. 2022) (no Cre driver); Ngn1-GFP (Magklara et al. 2011) - Ngn1 GFP+ cells

value: Main olfactory epithelium (MOE)

value: Mex3a fl/fl; Ngn1-GFP


title: WT_1h_B


title: Riboseq-Mex3aKO_Ngn_rep1


title: Riboseq-Mex3aWT_Ngn_rep1

description:
RNA from ribosome footprints
Mex3a flox/flox or Mex3a flox/+  (Alvarez-Varela et al. 2022) (no Cre driver); Ngn1-GFP (Magklara et al. 2011) - Ngn1 GFP + cells


title: Riboseq-Mex3aWT_OMP_rep1

value: OMP-GFP positive mature OSNs

value: Mex3a fl/fl; OMP-ires-GFP


title: Endosperm 75, MuActive plant ND58-75

description:
MuSeq2 Endosperm chip from MuActive plant ND58-75
Library name: E75

value: W22 MuActive


title: YY527, DSB, , biol rep 2

description: Library name: YY527 biol rep 2


title: YY527, DSB, , biol rep 1

description: Library name: YY527 biol rep 1


title: Endosperm 74, MuActive plant ND58-74

description:
MuSeq2 Endosperm chip from MuActive plant ND58-74
Library name: E74

value: B73 MuKiller & W22 MuActive


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 2, lane1


title: WT_0h_B

value: Untreated


title: abh1, Cytoplasmic RNA, replicate 1

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

description: Library name: S16_5C

data_processing:
Raw read quality was diagnosed using FastQC.
Trim Galore (Babraham Bioinformatics) was used for adapter and low-quality read trimming with PHRED score < 20.
Reads were aligned to the TAIR10 genome assembly using STAR (Dobin et al 2014).
FeatureCounts (Liao et al 2014) was used for determine transcript abundance on gene-level features extracted from the TAIR10 annotation retrived from EnsemblPlants (Kersey et al 2016).
Bedtools (genomecov -bga -split -scale -5) was used to generate a bedGraph file from the BAM files. The flag -5 was included to only consider read depth at the first nucleotide of the read for GMUCT libraries. A per-million scaling factor was provided to the -scale flag, determined by 1,000,000/total fragments (total fragments = [samtools view -F 260 -c]/2).
bedGraphToBigWig (kentUtils) was used to generate bigWig files (using the .bed files) for visualizing read depth across TAIR10 features.
Assembly: TAIR10
Supplementary files format and content: .bg: bedgraph file of scaled counts (RPM) across TAIR10 genome coordinates for each sample.
Supplementary files format and content: .bigWig: files for visualizing read coverage (scaled to reads per million, RPM) in a genome browser (e.g. IGV) for each sample.
Supplementary files format and content: .counts: raw counts for gene-level featres in each sample computed by FeatureCounts
Library strategy: GMUCT

molecule: cytoplasmic RNA

organism: Arabidopsis thaliana

source_name: Early-stage flower bud

growth_protocol: Seeds were sown onto moist soil (treated overnight with diatomaceous earth), supplemented with 10 g/L Jack’s Professional 15-16-17 Peat-Lite water-soluble fertilizer (JR Peters, Allentown, PA, USA) and NemAttack (Arbico Organics, Tucson, AZ, USA), and stratified in the dark for 48 h at 4 °C. Plants were grown at 22 °C under a 16-h-light (100-150 µmol m-2 s-1)/8-h-dark photoperiod. Approximately 20-30 mg of early-stage flower buds (stages 1-1235) were harvested from 10-week old plants. Early-stage flower buds were used owing to their numerosity, ability to produce a large number of small RNAs, and being cell dense structures. Excised buds were immediately frozen in liquid nitrogen and stored at -80 °C. Biological replicates represent pooled flower buds collected from independently grown plants.

extract_protocol:
Nucleoplasmic- and cytoplasmic-enriched RNA fractions were isolated using the Cytoplasmic and Nuclear RNA Purification Kit (Norgen Biotek, Thorold, ON, CAN) following manufacturer’s instructions, including on-column DNA nuclease treatment of the nuclear RNA fraction (RNase-Free DNase I Kit, Norgen Biotek, Thorold, ON, CAN). A detailed protocol is available on Protocols.io (dx.doi.org/10.17504/protocols.io.kqdg3x2nqg25/v1).
GMUCT libraries were constructed using an adapted protocol (Willmann et al., 2014). Details are described on Protocols.io (dx.doi.org/10.17504/protocols.io.yxmvm2jjbg3p/v1).

value: Early-stage flower bud

tag: ecotype


title: JL20, DSB, , biol rep 1

description: Library name: JL20 biol rep 1


title: WT_0h_A

value: HEK 293T

value: WT


title: JL108, DSB, , biol rep 1

description: Library name: JL108 biol rep 1


title: JL95, DSB, , biol rep 1

description: Library name: JL95 biol rep 1


title: JL94, DSB, , biol rep 1

description: Library name: JL94 biol rep 1


title: abh1, Nucleoplasmic RNA, replicate 1

description: Library name: S15_5N

molecule: nuclear RNA


title: ELP1_2h_B

value: s4U treated


title: Endosperm 69, MuActive plant ND58-69

description:
MuSeq2 Endosperm chip from MuActive plant ND58-69
Library name: E69


title: ELP1_2h_A


title: JL28, DSB, , biol rep 1

description: Library name: JL28 biol rep 1


title: Endosperm 61, MuActive plant ND58-61

description:
MuSeq2 Endosperm chip from MuActive plant ND58-61
Library name: E61

value: W22 MuActive & B73 MuKiller


title: Endosperm 76, MuActive plant ND58-76

description:
MuSeq2 Endosperm chip from MuActive plant ND58-76
Library name: E76


title: WT, Cytoplasmic RNA, replicate 3

description: Library name: S12_10C


title: ELP1_1h_B


title: Endosperm 63 MuActive plant ND58-63

description:
MuSeq2 Endosperm chip from MuActive plant ND58-63
Library name: E63


title: WT, Cytoplasmic RNA, replicate 2

description: Library name: S8_4C


title: WT, Cytoplasmic RNA, replicate 1

description: Library name: S6_3C


title: WT_1h_A


title: ELP1_1h_A


title: JL36, DSB, , biol rep 1

description: Library name: JL36 biol rep 1


title: WT, Nucleoplasmic RNA, replicate 3

description: Library name: S11_10N


title: Endosperm 52, MuActive plant ND67-52

description:
MuSeq2 Endosperm chip from MuActive plant ND67-52
Library name: E52


title: YY89, DSB, , biol rep 2

description: Library name: YY89 biol rep 2


title: AAVhu37-EGFP, drug substance

city: Woburn

first: Hsin-I

last: Jen

state: Massachusetts

address: 19 presidential way

department: Analytical Development

institute: Ultragenyx

data_processing:
CCS reads with length >200 bp and average quality score of 99% were used for mapping and alignment. Reference sequences of expression cassette, residual plasmid DNA were used for mapping.
To get the size of residual plasmid DNA and residual host cell DNA, CCS reads were first mapped to expression cassette (excluding ITR sequences) by MiniMap2 and unmapped reads were extracted by Samtools and mapped to plasmid backbone sequence including AAV2 Rep, Hu37 Cap, KanR and the rest of the Ad genes from helper plasmids. The unmapped reads were then mapped to human genomic DNA sequences. Sizes of reads that mapped to different reference sequences were checked by FastQC. The reads mapped to different impurities and human genome DNA sequences were remapped to ITR sequences via MiniMap2 to quantify the percentage of reads containing ITR.
To identify the genomic loci for the impurity host cell DNA, the PacBio reads that mapped to the human genome (hg38) were annotated using Homer annotatePeak.pl. The results were then further analyzed using JMP.
For RNA-seq, Adapters and short reads (<50 bps) and read with more than 4 ‘Ns’ were removed using Flexbar FASTQ Read Trimmer. The quality and size of the reads were checked with FastQC. The processed reads were mapped to mouse genome mm10 using Bowtie2 FASTQ Read Mapping. The unmapped reads were extracted using Samtools and Bedtools. The unmapped reads were then mapped to EGFP reference genome using Bowtie2 FASTQ Read Mapper, to identify reads mapped to EGFP. Same Samtools and Bedtools commands were used to extract reads that are not mapped to either mouse genome mm10 or EGFP reference genome. The FASTQ files for the unmapped reads were then mapped to pAAV2/8 and then to pAdF6 using Bowtie2 FASTQ Read Mapper.
Assembly: hg38
Supplementary files format and content: txt - mapped bed files

organism: synthetic construct

extract_protocol:
2 weeks and 3 weeks later, mice were perfused, and liver tissues were isolated. The whole median lobe was collected. Three 3-4mm punches from the Median Lobe were collected and placed in separate cryotubes, snap frozen in liquid nitrogen, and stored in -80°C. Remains from the median lobe were placed in a cryotube, snap frozen in liquid nitrogen, and stored in -80°C.
To prepare viral DNA for long-read sequencing,100 uL of rAAV material was digested in proteinase K reaction at 55°C for 30 minutes followed by deactivation of proteinase K at 80°C for 15 minutes, and gradually dropping the temperature to 4°C to allow single stranded DNA to anneal to double stranded DNA. After this, DNA was purified by Monarch DNA and PCR Purification Kit (NEB, Cat: #T1130) following the manufacturing protocol starting mixture of one volume of sample buffer and three volumes of binding buffer.  DNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and sample purity and integrity was checked using Nanodrop and Agilent TapeStation. Following quality control, PacBio SMRTbell amplicon libraries for PacBio Sequel were constructed using SMRTbell prep kit 3.0 (PacBio, Menlo Park, CA, USA) using the manufacturer recommended protocol. Primer annealing, polymerase binding, and complex cleanup was performed using the Sequel binding kit 3.1 & cleanup beads (PacBio) and loaded onto PacBio Sequel IIe. Sequencing was performed on PacBio Sequel IIe SMRT cell with AAV Mode enabled. Sequel IIe sequencing generated subread files, as well as HiFi reads via on-board circular consensus sequencing (CCS) analysis.RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Cat: 74881). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). ERCC Ex-fold RNA reagent (Cat: 4456739) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. Samples were treated with TURBO DNase (Thermo Fisher Scientific, Cat: AM2238) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Cat: 334386), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina (NEB, Cat: E7770) by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: C56BL/6 adult male mice between 7 to 8 weeks old were used for this study. Individual doses for AAVhu37-CAG-EGFP were calculated based on individual body weights for intravenous tail vein administration. Each mice received 2.0E14 vg/kg.

value: rAAV


title: ELP1_0h_B


title: YY89, DSB, , biol rep 1

description: Library name: YY89 biol rep 1


title: ELP1_0h_A


title: WT, Nucleoplasmic RNA, replicate 2

description: Library name: S7_4N


title: JL19, DSB, Room temperature, biol rep 1

description: Library name: JL19 biol rep 1 exp9

value: Room temperature


title: WT, Nucleoplasmic RNA, replicate 1

description: Library name: S5-3N


title: CTU2_2h_B


title: Endosperm 106, MuActive plant ND58-106

description:
MuSeq2 Endosperm chip from MuActive plant ND58-106
Library name: E106

value: Endosperm


title: 5xFAD-H151-NP5

city: NanJing

first: Limin

last: Tian

address: Longmian Avenue, Jiangning District

country: China

institute: China Pharmaceutical University

description:
Library name: H5
The hippocampus in the brain, collected from brain of 5xFAD mice treated with H151-NP, rep5

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-101/fasta/mus musculus c57bl6nj/dna/) to map reads to the reference genome of mus musculus Ensembl_v101. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mus musculus Ensembl_v101
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

molecule: polyA RNA

organism: Mus

source_name: hippocampus

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Extraction of mouse hippocampus, centrifugation, extraction of supernatant

value: hippocampus


title: CTU2_2h_A


title: Endosperm 105, MuActive plant ND58-105

description:
MuSeq2 Endosperm chip from MuActive plant ND58-105
Library name: E105


title: JL19, DSB, 10mM GSH 6hr, biol rep 1

description: Library name: JL19 biol rep 1 exp7

value: mutant isogenic to JKM139

value: 10mM GSH 6hr


title: 5xFAD-H151-NP4

description:
Library name: H4
The hippocampus in the brain, collected from brain of 5xFAD mice treated with H151-NP, rep4


title: JL19, DSB, 3mM Fe 6hr, biol rep 1

description: Library name: JL19 biol rep 1 exp5

value: 3mM Fe 6hr


title: CTU2_1h_B


title: 5xFAD-H151-NP3

description:
Library name: H3
The hippocampus in the brain, collected from brain of 5xFAD mice treated with H151-NP, rep3


title: JL19, DSB, 500nM ConcA 6hr, biol rep 1

description: Library name: JL19 biol rep 1 exp4

value: 500nM ConcA 6hr


title: CTU2_1h_A


title: JL19, DSB, 500nM ConcA 4hr, biol rep 1

description: Library name: JL19 biol rep 1 exp3

value: 500nM ConcA 4hr


title: CTU2_0h_B


title: 5xFAD-H151-NP2

description:
Library name: H2
The hippocampus in the brain, collected from brain of 5xFAD mice treated with H151-NP, rep2


title: Endosperm 42, MuActive plant ND67-42

description:
MuSeq2 Endosperm chip from MuActive plant ND67-42
Library name: E42

value: W22 MuActive


title: 5xFAD-H151-NP1

description:
Library name: H1
The hippocampus in the brain, collected from brain of 5xFAD mice treated with H151-NP, rep1


title: 5xFAD-ASSIST5

description:
Library name: Z5
The hippocampus in the brain, collected from brain of 5xFAD mice treated with ASSIST, rep5

value: ASSIST


title: JL19, DSB, 500nM ConcA 2hr, biol rep 1

description: Library name: JL19 biol rep 1 exp2

value: 500nM ConcA 2hr


title: Endosperm 107, MuActive plant ND58-107

description:
MuSeq2 Endosperm chip from MuActive plant ND58-107
Library name: E107


title: JL19, DSB, DMSO 6hr, biol rep 1

description: Library name: JL19 biol rep 1 exp1

value: DMSO 6hr


title: YY528, DSB, , biol rep 2

description: Library name: YY528 biol rep 2


title: RPF_CTU2_KO_rep3

data_processing:
Ribosome profiling reads were processed by clipping the adapter sequence (CTGTAGGCACCATCAAT) and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13
Processed reads were mapped to rRNA using bowtie version 1.2.1.1
Residual reads were uniquely mapped to non-dubious ORFs (hg38) extended by 18 nt into the UTRs
Genome_build: hg38
Supplementary_files_format_and_content: A-site codon occupancy

source_name: HEK 293T_RPF_CTU2_KO

extract_protocol:
Total RNA was extracted using phenol:chloroform method.
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

value: HEK 293T

value: Human embryonic kidney cells

tag: genotype/variation

value: CTU2 KO


title: RPF_CTU2_KO_rep2


title: YY528, DSB, , biol rep 1

description: Library name: YY528 biol rep 1


title: 5xFAD-ASSIST2

description:
Library name: Z2
The hippocampus in the brain, collected from brain of 5xFAD mice treated with ASSIST, rep2


title: RPF_CTU2_KO_rep1


title: RPF_ELP1_KO_rep3

source_name: HEK 293T_RPF_ELP1_KO

value: ELP1 KO


title: JL106, DSB, , biol rep 1

description: Library name: JL106 biol rep 1


title: YY526, DSB, , biol rep 1

description: Library name: YY526 biol rep 1


title: 5xFAD-ASSIST1

description:
Library name: Z1
The hippocampus in the brain, collected from brain of 5xFAD mice treated with ASSIST, rep1


title: RPF_ELP1_KO_rep2


title: 5xFAD-Saline5

description:
Library name: A5
The hippocampus in the brain, collected from brain of 5xFAD mice treated with Saline, rep5

value: Saline


title: CTU2_0h_A

value: Untreated


title: YY211, DSB, , biol rep 2

description: Library name: YY211 biol rep 2


title: RPF_ELP1_KO_rep1


title: HCT116_IND_T8_Rep3

type: genomic

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description: T8 Timepoint Replicate 3

hyb_protocol: hybing was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

scan_protocol: scanning was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

data_processing: The raw intensity data extracted from the CEL files were normalized with quantile normalization and log transformed.

label: biotin

source_name: Colon

label_protocol: labeling was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

growth_protocol: Cells were collected as describled in the manuscript Cunningham et al.

extract_protocol: genomic DNA was extracted as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

treatment_protocol: cell were treated as described in the manuscript Cunningham et al.

value: Induced for PLK1 over-expression

tag: timepoint


title: HCT116_UNIND_T16_Rep3

description: T16 Timepoint Replicate 3

value: Uninduced


title: 5xFAD-Saline4

description:
Library name: A4
The hippocampus in the brain, collected from brain of 5xFAD mice treated with Saline, rep4

value: hippocampus


title: 5xFAD-ASSIST4

description:
Library name: Z4
The hippocampus in the brain, collected from brain of 5xFAD mice treated with ASSIST, rep4


title: RPF_WT_rep3

source_name: HEK 293T_RPF_WT

value: WT


title: HCT116_UNIND_T16_Rep2

description: T16 Timepoint Replicate 2


title: YY211, DSB, , biol rep 1

description: Library name: YY211 biol rep 1

value: mutant isogenic to JKM139


title: 5xFAD-ASSIST3

description:
Library name: Z3
The hippocampus in the brain, collected from brain of 5xFAD mice treated with ASSIST, rep3


title: HCT116_IND_T16_Rep1

description: T16 Timepoint Replicate 1


title: HCT116_IND_T16_Rep3

description: T16 Timepoint Replicate 3


title: YY390, DSB, , biol rep 1

description: Library name: YY390 biol rep 1


title: HCT116_IND_T8_Rep2

description: T8 Timepoint Replicate 2


title: HCT116_IND_T16_Rep2

description: T16 Timepoint Replicate 2


title: HCT116_IND_T8_Rep1

description: T8 Timepoint Replicate 1


title: RPF_WT_rep2


title: RPF_WT_rep1


title: 5xFAD-Saline2

description:
Library name: A2
The hippocampus in the brain, collected from brain of 5xFAD mice treated with Saline, rep2


title: YY532, DSB, , biol rep 1

description: Library name: YY532 biol rep 1 exp1

value: WT (respiration deficient)


title: YY532, DSB, , biol rep 2

description: Library name: YY532 biol rep 2


title: 5xFAD-Saline1

description:
Library name: A1
The hippocampus in the brain, collected from brain of 5xFAD mice treated with Saline, rep1


title: HCT116_UNIND_T16_Rep1

description: T16 Timepoint Replicate 1


title: HCT116_UNIND_T8_Rep2

description: T8 Timepoint Replicate 2


title: Human milk-fed infant, PBMCs, HT186

status: Public on May 08 2025

city: College Station

first: Destiny

middle: A

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

description:
Library name: HT186
10x Genomics for Chromium Fixed RNA Profiling

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.0.
Assembly: Human GRCh38-2024-A
Supplementary files format and content: tab separated value files and matrix files

source_name: Blood

extract_protocol:
Blood was collected and peripheral blood mononuclear cells (PBMCs) were isolated and cryoperserved until all samples were collected and ready for downstream processing. Samples were then thawed according to the 10X Genomics Cell Preparation for Single Cell Protocol. Cells were then fixed and prepared for downstream processing utiling the 10X Genomics Chromium Fixed RNA Profiling (Flex) Reagent Multiplex Kits.
Library prepartation and construction was performed according to the 10X Genomics Chromium Fixed RNA Profiling (Flex) Reagent Kits for Multiplexed Samples protocol.

value: Blood

value: peripheral blood mononuclear cells

value: Human milk-fed


title: Formula-fed infant, PBMCs, HT195

description:
Library name: HT195
10x Genomics for Chromium Fixed RNA Profiling

value: Formula-fed


title: Human milk-fed infant, PBMCs, HT185

description:
Library name: HT185
10x Genomics for Chromium Fixed RNA Profiling


title: Human milk-fed infant, PBMCs, HT205

description:
Library name: HT205
10x Genomics for Chromium Fixed RNA Profiling


title: Formula-fed infant, PBMCs, HT181

description:
Library name: HT181
10x Genomics for Chromium Fixed RNA Profiling


title: Formula-fed infant, PBMCs, HT180, Part2

description:
Library name: HT180-4
10x Genomics for Chromium Fixed RNA Profiling


title: 5xFAD-Saline3

description:
Library name: A3
The hippocampus in the brain, collected from brain of 5xFAD mice treated with Saline, rep3


title: Formula-fed infant, PBMCs, HT180, Part1

description:
Library name: HT180-1
10x Genomics for Chromium Fixed RNA Profiling


title: Human milk-fed infant, PBMCs, HT189

description:
Library name: HT189
10x Genomics for Chromium Fixed RNA Profiling


title: HCT116_UNIND_T8_Rep1

description: T8 Timepoint Replicate 1


title: Human milk-fed infant, PBMCs, HT201

description:
Library name: HT201
10x Genomics for Chromium Fixed RNA Profiling


title: HCT116_UNIND_T8_Rep3

description: T8 Timepoint Replicate 3


title: Human milk-fed infant, PBMCs, HT191

description:
Library name: HT191
10x Genomics for Chromium Fixed RNA Profiling


title: HCT116_T0

description: T0 Timepoint


title: Patient-Derived Xenograft, Treated with Vehicle, 3 days, replicate 6

first: Alessandro Mauro

last: Mozzarelli

state: New York

address: 450 East 29th Street, ACLS - East Tower, New York, NY 10016

department: Biochemistry and Molecular Pharmacology

institute: NYU Grossman School of Medicine

description:
Library name: PDX_V6
Column name in gene_count.xls: H2110_V6

data_processing:
Raw reads in FASTQ format were processed with fastp, calculating Q20, Q30, and GC content. High-quality clean reads were mapped to the reference genome (downloaded from the genome website) using Hisat2 v2.0.5, which improves mapping by incorporating splice junctions. Gene expression levels were quantified with featureCounts v1.5.0-p3, and FPKM values were calculated, normalizing for gene length and sequencing depth
For DESeq2 (with replicates), differential expression was analyzed using DESeq2 (v1.20.0) with a negative binomial model. P-values were adjusted via Benjamini-Hochberg (FDR ≤ 0.05), with |log2FC| ≥ 1 as the significance threshold. For edgeR (without replicates), read counts were normalized for sequencing depth using edgeR (v3.22.5) before differential analysis, applying the same FDR and log2FC thresholds.
Assembly: hg38
Supplementary files format and content: Excel

source_name: Tumor

growth_protocol: MSK-LX1033, which was derived from a RIT1 M90I NSCLC brain metastasis cells were injected, and tumors were allowed to grow to approximately 300 mm³.

extract_protocol:
Total RNA was extracted using Rneasy RNA purification extractrion kit (Qiagen)
In strand-specific libraries, dUTP replaced dTTP in second-strand synthesis. Libraries underwent end repair, adapter ligation, size selection, amplification, and purification. Quality was checked with Qubit, PCR, and Bioanalyzer.

treatment_protocol: The tumors were then treated orally for three consecutive days with RMC-7977 (10 mg/kg), RMC-4550 (30 mg/kg), and Vehicle

value: Tumor

value: Lung Adenocarcinoma

value: Vehicle


title: Patient-Derived Xenograft, Treated with Vehicle, 3 days, replicate 3

description:
Library name: PDX_V3
Column name in gene_count.xls: H2110_V3


title: Patient-Derived Xenograft, Treated with Vehicle, 3 days, replicate 4

description:
Library name: PDX_V4
Column name in gene_count.xls: H2110_V4


title: Patient-Derived Xenograft, Treated with Vehicle, 3 days, replicate 2

description:
Library name: PDX_V2
Column name in gene_count.xls: H2110_V2


title: Patient-Derived Xenograft, Treated with Vehicle, 3 days, replicate 5

description:
Library name: PDX_V5
Column name in gene_count.xls: H2110_V5


title: Patient-Derived Xenograft, Treated with RMC-4550, 3 days, replicate 4

description:
Library name: PDX_SHP2_4
Column name in gene_count.xls: H2110_SHP2_4


title: Patient-Derived Xenograft, Treated with RMC-7977, 3 days, replicate 3

description:
Library name: PDX_7977_3
Column name in gene_count.xls: H2110_7977_3


title: Patient-Derived Xenograft, Treated with RMC-7977, 3 days, replicate 2

description:
Library name: PDX_7977_2
Column name in gene_count.xls: H2110_7977_2


title: Patient-Derived Xenograft, Treated with RMC-4550, 3 days, replicate 1

description:
Library name: PDX_SHP2_1
Column name in gene_count.xls: H2110_SHP2_1


title: Patient-Derived Xenograft, Treated with RMC-7977, 3 days, replicate 1

description:
Library name: PDX_7977_1
Column name in gene_count.xls: H2110_7977_1


title: Patient-Derived Xenograft, Treated with RMC-7977, 3 days, replicate 4

description:
Library name: PDX_7977_4
Column name in gene_count.xls: H2110_7977_4


title: H2110 Xenograft, Treated with Vehicle, 3 days, replicate 6

description:
Library name: H2110_V6
Column name in gene_count.xls: H2110_V6

data_processing:
Raw reads in FASTQ format were processed with fastp, calculating Q20, Q30, and GC content. High-quality clean reads were mapped to the reference genome (downloaded from the genome website) using Hisat2 v2.0.5, which improves mapping by incorporating splice junctions. Gene expression levels were quantified with featureCounts v1.5.0-p3, and FPKM values were calculated, normalizing for gene length and sequencing depth
For DESeq2 (with replicates), differential expression was analyzed using DESeq2 (v1.20.0) with a negative binomial model. P-values were adjusted via Benjamini-Hochberg (FDR ≤ 0.05), with |log2FC| ≥ 1 as the significance threshold. For edgeR (without replicates), read counts were normalized for sequencing depth using edgeR (v3.22.5) before differential analysis, applying the same FDR and log2FC thresholds.
Assembly: hg38
Supplementary files format and content: excel

growth_protocol: Lung adenocarcinoma H2110 cells were injected, and tumors were allowed to grow to approximately 300 mm³.

treatment_protocol: The tumors were then treated orally for three consecutive days with RMC-7977 (10 mg/kg), RMC-4550 (30 mg/kg), Trametinib (0.3 mg/kg), Cobimetinib (3 mg/kg), and Vehicle.


title: H2110 Xenograft, Treated with Vehicle, 3 days, replicate 7

description:
Library name: H2110_V7
Column name in gene_count.xls: H2110_V7


title: H2110 Xenograft, Treated with Vehicle, 3 days, replicate 2

description:
Library name: H2110_V2
Column name in gene_count.xls: H2110_V2


title: H2110 Xenograft, Treated with Vehicle, 3 days, replicate 5

description:
Library name: H2110_V5
Column name in gene_count.xls: H2110_V5


title: H2110 Xenograft, Treated with Trametinib, 3 days, replicate 3

description:
Library name: H2110_T3
Column name in gene_count.xls: H2110_T3

value: Trametinib


title: H2110 Xenograft, Treated with Trametinib, 3 days, replicate 2

description:
Library name: H2110_T2
Column name in gene_count.xls: H2110_T2


title: H2110 Xenograft, Treated with Vehicle, 3 days, replicate 3

description:
Library name: H2110_V3
Column name in gene_count.xls: H2110_V3


title: H2110 Xenograft, Treated with Trametinib, 3 days, replicate 4

description:
Library name: H2110_T4
Column name in gene_count.xls: H2110_T4


title: H2110 Xenograft, Treated with Trametinib, 3 days, replicate 1

description:
Library name: H2110_T1
Column name in gene_count.xls: H2110_T1


title: Patient-Derived Xenograft, Treated with Vehicle, 3 days, replicate 1

description:
Library name: PDX_V1
Column name in gene_count.xls: H2110_V1


title: H2110 Xenograft, Treated with RMC-4550, 3 days, replicate 4

description:
Library name: H2110_SHP2_4
Column name in gene_count.xls: H2110_SHP2_4


title: Patient-Derived Xenograft, Treated with RMC-4550, 3 days, replicate 3

description:
Library name: PDX_SHP2_3
Column name in gene_count.xls: H2110_SHP2_3


title: Patient-Derived Xenograft, Treated with RMC-4550, 3 days, replicate 2

description:
Library name: PDX_SHP2_2
Column name in gene_count.xls: H2110_SHP2_2


title: H2110 Xenograft, Treated with RMC-4550, 3 days, replicate 3

description:
Library name: H2110_SHP2_3
Column name in gene_count.xls: H2110_SHP2_3


title: H2110 Xenograft, Treated with RMC-4550, 3 days, replicate 2

description:
Library name: H2110_SHP2_2
Column name in gene_count.xls: H2110_SHP2_2


title: H2110 Xenograft, Treated with RMC-4550, 3 days, replicate 1

description:
Library name: H2110_SHP2_1
Column name in gene_count.xls: H2110_SHP2_1


title: H2110 Xenograft, Treated with Cobimetinib, 3 days, replicate 3

description:
Library name: H2110_C3
Column name in gene_count.xls: H2110_C3

value: Cobimetinib


title: H2110 Xenograft, Treated with Cobimetinib, 3 days, replicate 4

description:
Library name: H2110_C4
Column name in gene_count.xls: H2110_C4


title: H2110 Xenograft, Treated with Cobimetinib, 3 days, replicate 2

description:
Library name: H2110_C2
Column name in gene_count.xls: H2110_C2


title: H2110 Xenograft, Treated with Cobimetinib, 3 days, replicate 1

description:
Library name: H2110_C1
Column name in gene_count.xls: H2110_C1


title: H2110 Xenograft, Treated with RMC-7977, 3 days, replicate 2

description:
Library name: H2110_7977_2
Column name in gene_count.xls: H2110_7977_2


title: H2110 Xenograft, Treated with RMC-7977, 3 days, replicate 4

description:
Library name: H2110_7977_4
Column name in gene_count.xls: H2110_7977_4


title: H2110 Xenograft, Treated with RMC-7977, 3 days, replicate 3

description:
Library name: H2110_7977_3
Column name in gene_count.xls: H2110_7977_3


title: A498_PladB_Rep3

city: Chapel Hill

first: Gilbert

last: Giri

state: NC

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

description: Library name: A30

data_processing:
Raw FASTQ files were first preprocessed with fastp v0.23.4 to remove any paired-end reads shorter than 150 base pairs. The remaining reads were then aligned to the human reference genome GRCh38 using STAR v2.7.11b. During alignment, we incorporated the comprehensive Gencode v47 annotation and applied the parameters --twopassMode Basic and --alignEndsType EndToEnd to optimize mapping quality. Finally, the aligned reads were analyzed with rMATS v4.3.0 (using default parameters) to quantify event-based percent spliced in (PSI) values.
Assembly: hg38
Supplementary files format and content: Gene expression raw count using RSEM

source_name: Kidney

growth_protocol: Cells were cultured in MEM supplemented with 10% FBS, penicillin and streptomycin, and incubated at 37° C with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions, with an additional in-column DNase I treatment (RNase-Free DNase Set, Qiagen). Total RNA was sent to Novogene (Sacramento, CA) for polyA selection and library preparation followed by Illumina sequencing (paired end, 150 cycles).
PolyA selection. Performed by Novogene.

treatment_protocol: Once cells reached 70–80% confluence, the medium was replaced with fresh medium containing either 0.1% DMSO or one of the following inhibitors at the indicated concentrations: Pladienolide B (100 nM), Sapanisertib (100 nM), Torin-2 (300 nM), or hSMG-1 inhibitor 11j (300 nM). After 24 hours, cells were washed with ice-cold PBS, scraped into ice-cold PBS, and centrifuged at 300 × g for 5 minutes. The supernatant was discarded, and the cell pellets were flash-frozen in a dry ice–ethanol bath before storage at –80°C until RNA extraction.

value: Kidney

value: PladB


title: H2110 Xenograft, Treated with Vehicle, 3 days, replicate 1

description:
Library name: H2110_V1
Column name in gene_count.xls: H2110_V1


title: A498_Torin 2_Rep3

description: Library name: A27


title: A498_Torin 2_Rep2

description: Library name: A26


title: A498_PladB_Rep2

description: Library name: A29


title: A498_PladB_Rep1

description: Library name: A28


title: A498_SMG1inh_Rep2

description: Library name: A23


title: A498_Torin 2_Rep1

description: Library name: A25


title: A498_Sapanisertib_Rep3

description: Library name: A21

value: Sapanisertib


title: A498_SMG1inh_Rep1

description: Library name: A22


title: A498_DMSO_Rep3

description: Library name: A18

value: DMSO


title: A498_SMG1inh_Rep3

description: Library name: A24


title: A498_Sapanisertib_Rep1

description: Library name: A19


title: A498_Sapanisertib_Rep2

description: Library name: A20


title: A704_PladB_Rep3

description: Library name: A15


title: A498_DMSO_Rep1

description: Library name: A16


title: A704_PladB_Rep2

description: Library name: A14


title: A704_PladB_Rep1

description: Library name: A13


title: A704_Torin 2_Rep3

description: Library name: A12


title: A704_Torin 2_Rep2

description: Library name: A11


title: A704_Torin 2_Rep1

description: Library name: A10


title: H2110 Xenograft, Treated with RMC-7977, 3 days, replicate 1

description:
Library name: H2110_7977_1
Column name in gene_count.xls: H2110_7977_1


title: A704_SMG1inh_Rep3

description: Library name: A9


title: A704_SMG1inh_Rep2

description: Library name: A8


title: A704_Sapanisertib_Rep2

description: Library name: A5


title: A704_Sapanisertib_Rep3

description: Library name: A6


title: A704_SMG1inh_Rep1

description: Library name: A7


title: A704_DMSO_Rep3

description: Library name: A3


title: A704_DMSO_Rep1

description: Library name: A1


title: A704_Sapanisertib_Rep1

description: Library name: A4


title: A704_DMSO_Rep2

description: Library name: A2


title: RNA-Seq, U2OS-MYC-KO, MYC-7A, Dox

city: Pittsburgh

first: Da

last: Yang

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were done by cuffdiff.
bw files were generated by STAR wig output.
Assembly: hg38
Supplementary files format and content: bw files showing the read distribution across the genome.

growth_protocol: U2OS-MYC-KO-MYC-Tet-On cells at low passage numbers (< 5) were maintained in McCoy's 5a Medium Modified supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen). 10 µg total RNA was treated with RNase-free DNase I (Promega) for 30 min at 37 °C and RNA cleanup was performed using the RNA Clean & Concentrator-5 columns (Zymo). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) following manufacturer's protocols.

treatment_protocol: Cells at exponential phase were treated with 1 µg/ml dox for 24 h and cells without Dox (with PBS treatment) as controls.

value: 1 ug/mL Dox, 24 h


title: RNA-Seq, U2OS-MYC-KO, MYC-3A, noDox

value: PBS, 24 h


title: RNA-Seq, U2OS-MYC-KO, MYC-7A, noDox


title: RNA-Seq, U2OS-MYC-KO, MYC-WT, Dox


title: RNA-Seq, U2OS-MYC-KO, MYC-3A, Dox


title: RNA-Seq, U2OS-MYC-KO, MYC-WT, noDox


title: A498_DMSO_Rep2

description: Library name: A17

value: WT


title: ChIP-Rx, U2OS-MYC-KO, MYC-7A, Dox, MAX, IP, rep2

data_processing:
The adapters were trimmed using Cutadapt with “--match-read-wildcards --trim-n -O 1 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” parameters. Since the library contains reads from both human and mouse samples, we first generated a “genome” concatenated by human (hg19) and mouse (mm10) genome. To distinguish the chromosome names, we added a suffix “__mm10” to all mouse chromosome names. A custom Bowtie2 library was built based on this combined genome sequence using “bowtie2-build” command. Reads were first mapped using bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 800”.
The SAM files were converted to BAM files using samtools. Read pairs with XS tag and MAPQ score >= 30 were retained using samtools. Duplicates were removed using Picard MarkDuplicates. Then the reads were split to two files such that hg38 reads were stored in one file and mm10 reads were stored in the other one. All suffix “__mm10” were removed for the mm10 SAM file. Alignment files were then parsed and converted in a bed format using MACS2 “filterdup” command with “--keep-dup -f BAMPE” parameters.
Next, the peaks were called by MACS2 with “--keep-dup all -f BEDPE” parameters using the similar steps with eCLIP-Seq. Final peaks overlapped with “blacklist” regions were removed.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using MACS2 “pileup” command with “-f BEDPE” parameters. Then the counts in the bedgraph were RRPM (reference-adjusted reads per million) normalized using MACS2 “bdgopt” command. Next, the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.

growth_protocol: U2OS cells were maintained in McCoy's 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37°C. Mouse embryonic fibroblast cell line NIH/3T3 was maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS, 1% MEM non-essential amino acids (Gibco), 10 mM HEPES (Gibco), and 1% penicillin/streptomycin.

extract_protocol:
After reverse cross-linking, RNase A, and proteinase K treatment on MYC-DNA adducts enriched with anti-FLAG antibodies, DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 cycles on the thermocycler. Post-amplification libraries were size selected at 200 - 500 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the 1× dsDNA High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Both NIH3T3 cells at exponential growth phase and U2OS cells induced for 24 h with 1 µg/mL of doxycycline (Dox) or without Dox treatment were fixed with 1% formaldehyde for 10 min. After quenching by glycine, 10% of NIH3T3 cells were  mixed with U2OS cells, mixed chromatin were sheared to a size of 200 - 500 bp using a Bioruptor Pico (Diagenode) and incubated for overnight with an anti-FLAG (Sigma, F3165) antibody at 4°C.

tag: chip antibody

value: MAX (Novus, NBP1-49963)


title: ChIP-Rx, U2OS-MYC-KO, MYC-7A, Dox, MAX, IP, rep1


title: ChIP-Rx, U2OS-MYC-KO, MYC-3A, Dox, MAX, IP, rep2


title: ChIP-Rx, U2OS-MYC-KO, MYC-7A, no Dox, MAX, IP, rep1


title: ChIP-Rx, U2OS-MYC-KO, MYC-3A, Dox, MAX, IP, rep1


title: ChIP-Rx, U2OS-MYC-KO, MYC-3A, no Dox, MAX, IP, rep2


title: ChIP-Rx, U2OS-MYC-KO, MYC-7A, no Dox, MAX, IP, rep2


title: ChIP-Rx, U2OS-MYC-KO, MYC-3A, no Dox, MAX, IP, rep1


title: ChIP-Rx, U2OS-MYC-KO, MYC-WT, Dox, MAX, IP, rep2


title: ChIP-Rx, U2OS-MYC-KO, MYC-WT, no Dox, MAX, IP, rep2


title: ChIP-Rx, U2OS-MYC-KO, MYC-WT, Dox, MAX, IP, rep1

value: 1 ug/ml Dox, 24 h


title: ChIP-Rx, U2OS-MYC-KO, MYC-WT, no Dox, MAX, IP, rep1


title: ChIP-Rx, U2OS-MYC-KO, MYC-7A, no Dox, input


title: ChIP-Rx, U2OS-MYC-KO, MYC-3A, Dox, input


title: ChIP-Rx, U2OS-MYC-KO, MYC-7A, Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-7A, Dox, IP rep2

data_processing:
Briefly, we followed CLIP Tool Kit (CTK) pipeline for most of the data processing steps and used MACS2 to do peak calling.
eCLIP-Seq data were first demultiplexed using fastx_barcode_splitter.pl from fastx-toolkit, with default parameters, yielding two IP replicates and one input sample. The adapters were trimmed using Cutadapt with “--match-read-wildcards --times 1 --quality-cutoff 5 -O 1 -m 15 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTA -a ATTGCTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a ACAAGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a AACTTGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a AGGACCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG ” parameters and the low-quality reads were dropped.
Then, the analysis was mainly based on CTK pipeline. Briefly, the exact PCR duplicates were collapsed using fastq2collapse.pl with default parameters. The 10-nt random-mers were removed from read 2 and stored in the read ID for further analysis, using stripBarcode.pl with default parameters. The processed read 2 sequences were mapped to the hg38 genome using bwa, with parameters “-t 4 -n 0.06 -q 20”. Only uniquely mapped reads were kept for further analysis. Tags from rRNA and repetitive RNA were removed using tagoverlap.pl with recommended parameters. Then, based on the random-mers, the PCR duplicates were collapsed using tag2collpase.pl with recommended parameters. For each replicate, we separated the reads into plus and minus strand.
Next, we used MACS2 to do peak calling by the following steps. (1) For each replicate, we first call peaks in IP to identify the potential RNA binding sites with “--keep-dup all --nomodel -s $tagsize --extsize 100 --max-gap 50 -q 1e-2” parameters. Since the length eCLIP-Seq reads various a lot after adapter trimming, the average “tagsize” was calculated by an ad hoc script. These peaks are considered as “IP-only” peaks. (2) To identify MYC-specific binding peaks, we called peak by comparing IP versus input with the same parameters. These peaks are considered as “enriched” peaks. (3) “IP-only” peaks that are overlapped with the “enriched” peaks are considered as MYC-specific binding sites (enriched in IP). (4) Then the overlapped MYC-specific binding sites from the two replicates were considered as the reproducible MYC-specific binding sites. (5) To make downstream analysis simple and get a uniform peak list for each cell line, replicates of IP were merged and then used to call peaks by comparing the merged IP with input using the same parameters. The peaks that overlap with the reproducible MYC-specific binding sites will be considered as the final peak list and used for following analysis. Finally, for each sample, peaks from plus and minus strands were merged as the MYC eCLIP-Seq peaks for each sample. Here, the non-Dox-treated IP samples of WT, 3A, and 7A are merged and considered as 'input' when do peak calling.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using CTK “tag2profile.pl” with “-ss -exact --normalize multiply==$factor -of bedgraph” in which factor indicates the counts per million (CPM) normalization factor. The bedgraph files with original counts were also generated, in which the 'nTtotal' in the file name indicates the total read numbers. Then the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.
Library strategy: eCLIP-Seq

growth_protocol: U2OS cells were maintained in McCoy's 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Protein-associated RNAs by eCLIP and input RNAs were extracted using acid phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6) (Invitrogen) and RNA cleanup was performed with RNA Clean & Concentrator-5 columns (Zymo). After reverse transcription, qPCR was performed to the Ct value of the cDNA with Power SYBR Green Master Mix (Applied Biosystems).
eCLIP-seq libraries were prepared with primers containing Illumina adapter sequences using Q5 High-Fidelity 2× Master Mix (NEB) for 9 to 18 cycles and PCR products were purified with Agencourt AMPureXP beads (Beckman Coulter). After separating on a 3% Nusieve GTG agarose gel (Lonza), DNA ranging from 175 - 300 bp gel fragments was excised and extracted using the MinElute Gel Extraction Kit (Qiagen) and libraries were validated using the 1× High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: U2OS cells at the exponential phase were induced for 24 h with 1 µg/mL of doxycycline (Dox) or PBS, and washed twice with ice-cold PBS, UV-crosslinked on ice with 254 nm at 400 mJ/cm2 with a UV crosslinker (XL-1000, Spectrolinker). For each reaction, 20 million cells were lysed in eCLIP lysis buffer for 15 min on ice and incubated at 37°C for 5 min with RNase I (Ambion) and Turbo DNase (Ambion) on a ThermoMixer C (Eppendorf).

tag: eclip antibody

value: FLAG (Sigma, #F3165)


title: ChIP-Rx, U2OS-MYC-KO, MYC-WT, no Dox, input


title: ChIP-Rx, U2OS-MYC-KO, MYC-3A, no Dox, input


title: ChIP-Rx, U2OS-MYC-KO, MYC-WT, Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-7A, Dox, IP rep1


title: eCLIP, U2OS-MYC-KO, MYC-7A, no Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-7A, no Dox, IP rep2


title: eCLIP, U2OS-MYC-KO, MYC-3A, Dox, IP rep2


title: eCLIP, U2OS-MYC-KO, MYC-3A, Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-7A, Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-7A, no Dox, IP rep1


title: eCLIP, U2OS-MYC-KO, MYC-3A, no Dox, IP rep2


title: eCLIP, U2OS-MYC-KO, MYC-3A, Dox, IP rep1


title: eCLIP, U2OS-MYC-KO, MYC-3A, no Dox, IP rep1


title: eCLIP, U2OS-MYC-KO, MYC-WT, Dox, IP rep1


title: eCLIP, U2OS-MYC-KO, MYC-WT, no Dox, IP rep1


title: eCLIP, U2OS-MYC-KO, MYC-WT, Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-3A, no Dox, input


title: eCLIP, U2OS-MYC-KO, MYC-WT, no Dox, IP rep2


title: eCLIP, U2OS-MYC-KO, MYC-WT, no Dox, input


title: Si NPs_3

city: Xianyang

first: Meng

last: Li

address: No. 3 Taicheng Road, Yangling District

institute: Northwest A&F University

description: Library name: sample 18

data_processing:
Firstly, Cutadapt were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with FDR < 0.05) by R package edgeR.
Supplementary files format and content: gene_expression.xlsx

organism: Lolium arundinaceum

source_name: leaf

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

value: leaf

value: well-watered + 300 mg/L silicon nanoparticles


title: eCLIP, U2OS-MYC-KO, MYC-WT, Dox, IP rep2


title: Si NPs_2

description: Library name: sample 17


title: DS_Si NPs_3

description: Library name: sample 15

value: drought Stress + 300 mg/L silicon nanoparticles


title: Si NPs_1

description: Library name: sample 16


title: DS_CNCs_1

description: Library name: sample 10

value: drought Stress + 100 mg/L cellulose nanocrystals


title: DS_Si NPs_2

description: Library name: sample 14


title: DS_Si NPs_1

description: Library name: sample 13


title: DS_CNCs_2

description: Library name: sample 11


title: DS_1

description: Library name: sample 7

value: drought Stress


title: DS_2

description: Library name: sample 8


title: DS_CNCs_3

description: Library name: sample 12


title: CNCs_2

description: Library name: sample 5

value: well-watered + 100 mg/L cellulose nanocrystals


title: DS_3

description: Library name: sample 9


title: CNCs_3

description: Library name: sample 6


title: CNCs_1

description: Library name: sample 4


title: CK_3

description: Library name: sample 3

value: Control, Well-watered


title: CK_2

description: Library name: sample 2


title: HltfdTAG_Rep2_DMSO_TTseq

first: Sarah

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

description:
Library name: HltfdTAG_Rep2_DMSO_TTseq
4sU-labelled RNA

data_processing:
Barcode adapter sequences removed using cutadapt and trimmed using trimmomatic
Reads mapped to mm10 genome using STAR, with options options --outSAMtype SAM, --outFilterMismatchNoverReadLmax 0.02, and --outFilterMultimapNmax 1, and quality filtered using samtools view with options -q 7, -f 2, -bS.
Counts were generated using featureCounts, with options -B -t "exon" -g "gene_name" -F GTF -p -s 2 for Gencode mouse V23 features
In R/Bioconductor environment, raw count matrices were corrected for batch effects using Combat-seq and differiential expression analysis was performed using DEseq2 for all replicates of each condition
Aligned reads were processed to generate strand specific bigwigs using deeptools bamCoverage with binsize 1 and DEseq2-derived scaling factors
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Excel file containing all DEseq2 results for each condition for TTseq
Supplementary files format and content: tab-delimited matrix of raw TTseq counts for each sample for all features
Supplementary files format and content: tab-delimited matrix of Combatseq corrected raw TTseq counts for each sample for all features
Supplementary files format and content: tab-delimited table containing information for Combatseq batch corrected for TT-seq data
Supplementary files format and content: bed file for all non-coding features in this study

growth_protocol: ES-E14TG2a (E14) embryonic stem cells from male Mus musculus origin were grown at 37°C and 5% CO2 in DMEM base medium (Sigma) supplemented with 10% FBS (Sigma, 18N103), 1X nonessential amino acids (Corning), 2mM L-glutamine (Corning), β-mercaptoethanol (Acros Organics), and LIF on 10-cm plates precoated with 0.2% gelatin. Cells were passaged every ~48 h using trypsin (Corning) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma TC hood cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened to confirm no mycoplasma presence.

extract_protocol:
RNA was extracted with TRIzol
nascent RNA was rRNA depleted using antisense oligos, purified. Nascent RNA-seq libraries were built using the NEBNext Ultra II RNA Library Prep kit according according to the manufacturer's modifications, but with modifications to account for higher volume input.

treatment_protocol: After 48 hours of growth to confluency, reverse transfections were performed using 3500-5000 ng of either target or control (GFP) esiRNAs, 25 µL of Lipofectamine 3000 (Invitrogen), and 2 mL of OptiMEM media (Gibco), incubated for 15-30 min at room temperature (RT). During this incubation, ES cells were counted and diluted to 350,000 cells/mL in ES cell media. After incubation, the transfection reaction was added to 4 mL diluted cell suspension and transferred to a pre-gelatinized 10 cm plate. After 16-18 h, the media was replaced with 6 mL fresh ES cell media. Cells were treated with 4sU and harvested 48 h post-transfection.

value: embryonic stem cells

value: wild-type

value: HltfdTAG 3hr DMSO


title: HltfdTAG_Rep2_dTAG_TTseq

description:
Library name: HltfdTAG_Rep2_dTAG_TTseq
4sU-labelled RNA

value: HltfdTAG 3hr dTAG


title: Chd8dTAG_Clone1_dTAG_TTseq

description:
Library name: Chd8dTAG_Clone1_dTAG_TTseq
4sU-labelled RNA

value: Chd8dTAG 3hr dTAG


title: Chd8dTAG_Clone1_DMSO_TTseq

description:
Library name: Chd8dTAG_Clone1_DMSO_TTseq
4sU-labelled RNA

value: Chd8dTAG 3hr DMSO


title: Chd4dTAG_Clone1_DMSO_TTseq

description:
Library name: Chd4dTAG_Clone1_DMSO_TTseq
4sU-labelled RNA

value: Chd4dTAG 3hr DMSO


title: Chd4dTAG_Clone2_dTAG_TTseq

description:
Library name: Chd4dTAG_Clone2_dTAG_TTseq
4sU-labelled RNA

value: Chd4dTAG 3hr dTAG


title: HltfdTAG_Rep1_dTAG_TTseq

description:
Library name: HltfdTAG_Rep1_dTAG_TTseq
4sU-labelled RNA


title: Chd8dTAG_Clone2_DMSO_TTseq

description:
Library name: Chd8dTAG_Clone2_DMSO_TTseq
4sU-labelled RNA


title: Chd4dTAG_Clone1_dTAG_TTseq

description:
Library name: Chd4dTAG_Clone1_dTAG_TTseq
4sU-labelled RNA


title: Chd8dTAG_Clone2_dTAG_TTseq

description:
Library name: Chd8dTAG_Clone2_dTAG_TTseq
4sU-labelled RNA


title: HltfdTAG_Rep1_DMSO_TTseq

description:
Library name: HltfdTAG_Rep1_DMSO_TTseq
4sU-labelled RNA


title: Smarca5KD_Rep3_TTseq

description:
Library name: Smarca5KD_Rep3_TTseq
4sU-labelled RNA

value: Smarca5 knockdown for 48 hours


title: SrcapKD_Rep3_TTseq

description:
Library name: SrcapKD_Rep3_TTseq
4sU-labelled RNA

value: Srcap knockdown for 48 hours


title: Smarcal1KD_Rep3_TTseq

description:
Library name: Smarcal1KD_Rep3_TTseq
4sU-labelled RNA

value: Smarcal1 knockdown for 48 hours


title: Chd4dTAG_Clone2_DMSO_TTseq

description:
Library name: Chd4dTAG_Clone2_DMSO_TTseq
4sU-labelled RNA


title: Smarca4KD_Rep3_TTseq

description:
Library name: Smarca4KD_Rep3_TTseq
4sU-labelled RNA

value: Smarca4 knockdown for 48 hours


title: Smarca2KD_Rep3_TTseq

description:
Library name: Smarca2KD_Rep3_TTseq
4sU-labelled RNA

value: Smarca2 knockdown for 48 hours


title: Chd8KD_Rep3_TTseq

description:
Library name: Chd8KD_Rep3_TTseq
4sU-labelled RNA

value: Chd8 knockdown for 48 hours


title: Chd9KD_Rep3_TTseq

description:
Library name: Chd9KD_Rep3_TTseq
4sU-labelled RNA

value: Chd9 knockdown for 48 hours


title: Ino80KD_Rep3_TTseq

description:
Library name: Ino80KD_Rep3_TTseq
4sU-labelled RNA

value: Ino80 knockdown for 48 hours


title: Smarcal1KD_CandR_Smarcal1

description: Library name: Smarcal1KD_CandR_Smarcal1

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads were divided into size classes: 1-120 for DNA binding proteins or 130-500 for histone variants or histone modifications
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol: After treatment, nuclei were extracted as outlined in CUT&RUN. Nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by Ca** addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

treatment_protocol: For cross linked WT cells: cells were washed with 1X PBS, typsinized, counted, and 1 million cells were collected in 1.5 mL microfuge tubes and placed on ice. Cells were centrifuged at 600 rcf at 4°C for 5 min, and the supernatant was removed without disturbing the pellet. The cell pellet was resuspended gently in 1 mL ESC media + 0.1% formaldehyde, inverted 3 times, and crosslinked for 5 min at RT. The reaction was then quenched with 100 uL of 2.5M glycine. For RNAi treated cells: after 48 hours of growth to confluency, reverse transfections were performed using 3500-5000 ng of either target or control (GFP) esiRNAs, 25 µL of Lipofectamine 3000 (Invitrogen), and 2 mL of OptiMEM media (Gibco), incubated for 15-30 min at room temperature (RT). During this incubation, ES cells were counted and diluted to 350,000 cells/mL in ES cell media. After incubation, the transfection reaction was added to 4 mL diluted cell suspension and transferred to a pre-gelatinized 10 cm plate. After 16-18 h, the media was replaced with 6 mL fresh ES cell media. Nuclei were harvested 48 h post-transfection.

value: Control knockdown for 48 hours

tag: antibody


title: Rad54bKD_Rep3_TTseq

description:
Library name: Rad54bKD_Rep3_TTseq
4sU-labelled RNA

value: embryonic stem cells

value: Rad54b knockdown for 48 hours


title: CK_1

description: Library name: sample 1

value: leaf

value: Control, Well-watered


title: Chd8KD_CandR_Chd8

description: Library name: Chd8KD_CandR_Chd8

value: wild-type


title: SRCAPKD_CandR_SRCAP

description: Library name: SRCAPKD_CandR_SRCAP

value: SRCAP


title: RNASEQ_Cro_E2C_2

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

description: Library name: RNASEQ_Cro_E2C_2

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file includes FPKM values for each sample

source_name: embryo

extract_protocol:
5-10 early embryos per group were collected in tubes with lysis component and ribonuclease inhibitor.
We carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2KB. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip GX Touch and Step OnePlus Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.

value: embryo

value: WT

value: sodium crotonate


title: RNASEQ_Cro_E2C_1

description: Library name: RNASEQ_Cro_E2C_1


title: RNASEQ_Ace_E2C_2

description: Library name: RNASEQ_Ace_E2C_2

value: sodium acetate


title: RNASEQ_Ace_E2C_1

description: Library name: RNASEQ_Ace_E2C_1


title: ControlKD_CandR_Chd8

description: Library name: ControlKD_CandR_Chd8


title: RNASEQ_Con_E2C_2

description: Library name: RNASEQ_Con_E2C_2

value: DMSO


title: Smarcad1KD_Rep3_TTseq

description:
Library name: Smarcad1KD_Rep3_TTseq
4sU-labelled RNA

value: Smarcad1 knockdown for 48 hours


title: RNASEQ_Con_E2C_1

description: Library name: RNASEQ_Con_E2C_1


title: ControlKD_Rep15_RNAseq

description: Total RNA

data_processing:
Barcode adapter sequences removed using cutadapt and trimmed using trimmomatic.
Reads mapped to mm10 genome using STAR, with options --outSAMtype SAM, --outFilterMismatchNoverReadLmax 0.02, and --outFilterMultimapNmax 1, and quality filtered using samtools view with options -q 7, -f 2, -bS.
Counts were generated using featureCounts, with options -B -t "exon" -g "gene_name" -F GTF -p -s 2 for Gencode mouse V23 features, with options -B -F SAF -p -s 2 for stranded features, and options -B -F SAF -p -s 0 for unstranded features.
In R/Bioconductor environment, raw count matrices were corrected for batch effects using Combat-seq and differential expression analysis was performed using DEseq2 for all replicates of each condition.
Aligned reads were processed to generate strand specific bigwigs using deeptools bamCoverage with binsize 1 and DEseq2-derived scaling factors.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Excel file containing all DEseq2 results for each condition for RNAseq.
Supplementary files format and content: Tab-delimited matrix of raw RNAseq counts for each sample for all features.
Supplementary files format and content: Tab-delimited matrix of Combatseq corrected raw RNA-seq counts for each sample for all features.
Supplementary files format and content: Tab-delimited table containing information for Combatseq batch corrected for RNAseq data.

extract_protocol:
48 h post transfection, media was aspirated from transfected plates and replaced with 10 mL of 500 nM 4-thio-uridine (4sU) containing ESC media and the plates incubated at 37°C with 5% CO2 for 5 min. After 5 min, the 4sU-containing media was aspirated and the cells were washed with PBS, trypsinized, and then pelleted by centrifugation. Total RNA was collected from cell pellets with a TRIzol extraction followed by an isopropanol/salt precipitation and resuspended in 100 µL 1XTE, according to ThermoFisher’s recommendations. 100 µg of total RNA was diluted to a concentration of 240 ng/µL at a volume of 416.67 µL in 1XTE and then fragmented with a Bioruptor Pico (Diagenode) on high power for one 30 second cycle. The fragmented RNA was then separated using thiol-specific biotinylation followed by streptavadin bead treated to isolate 4sU-labelled RNA from total RNA. 1 ug of total RNA and 100 ng nascent RNA from each sample were used to build RNA-seq and TT-seq libraries, respectively.
Total RNA was rRNA depleted using antisense oligos and purified. Total RNA-seq libraries were built using a strand-specific RNA-seq library build protocol.

value: Control KD for 48 hours


title: ControlKD_Rep14_RNAseq

description: Total RNA


title: ControlKD_Rep17_RNAseq

description: Total RNA


title: ControlKD_Rep16_RNAseq

description: Total RNA


title: RNAseq_L2C_siEchs1_2

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file includes FPKM values for each samples

extract_protocol:
5-10 early embryos per group were collected in tubes with lysis component and ribonuclease inhibitor.
we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2KB. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip GX Touch and Step OnePlus Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.


title: L2C_H3K9cro_1

description: Library name: L2C_H3K9cro_1

data_processing:
Raw reads were processed with Trim Galore to remove adaptor sequences and poor quality bases.
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Picard was used to remove PCR duplicates.
Peaks were called using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig file for each sample

extract_protocol:
A total of 100-200 early embryos were used in each ChIP-seq experiment
ChIP-seq libraries were prepared using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China) according to the manufacturer’s protocol. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.


title: L2C_H3K9cro_2

description: Library name: L2C_H3K9cro_2


title: ControlKD_Rep13_RNAseq

description: Total RNA


title: RNAseq_L2C_siEchs1_1


title: RNAseq_L2C_siEchs1_3


title: ControlKD_Rep12_RNAseq

description: Total RNA


title: ControlKD_Rep11_RNAseq

description: Total RNA


title: RNAseq_L2C_siCon_3


title: RNAseq_L2C_siCon_1


title: ControlKD_Rep8_RNAseq

description: Total RNA


title: RNAseq_E2C_siEchs1_3


title: ControlKD_CandR_Smarcal1

description: Library name: ControlKD_CandR_Smarcal1


title: ControlKD_Rep10_RNAseq

description: Total RNA


title: ControlKD_CandR_SRCAP

description: Library name: ControlKD_CandR_SRCAP


title: ControlKD_Rep7_RNAseq

description: Total RNA


title: ControlKD_Rep9_RNAseq

description: Total RNA


title: RNAseq_E2C_siCon_2


title: ControlKD_Rep5_RNAseq

description: Total RNA


title: ControlKD_Rep3_RNAseq

description: Total RNA


title: ControlKD_Rep4_RNAseq

description: Total RNA


title: RNAseq_E2C_siEchs1_2


title: RNAseq_E2C_siCon_1


title: ControlKD_Rep1_RNAseq

description: Total RNA


title: siEchs1_E2C_Pol_1


title: siCon_E2C_Pol_2


title: siEchs1_E2C_Pol_2


title: siCon_E2C_Pol_1


title: RNAseq_L2C_siCon_2


title: Mla_H3K9cr_2


title: Ttf2KD_Rep1_RNAseq

description: Total RNA

value: Ttf2 knockdown for 48 hours


title: GV_H3K9cr_2


title: Mla_H3K9cr_1


title: SrcapKD_Rep2_RNAseq

description: Total RNA

value: Srcap knockdown for 48 hours


title: GV_H3K9cr_1


title: Ttf2KD_Rep2_RNAseq

description: Total RNA


title: SrcapKD_Rep1_RNAseq

description: Total RNA


title: ControlKD_Rep6_RNAseq

description: Total RNA


title: RNAseq_E2C_siEchs1_1


title: RNAseq_E2C_siCon_3


title: FourC_H3K9cr_2


title: ControlKD_Rep2_RNAseq

description: Total RNA


title: FourC_H3K9cr_1


title: Zranb3KD_Rep2_RNAseq

description: Total RNA

value: Zranb3 knockdown for 48 hours


title: Smarcad1KD_Rep2_RNAseq

description: Total RNA


title: EightC_H3K9cr_1


title: Smarcad1KD_Rep1_RNAseq

description: Total RNA


title: EightC_H3K9cr_2


title: FourC_H3K4cr_2


title: Zranb3KD_Rep1_RNAseq

description: Total RNA


title: Smarca4KD_Rep2_RNAseq

description: Total RNA

value: Smarca4 knockdown for 48 hours


title: FourC_H3K4cr_1


title: Smarca5KD_Rep2_RNAseq

description: Total RNA

value: embryonic stem cells

value: Smarca5 knockdown for 48 hours


title: Smarca4KD_Rep1_RNAseq

description: Total RNA


title: Smarca2KD_Rep2_RNAseq

description: Total RNA

value: Smarca2 knockdown for 48 hours


title: E2C_H3K9cr_1


title: E2C_H3K4cr_1


title: Smarcal1KD_Rep2_RNAseq

description: Total RNA

value: Smarcal1 knockdown for 48 hours


title: Smarca2KD_Rep1_RNAseq

description: Total RNA

value: wild-type


title: E2C_H3K4cr_2


title: ShprhKD_Rep1_RNAseq

description: Total RNA

value: Shprh knockdown for 48 hours


title: E2C_H3K9cr_2

value: embryo


title: Rad54l2KD_Rep2_RNAseq

description: Total RNA

value: Rad54l2 knockdown for 48 hours


title: ShprhKD_Rep2_RNAseq

description: Total RNA


title: DRB_E2C_Pol_1


title: DRB_E2C_Pol_2


title: DRB_E2C_K9cr_2


title: Rad54l2KD_Rep1_RNAseq

description: Total RNA


title: Smarcal1KD_Rep1_RNAseq

description: Total RNA


title: DRB_E2C_K9cr_1


title: Rad54lKD_Rep2_RNAseq

description: Total RNA

value: Rad54l knockdown for 48 hours


title: Smarca5KD_Rep1_RNAseq

description: Total RNA


title: DMSO_E2C_Pol_2


title: Rad54lKD_Rep1_RNAseq

description: Total RNA


title: DMSO_E2C_Pol_1


title: DMSO_E2C_K9cr_2


title: Cro_treat_E2C_Pol_2


title: Rad54bKD_Rep2_RNAseq

description: Total RNA

value: Rad54b knockdown for 48 hours


title: Ino80KD_Rep2_RNAseq

description: Total RNA

value: Ino80 knockdown for 48 hours


title: Rad54bKD_Rep1_RNAseq

description: Total RNA


title: DMSO_E2C_K9cr_1


title: HltfKD_Rep2_RNAseq

description: Total RNA

value: Hltf knockdown for 48 hours


title: Echs1KD_E2C_2

data_processing:
Raw reads were processed with Trim Galore (v0.6.4) to remove adaptor sequences and poor quality bases. Trimmed reads were then aligned to the to the mouse reference genome (mm10) using Bismark (v0.22.3). PCR duplicates were removed using Picard (v2.23.3).
Assembly: mm10
Supplementary files format and content: bw file for each sample

extract_protocol:
A total of 5-10 mouse 2-cell embryos were collected.
The WGBS libraries were prepared using a Post-bisulfite adapter tagging (PBAT) approach by Annoroad Gene Technology


title: Cro_treat_E2C_Pol_1


title: HltfKD_Rep1_RNAseq

description: Total RNA


title: HellsKD_Rep2_RNAseq

description: Total RNA

value: Hells knockdown for 48 hours


title: HellsKD_Rep1_RNAseq

description: Total RNA


title: Echs1KD_E2C_1


title: Con_E2C_2


title: Ercc6lKD_Rep1_RNAseq

description: Total RNA

value: Ercc6l knockdown for 48 hours


title: Con_E2C_1


title: Ercc6lKD_Rep2_RNAseq

description: Total RNA


title: Progenitor renal cells_donor 06

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description: Progenitor Renal Cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Minfi R package standard protocol
Processed data: Minfi preprocessNoob (single-sample) normalized Average Beta

label: Cy5 and Cy3

source_name: Progenitor renal cells, nephrectomy

label_protocol: Standard Illumina labelling protocol

growth_protocol: Urinary renal progenitor cells (uRPC) and progenitor renal cells from nephrectomy (PEC) isolation was performed as previously described (Manonelles A et al, Front Physiol 2018 DOI:/10.3389/fphys.2018.01412; Lazzeri E et al. J Am Soc Nephrol 2015 doi: 10.1681/ASN.2014010057). Patients with sample contamination were also considered as screening failure. After cell isolation and expansion, samples with ≥80% CD133+CD24+ positivity by FACs analysis were suitable to study.

extract_protocol: Total DNA was isolated by standard procedures

tag: group

value: nephrectomy

value: Progenitor renal cells


title: Ercc6KD_Rep2_RNAseq

description: Total RNA

value: Ercc6 knockdown for 48 hours


title: Ercc6KD_Rep1_RNAseq

description: Total RNA

value: embryonic stem cells


title: Progenitor renal cells_donor 05

description: Progenitor Renal Cells


title: Ep400KD_Rep2_RNAseq

description: Total RNA

value: Ep400 knockdown for 48 hours


title: Progenitor renal cells_donor 04

description: Progenitor Renal Cells


title: Progenitor renal cells_donor 03

description: Progenitor Renal Cells


title: Ino80KD_Rep1_RNAseq

description: Total RNA


title: Ep400KD_Rep1_RNAseq

description: Total RNA


title: Progenitor renal cells_donor 02

description: Progenitor Renal Cells


title: Progenitor renal cells_donor 01

description: Progenitor Renal Cells


title: Chd8KD_Rep2_RNAseq

description: Total RNA

value: Chd8 knockdown for 48 hours