title: Acrylamide_IC20_100-2

description:
Acrylamide_IC20_100-2_S3
counttable.txt

tag: exposure

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_E17

status: Public on Jun 01 2021

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: total RNA

organism: Mus musculus

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: basophil

tag: mousename

tag: coverage

tag: number of genes


title: IND-PALF_CC-12

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

organism: Homo sapiens

source_name: Liver tissue

extract_protocol:
Total RNA was extracted from archived frozen liver tissue using a TissueLyser LT and the RNeasy® Mini Kit protocol (QIAGEN, Hilden, Germany). RNA purity and concentration were confirmed using the NanoDrop 2000™ Spectrophotometer (Thermo Scientific, DE, USA). RNA quantity was determined with Qubit fluorometer. Total RNA samples were checked for quality based on fragment size using Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

tag: diagnosis

value: pediatric acute liver failure (PALF)


title: F_P7_hyperoxia_CD45_2_DC35_M18

value: Mac III


title: IND-PALF_CC-11


title: genomic DNA from cultured airway epithelial cells (basal cells) [d45f_44b0-2A]

type: genomic

first: Carole

last: Ober

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description:
200517480202_R08C01
d45f_44b0-2A

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

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 90% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5% in either African Americans or European Americans) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
normalized data: Average Beta

label: cy3, cy5

molecule: genomic DNA

source_name: Cultred airway epithelial cells

label_protocol: Standard Illumina protocol.

value: vehicle

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

value: Never

value: Male

tag: ethnicity

value: White

tag: age

tag: array


title: Acrylamide_IC20_100-1

city: Bilthoven

first: Victoria

middle: C

last: de Leeuw

address: PO box 1

country: Netherlands

institute: National Institute for Public Health and the Environment

description:
Acrylamide_IC20_100-1_S3
counttable.txt

data_processing:
Sequencing was performed on the NextSeq 500 sequencer (Illumina) using the NextSeq 500/550 High Output Kit version 2.5 (75 cycles).
Raw bcl files were base called and demultiplexed into FASTQ files with Bcl2fastq (Illumina, version 2.20.0.422).
Quality control reports (FastQC, version 0.11.8) were generated using MultiQC (version 1.0).
Transcripts were quantified using Salmon (version 1.3.0).
Transcript level information was summarized into genes using tximport (version 1.16.1).
Normalized gene counts were generated using DESeq2 (version 1.30.0).
Genome_build: Human transcriptome (GRCh38, version 30, Ensembl 96).
Supplementary_files_format_and_content: counttable.txt: Count matrix containing normalized gene counts.

source_name: Neuronal-astrocyte co-culture

growth_protocol: For each experiment, NPCs were thawed and maintained according to the neuronal induction protocol from Stemcell (Document #28782, Stemcell Technologies). Briefly, cells were kept in a humidified chamber (37 °C, 5% CO2, 3% O2) in STEMdiff™ Neural Progenitor (NP) medium (Stemcell) on Poly-L-Ornithine (PLO, 15 µg/mL, Sigma-Aldrich, Saint Louis, MO, USA) - laminin (10 µg/mL, Sigma-Aldrich) coated 6-well plates (Corning, New York, NY, USA). Culture medium was refreshed daily for a week until the NPCs were confluent. For neuron-astrocyte generation, NPCs were dissociated and seeded at 2.56 × 10^5 cells/cm2 on PLO-laminin-coated 8-well micro-slides (Ibidi), 12 or 24-well plates (Corning). Cells were kept for one day in NP medium, after which they were switched to differentiation medium consisting of neurobasal medium, 10 µl/mL N2 supplement, 20 µl/mL B-27-retinoic acid supplement, 10 µl/mL 5000 IU/mL Penicillin / 5000 µg/mL Streptomycin, 10 µl/mL nonessential amino acids, 20 ng/mL glial cell line-derived neurotrophic factor and 20 ng/mL brain-derived neurotrophic factor (all from Gibco), 1 μM dibutyryl cyclic adenosine monophosphate (Sigma-Aldrich), 200 μM ascorbic acid (Sigma-Aldrich) and 2 μg/mL laminin (Sigma-Aldrich). Ciliary neurotrophic factor (Gibco) was added during the first week of neuron-astrocyte generation at a final concentration of 10 ng/mL. Half of the medium was refreshed every two to three days.

extract_protocol:
Eight samples per condition (all technical replicates from one experiment) were fixated in QIAzol (Qiagen) and stored at -80 °C until further processing. Whole RNA extraction was performed following the manufacturer’s protocol using the RNeasy® mini kit (Qiagen) with a DNase digestion step (Qiagen). RNA concentration was determined using the Qubit3 (Invitrogen) and RNA quality was analyzed using the 2100 Bioanalyzer (Agilent Technologies).
Samples were processed according to the TruSeq Stranded mRNA protocol (Illumina, San Diego, CA, USA). Enrichment of mRNA was done using polyA-affinity purification converting it into a multiplex library of 16 samples.

treatment_protocol: Compounds were freshly prepared for each exposure. Acrylamide (CAS# 79-06-1) and valproic acid sodium (CAS# 1069-66-5) were dissolved in medium, and chlorpyrifos (CAS# 2921-88-2), fluoxetine hydrochloride (CAS# 59333-67-4) and methyl mercury chloride (CAS# 115-09-3) were dissolved in dimethyl sulfoxide (DMSO, CAS# 67-68-5). Final concentrations of DMSO in the medium was 0.25% (v/v).

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Acrylamide IC20/100

tag: batch


title: M_P7_hyperoxia_CD45_2_DC35_G3

tag: sequencing run

tag: gender

value: M

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: Mac IV


title: IND-PALF_CC-10

tag: tissue

tag: diagnosis


title: F_P7_hyperoxia_CD45_2_DC35_P2

value: F

value: hyperoxia

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: IND-PALF_CC-9

value: liver


title: genomic DNA from cultured airway epithelial cells (basal cells) [d45f_44b0-1A]

description:
200514030156_R03C01
d45f_44b0-1A

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: IND-PALF_CC-8

value: pediatric acute liver failure (PALF)


title: NPC-8

description:
NPC-8_S16
counttable.txt

source_name: Neural progenitor cells

tag: originating cell line

value: Neural progenitor cells

tag: time point

value: Day 0

tag: exposure

value: No exposure

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_D8

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: immune

tag: cell subtype


title: genomic DNA from cultured airway epithelial cells (basal cells) [7b33_43a0-1A]

description:
200514030112_R08C01
7b33_43a0-1A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

value: Nasal

value: Current

value: Male


title: Acrylamide_IC20_100-5

description:
Acrylamide_IC20_100-5_S4
counttable.txt

value: Neuronal-astrocyte co-culture

value: Day 10

value: Acrylamide IC20/100


title: M_P7_hyperoxia_CD45_1_DC35_B7

value: M

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: Acrylamide_IC20_100-3

description:
Acrylamide_IC20_100-3_S4
counttable.txt

tag: originating cell line

tag: time point


title: IND-PALF_CC-7

tag: tissue

tag: diagnosis


title: genomic DNA from cultured airway epithelial cells (basal cells) [7b33_43a0-2A]

description:
200516380173_R01C01
7b33_43a0-2A

value: vehicle

tag: smoking

tag: gender

tag: ethnicity

value: White

tag: age

tag: array


title: IND-PALF_CC-6

value: liver


title: genomic DNA from cultured airway epithelial cells (basal cells) [323b_40ff-2A]

description:
200512330148_R05C01
323b_40ff-2A

tag: treatment

value: CRS

value: Never


title: NPC-6

description:
NPC-6_S16
counttable.txt

tag: cell type

value: Neural progenitor cells

value: Day 0

tag: exposure

tag: batch


title: NPC-7

description:
NPC-7_S16
counttable.txt

value: No exposure


title: IND-PALF_CC-14

value: pediatric acute liver failure (PALF)


title: F_P7_hyperoxia_CD45_2_DC35_E20

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_G13

tag: mousename

tag: coverage

tag: number of genes


title: NPC-5

description:
NPC-5_S16
counttable.txt

tag: originating cell line

tag: time point


title: IND-PALF_CC-4

tag: tissue

tag: diagnosis


title: NPC-3

description:
NPC-3_S16
counttable.txt


title: genomic DNA from cultured airway epithelial cells (basal cells) [9623_473f-1A]

description:
200514030112_R06C01
9623_473f-1A

value: RV

tag: crs

tag: asthma

tag: steroid

value: Nasal

tag: smoking

value: Prior

tag: gender

value: Male

tag: ethnicity

tag: age

tag: array


title: IND-PALF_CC-3


title: NPC-2

description:
NPC-2_S15
counttable.txt

tag: cell type

tag: exposure

tag: batch


title: NPC-4

description:
NPC-4_S16
counttable.txt


title: genomic DNA from cultured airway epithelial cells (basal cells) [9623_473f-2A]

description:
200514030073_R04C01
9623_473f-2A

tag: treatment

value: vehicle


title: M_P7_hyperoxia_CD45_2_DC35_L4

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: IND-PALF_CC-2

tag: tissue

value: liver

tag: diagnosis


title: NPC-1

description:
NPC-1_S15
counttable.txt

tag: originating cell line

tag: time point


title: CONTROL_CC-22

value: normal


title: control-8

description:
control-8_S2
counttable.txt

value: Neuronal-astrocyte co-culture

value: Day 10


title: M_P7_hyperoxia_CD45_2_DC35_D22

tag: gender


title: genomic DNA from cultured airway epithelial cells (basal cells) [76b3_439a-2A]

description:
200517480202_R07C01
76b3_439a-2A

tag: crs

value: CRS

tag: asthma

value: No

tag: steroid

tag: smoking

value: Current

tag: ethnicity

value: White

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [db6c_413d-1A]

description:
200516380203_R06C01
db6c_413d-1A

tag: treatment

value: Never


title: control-7

description:
control-7_S2
counttable.txt

tag: cell type

tag: exposure

value: No exposure

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_A3

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: IL cell

tag: mousename

tag: coverage

tag: number of genes


title: CONTROL_CC-21

tag: tissue

tag: diagnosis


title: IND-PALF_CC-5

value: pediatric acute liver failure (PALF)


title: P_8_3

city: Birmingham

first: Kaleen

middle: M

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

institute: University of Alabama at Birmingham

description: Sex: 2

data_processing:
raw FASTQ sequence reads were passed through quality control using FastQC (v0.11.4) and compiled for all samples using MultiQC (v1.7)
adapter trimming and filtering of low-quality reads using fastp (v0.19.4)
reads were aligned using STAR aligner (v2.6.1b)
annotation using GENCODE annotations (gencode.v29.annotation.gtf)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file containing read counts for all genes and all samples, including all re-analyzed samples.

molecule: polyA RNA

source_name: vastus lateralis muscle

extract_protocol: bead homogenization in Qiazol, Qiagen miRNeasy Kit

value: Skeletal Muscle

tag: time point


title: control-6

description:
control-6_S1
counttable.txt

tag: originating cell line


title: M_P7_hyperoxia_CD45_1_DC35_F11

tag: gender

value: M

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_L7

tag: treatment


title: control-5

description:
control-5_S1
counttable.txt

tag: cell type


title: genomic DNA from cultured airway epithelial cells (basal cells) [db6c_413d-2A]

description:
200516380117_R03C01
db6c_413d-2A

value: vehicle

tag: crs

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

tag: age

tag: array


title: M_P7_hyperoxia_CD45_2_DC35_H23

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: T cell

tag: mousename


title: F_P7_hyperoxia_CD45_2_DC35_L6

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_H5

tag: gender

tag: treatment

value: Mac IV


title: control-4

description:
control-4_S1
counttable.txt

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

tag: batch


title: P_5_3

description: Sex: 2

tag: tissue

tag: age


title: P_5_1

description: Sex: 2


title: F_P7_hyperoxia_CD45_2_DC35_B22

tag: sequencing run

value: neutrophil


title: control-3

description:
control-3_S1
counttable.txt


title: genomic DNA from cultured airway epithelial cells (basal cells) [76b3_439a-1A]

description:
200514040052_R06C01
76b3_439a-1A

value: RV

tag: crs

value: CRS

tag: asthma

value: No

tag: steroid

tag: smoking

value: Current

tag: ethnicity

value: White

tag: array


title: EVL42_LS-Patient_28

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

description: colon mucosa from patient with Lynch Syndrome (LS)

data_processing:
Sequencing reads quality check - FastQC
Alignment: patient samples - STAR
Expression quantification - rsem-calculate-expression
Genome_build: patient samples - UCSC hg19;  mouse model samples - NCBI mm10
Supplementary_files_format_and_content: tab-delimited output with raw read counts

source_name: NORMAL

extract_protocol:
Intestinal (small) crypts from mice were isolated and prepared as single cells. Stem and non stem cells were FACS sorted. Total RNA and total cell extracts (proteins) were generated from a pool of cells.
Total RNA was sequenced on Illumina Hi-seq instrument using 78 base pairs paired end reads. For TCE, tryptic peptides were individually analyzed by nano-LC coupled Synapt G2-si ion-mobility mass spectrometry in HDMSE mode using Waters Masslynx (version 4.1, SCN 851).

value: NORMAL

tag: localization

value: COLON

tag: pathology

value: UM

tag: mmr status

value: HET


title: M_P7_hyperoxia_CD45_1_DC35_H3

tag: gender

value: M

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: control-2

description:
control-2_S1
counttable.txt

tag: originating cell line

tag: cell type

tag: time point

tag: exposure

value: No exposure

tag: batch


title: control-1

description:
control-1_S1
counttable.txt

value: Neuronal-astrocyte co-culture


title: GCGR-NS13-PP5W_EPZ_rep3

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description:
EPZ treated
GCGR-NS13-PP5W.counts

data_processing:
ChIP-RX data were aligned to a metagenome of the combined Human hg38 and mouse mm10 reference genomes (with 'mm10_' appended as a prefix of mouse chromosome names) using bowtie2 (v2.3.4.1) with the --no_unal parameter
Samtools (v1.7) was used to convert SAM to BAM files, sort them, remove duplicates and remove multimappers with the samtools view -q 2 parameter.
Aligned reads were seperated into those uniquely aligning to either the human or mouse genome by using grep for chromosome names containing 'mm10_'.
ChIP-RX normalisation factors were generated by counting the number of reads aligned to the human and mouse reference genomes with samtools flagstat and using the formula 1/(spike-in counts/1000000).
Bigwig files were generated using bamCoverage (deeptools v3.3.0) with the -of bigwig -bs10 parameters and scaled for the ChIP-RX normalisation factor with --scalefactor.
Peaks were called using Homer (v4.10.4) findPeaks and average plots generated using deeptools computeMatrix and plotProfile.
RNA-Seq data was processed using hisat2 (v2.1.0) to align reads to the hg38 genome and featureCounts (v1.6.4) to quantify gene abundance. DESeq2 (v1.24.0) was used to identify differentially expressed genes.
Genome_build: hg38 & mm10
Supplementary_files_format_and_content: bigWig files contain ChIP-RX RRPM scaled librarys. Tab delimited .tsv file contains RNA-Seq raw read counts for Ensemble geneIDs output from featureCounts (headers removed to be a suitable format for loading into R with read.table)

source_name: Neural stem cells

growth_protocol: Hindbrain dervice neural stem cell cultures were maintained in DMEM/HAMS-F12 serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Sigma, 1 µg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/protein-DNA complexes were isolated using antibodies.
Libraries were constructed using the Rubicon Genomics DNA ThruPlex library preparation kit, catalog number R400427, in accordance with the manufacturers instructions.

treatment_protocol: Cells were engineered to express either H3F3A wildtype of K27M-mutant histone H3.3 containing a C-terminal V epitope tag

value: Hindbrain derived neural stem cells

tag: genotype

tag: agent

value: EPZ


title: M_P7_hyperoxia_CD45_2_DC35_D23

tag: sequencing run

value: Mac III


title: ND29_LS-Patient_17

tag: tissue

tag: localization

tag: pathology

tag: mmr status


title: F_P7_hyperoxia_CD45_2_DC35_K1

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment


title: P_8_1

description: Sex: 2

value: Skeletal Muscle

tag: age


title: NA20_LS-Patient_15

source_name: TUMOR

value: TUMOR

value: T

value: KO


title: ND41_LS-Patient_16

value: NORMAL

value: COLON


title: F_P7_hyperoxia_CD45_2_DC35_D9

tag: cell type

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_N7

value: M

value: mast cell


title: EVL41_LS-Patient_15

value: UM

tag: batch

value: HET


title: GCGR-NS13-PP5W_EPZ_rep1

description:
EPZ treated
GCGR-NS13-PP5W.counts

tag: genotype

tag: agent


title: M_P7_hyperoxia_CD45_2_DC35_P12

tag: sequencing run

value: hyperoxia

value: immune

value: basophil


title: ND24_LS-Patient_14

tag: tissue

tag: localization

tag: pathology


title: GCGR-NS13-PP5W_DMSO_rep3

description:
DMSO treated
GCGR-NS13-PP5W.counts

value: Hindbrain derived neural stem cells

value: DMSO


title: M_P7_hyperoxia_CD45_1_DC35_N1

tag: gender

tag: plate


title: GCGR-NS13-PP5W_DMSO_rep1

description:
DMSO treated
GCGR-NS13-PP5W.counts


title: GCGR-NS13-PP5W_DMSO_rep2

description:
DMSO treated
GCGR-NS13-PP5W.counts


title: ND23_LS-Patient_14

tag: mmr status


title: ND28_LS-Patient_13


title: F_P7_hyperoxia_CD45_2_DC35_H23

value: F

tag: well

tag: timepoint

tag: treatment

value: Mac IV


title: M_P7_hyperoxia_CD45_1_DC35_C22

tag: cell type

tag: cell subtype

value: Mac III


title: GCGR-NS13-PP5K_EPZ_rep3

description:
EPZ treated
GCGR-NS13-PP5K.counts

value: EPZ


title: ND27_LS-Patient_13


title: M_P7_hyperoxia_CD45_1_DC35_J12

tag: mousename

tag: coverage


title: GCGR-NS13-PP5K_EPZ_rep2

description:
EPZ treated
GCGR-NS13-PP5K.counts


title: ND36_LS-Patient_18

tag: batch


title: M_P7_hyperoxia_CD45_1_DC35_A4

tag: number of genes


title: ND34_LS-Patient_12


title: GCGR-NS13-PP5K_EPZ_rep1

description:
EPZ treated
GCGR-NS13-PP5K.counts

tag: genotype

tag: agent


title: M_P7_hyperoxia_CD45_1_DC35_F9

tag: sequencing run


title: GCGR-NS13-PP5K_DMSO_rep3

description:
DMSO treated
GCGR-NS13-PP5K.counts


title: EVL39_LS-Patient_11

tag: tissue

tag: localization


title: GCGR-NS13-PP5W_EPZ_rep2

description:
EPZ treated
GCGR-NS13-PP5W.counts


title: EVL32_LS-Patient_10

tag: pathology


title: GCGR-NS13-PP5K_DMSO_rep2

description:
DMSO treated
GCGR-NS13-PP5K.counts


title: M_P7_hyperoxia_CD45_2_DC35_G20

tag: gender

tag: plate


title: GCGR-NS13-PP5K_DMSO_rep1

description:
DMSO treated
GCGR-NS13-PP5K.counts


title: ND39_LS-Patient_8

tag: mmr status


title: ND43_LS-Patient_9


title: F_P7_hyperoxia_CD45_2_DC35_O1

tag: well

tag: timepoint

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_B15

tag: treatment

tag: cell type

value: Mac II


title: H295R_total_rep3 [UO_AH_163]

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

data_processing:
Reads were mapped using Salmon with custom index containing ERCC spike-ins and precursor transcripts. Settings for salmon quant: -l A --allowDovetail --validateMappings
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output quant.sf files, tab-delimited text file of read counts and TPM for each sample

growth_protocol: H295R cells cultured in DMEM/F12 with 1% ITS and 10% CCS; cadeveric human adrenocortical cells were isolated and cultured as previously (PMC4475723)

extract_protocol:
H295R cells were washed and treated with TRIzol and RNA was extracted using ZYMO DirectZol RNA Miniprep kit. rRNA was depleted using ribozero gold; RNA from human adrenocortical cells was polyA-selected. For samples treated with 4-thiouridine, labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6).
All RNA was made into cDNA libraries using Kappa HyperPrep kit an sequenced on Nova-seq.

treatment_protocol: 24 hours prior to stimulation of H295R cells wiht 10 nM AngII media was replaced with low sera media (DMEM/F12 with 0.1% CCS, 1% ITS); human adrenocortical cells were treated with 10 nM and 10uM of AngII and ACTH respectively.

tag: cell line

value: steroid-producing adrenocortical cell line

value: Unstimulated, 20 minute 4-thiouridine


title: NA12_LS-Patient_7

value: TUMOR

value: COLON

value: T

value: KO


title: M_P7_hyperoxia_CD45_2_DC35_L1

value: M

value: hyperoxia

tag: cell subtype

value: DC I

tag: mousename

tag: coverage


title: M_P7_hyperoxia_CD45_2_DC35_E5

value: immune

tag: number of genes


title: NA30_LS-Patient_6

tag: batch


title: NA31_LS-Patient_6

source_name: POLYP

value: POLYP

value: AD-HGD


title: H295R_total_rep2 [UO_AH_162]


title: M_P7_hyperoxia_CD45_1_DC35_M3

tag: sequencing run

value: mast cell II


title: H295R_total_rep1 [UO_AH_161]


title: M_P7_hyperoxia_CD45_1_DC35_I18

value: Mac III


title: EVL35_LS-Patient_6

tag: tissue

value: NORMAL

value: UM

value: HET


title: EVL34_LS-Patient_5

tag: localization


title: H295R_label_rep2 [UO_AH_159]

value: steroid-producing adrenocortical cell line

tag: molecule subtype

value: 4-thiouridine labeled RNA


title: H295R_label_rep1 [UO_AH_158]

value: Unstimulated, 20 minute 4-thiouridine


title: ND20_LS-Patient_4

value: COLON

tag: pathology


title: M_P7_hyperoxia_CD45_1_DC35_D9

tag: gender

tag: plate

value: Mac IV


title: ND19_LS-Patient_4

tag: mmr status


title: F_P7_hyperoxia_CD45_2_DC35_P21

value: F

tag: well

tag: timepoint

value: Mac II


title: F_P7_hyperoxia_CD45_2_DC35_M2

tag: treatment

value: hyperoxia

tag: cell type


title: ND22_LS-Patient_3

value: TUMOR

value: T

value: KO


title: F_P7_hyperoxia_CD45_2_DC35_D10

value: immune

tag: cell subtype


title: ND21_LS-Patient_3


title: M_P7_hyperoxia_CD45_2_DC35_D11

value: M

tag: mousename


title: NA27_LS-Patient_2


title: H295R_label_rep3 [UO_AH_160]

tag: cell line


title: NA26_LS-Patient_2

value: POLYP

value: AD-HGD


title: F_P7_hyperoxia_CD45_2_DC35_L15

value: B cell

tag: coverage

tag: number of genes


title: GCGR-NS19-K27WT-H3K4me1_ChIP-RX

description: Mus musculus spike-in

library_source: genomic

value: Hindbrain derived neural stem cells

tag: genotype

tag: chip antibody


title: GCGR-NS13-K27WT-H3K4me1_ChIP-RX

description: Mus musculus spike-in


title: M_P7_hyperoxia_CD45_2_DC35_L7

tag: sequencing run

value: Mac III


title: GCGR-NS19-K27M-H3K4me1_ChIP-RX

description: Mus musculus spike-in


title: EVL30_LS-Patient_1

tag: tissue

value: NORMAL

tag: localization

value: UM

tag: batch

value: HET


title: GCGR-NS19-K27WT-BMI1_ChIP-RX

description: Mus musculus spike-in


title: GCGR-NS13-K27M-H3K4me1_ChIP-RX

description: Mus musculus spike-in


title: M_P7_hyperoxia_CD45_2_DC35_M8

tag: gender

tag: plate

value: Mac V


title: M_P7_hyperoxia_CD45_2_DC35_M10

tag: well

value: DC III


title: GCGR-NS13-K27M-BMI1_ChIP-RX

description: Mus musculus spike-in


title: NA21_LS-Patient_2

value: COLON

tag: pathology

tag: mmr status


title: GCGR-NS13-K27WT-BMI1_ChIP-RX

description: Mus musculus spike-in

tag: cell type


title: HDAC5kd_ortho_3 [ATAC-Seq]

city: zhengzhou

first: huizhi

last: zhao

address: No.100 Science Avenue

country: China

institute: zhengzhou university

data_processing:
read counts of protein coding genes were generated using kallisto for RNA-seq
peaks were called using MACS2 for ATAC-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: raw counts, peak text files

source_name: orthochromatic erythroblasts

growth_protocol: CD34+ cells were purified using magnetic beads from peripheral blood of healthy donors at the New York Blood Center. The CD34+ cells were differentiated towards the erythroid lineage using a three phase culture system and erythroid differentiation was monitored by analyzing the surface expression of glycophorin A (GPA), band 3 and α4 integrin.

extract_protocol:
RNA was extracted from FACS-sorted polychromatic and orthochromatic erythroblasts.nuclei were extracted from 50,000 cells of FACS-sorted polychromatic or orthochromatic erythroblasts following HDAC5 knockdown or luciferase control, followed by the transposition reaction performed with Tn5 transposase.
Approximately 100ng of total RNA was used as input for cDNA library preparation, which was preformed using an Illumina TruSeq kit followed by sequencing using an Illumina HiSeq 4000 platform (Beijing Genomics Institute, BGI, China). The transposed DNA was purified and amplified to generate sequencing libraries following manufacturer instructions (Nextera DNA Library Prep Kit, FC-121-1030).

treatment_protocol: Lentivirus particle preparation and shRNA-mediated knockdown in CD34+ cells was performed

tag: developmental stage

value: orthochromatic

tag: treatment

value: HDAC5 knockdown

value: PB-derived HSC cultured cells


title: M_P7_hyperoxia_CD45_2_DC35_F21

tag: timepoint

value: hyperoxia

tag: cell subtype

value: DC II

tag: mousename


title: M_P7_hyperoxia_CD45_1_DC35_I5

value: M

value: immune

value: Mac IV

tag: coverage

tag: number of genes


title: HDAC5kd_ortho_2 [ATAC-Seq]


title: AC112618-NA3

city: Syracuse

first: Wenyi

last: Feng

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

data_processing:
Sequence read mapping to hg19 by StarFusion using Galaxy; extraction of sequence reads to Entrez Gene ID by FeatureCounts (https://rdrr.io/bioc/Rsubread/man/featureCounts.html)
Genome_build: hg19
Supplementary_files_format_and_content: FeatureCounts

source_name: EBV-transformed lymphoblasts from normal (unaffected) individual

growth_protocol: EBV transformed lymphocytes derived from a normal individual(GM06990) and a Fragile X individual (GM03200) were grown in RPMI1640, supplemented with GlutaMAX, 15% heat-inactivated FBS, 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus Mini Kit. The RNA was run on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip to assess RNA quality and quantity.
1 µg of total RNA was used as input to the Illumina TruSeq Stranded Total RNA Library Prep Kit Ribo Zero Gold H/M/R.  Library size was assessed using the DNA 1000 chip on the Bioanalyzer, and the libraries were quantified using a Qubit fluorometer.  Pair-end sequencing was run on an Illumina NextSeq 500 instrument.  A total of four replicates were processed for treatment/conditions out of which three were biological replicates.

treatment_protocol: Cells were either treated with DMSO, 0.3 micro molar aphidicolin or left untreated for 24 h before harvest.  3x106 cells were harvested for RNA-seq.

tag: cell line

tag: drug treatment

value: 0.03 microM APH in 0.02percent DMSO

tag: biological replicate


title: GCGR-NS19-K27M-BMI1_ChIP-RX

description: Mus musculus spike-in

value: Hindbrain derived neural stem cells

tag: genotype

tag: chip antibody


title: M_P7_hyperoxia_CD45_1_DC35_N20

tag: sequencing run

tag: gender

tag: plate

value: Mac III


title: F_P7_hyperoxia_CD45_2_DC35_I9

value: F

tag: well

value: basophil


title: AC112618-NA1b

tag: technical replicate

value: b


title: AC112618-NA2


title: HDAC5kd_poly_3 [ATAC-Seq]

source_name: polychromatic erythroblasts

tag: developmental stage

value: polychromatic

tag: cell type


title: M_P7_hyperoxia_CD45_1_DC35_J1

tag: timepoint

tag: treatment

value: neutrophil


title: AC112618-NA1a

value: a


title: M_P7_hyperoxia_CD45_2_DC35_C10

tag: cell subtype

tag: mousename


title: AC112618-ND2

value: 0.02percent DMSO


title: HDAC5kd_poly_1 [ATAC-Seq]

value: HDAC5 knockdown


title: AC112618-ND3


title: M_P7_hyperoxia_CD45_2_DC35_J20

tag: coverage

tag: number of genes


title: PB_luci_ortho_3 [ATAC-Seq]

value: orthochromatic

value: luciferase control

value: PB-derived HSC cultured cells


title: HDAC5kd_poly_2 [ATAC-Seq]


title: M_P7_hyperoxia_CD45_1_DC35_O11

value: M

value: hyperoxia

value: DC I


title: AC112618-ND1b

tag: cell line

tag: drug treatment


title: PB_luci_poly_3 [ATAC-Seq]


title: M_P7_hyperoxia_CD45_2_DC35_O3

value: immune


title: PB_luci_ortho_2 [ATAC-Seq]


title: AC112618-NU2

value: no drug treatment

tag: biological replicate


title: AC112618-ND1a


title: M_P7_hyperoxia_CD45_1_DC35_B14

value: mast cell


title: AC112618-NU3


title: HDAC5kd_ortho_1 [ATAC-Seq]


title: PB_luci_ortho_1 [ATAC-Seq]


title: AC112618-NU1b


title: M_P7_hyperoxia_CD45_1_DC35_H6


title: M_P7_hyperoxia_CD45_2_DC35_G7


title: PB_luci_poly_2 [ATAC-Seq]


title: F_P7_hyperoxia_CD45_2_DC35_N19

value: F

value: Mac V


title: PB_luci_poly_1 [ATAC-Seq]


title: AC112618-FA3

source_name: EBV-transformed lymphoblasts from FX individual

value: 0.03 microM APH in 0.02percent DMSO


title: AC112618-NU1a


title: HDAC5kd_ortho_3 [RNA-Seq]


title: M_P7_hyperoxia_CD45_2_DC35_M9

value: Mac III


title: HDAC5kd_ortho_2 [RNA-Seq]


title: AC112618-FA2


title: M_P7_hyperoxia_CD45_2_DC35_L12


title: HDAC5kd_ortho_1 [RNA-Seq]


title: F_P7_hyperoxia_CD45_2_DC35_K17


title: HDAC5kd_poly_3 [RNA-Seq]

value: polychromatic


title: AC112618-FA1b

value: b


title: AC112618-FD3

value: 0.02percent DMSO


title: HDAC5kd_poly_2 [RNA-Seq]

value: HDAC5 knockdown


title: HDAC5kd_poly_1 [RNA-Seq]


title: PB_luci_ortho_3 [RNA-Seq]

value: orthochromatic


title: PB_luci_ortho_2 [RNA-Seq]

value: luciferase control


title: AC112618-FD1b


title: F_P7_hyperoxia_CD45_2_DC35_F7

value: neutrophil


title: M_P7_hyperoxia_CD45_2_DC35_L18

value: M


title: AC112618-FA1a

value: a


title: AC112618-FD2


title: F_P7_hyperoxia_CD45_2_DC35_O7

value: hyperoxia

value: Mac IV


title: PB_luci_ortho_1 [RNA-Seq]

value: PB-derived HSC cultured cells


title: M_P7_hyperoxia_CD45_1_DC35_H8

value: immune


title: M_P7_hyperoxia_CD45_2_DC35_L11

value: basophil


title: AC112618-FD1a


title: AC112618-FU1b

value: no drug treatment


title: AC112618-FU3


title: PB_luci_poly_2 [RNA-Seq]


title: AC112618-FU2


title: AC112618-FU1a


title: PB_luci_poly_1 [RNA-Seq]


title: F_P7_hyperoxia_CD45_2_DC35_P8

value: F


title: F_P7_hyperoxia_CD45_2_DC35_F18

value: Mac V


title: G2_NULL

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

country: Germany

institute: Bundeswehr Institute of Radiobiology

description:
rRNA depleted RNA
sham control
G2_80kVvsNULL.xlsx
G2_150kVvsNULL.xlsx
G2_DEvsNULL.xlsx

data_processing:
Differential gene expression analysis was based on a workflow suggested by Love et al.. In brief read mapping to the human reference transcriptome (GRCh37.67), quantifying transcript abundance and correcting for fragment-level gc-biases was performed with Salmon (version 0.8.1). Salmon results were imported  via tximport (version 1.4.0)into DeSeq2 (version 1.22.2). Significant differential gene expression was defined by a log2 fold change of FPKM (fragments per kilobase per million mapped fragments) > |0.5|  and Padj (FDR-adjusted p-value) < 0.1. This stringent analysis was complemented by an additional search for candidate genes using slackened criteria in order to accommodate to the subtle effects that can be expected in light of the very low doses applied during CT scans, i.e. a log2 fold change of FPKM (fragments per kilobase per million mapped fragments) > |0.5| and an uncorrected p value < 0.05 in at least two of the three probands.
Results were exported from R to Microsoft Excel and sorted in accordance to their fold changes and significance.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx-File, Results table from DESeq2 with gene-symbols

source_name: peripheral blood

extract_protocol:
After irradiation and incubation at 37°C for 6h, 2.5ml of blood were transferred to PAXgene™ Blood RNA tubes. Apart from irradiation matching non-irradiated sham controls samples were handled the very same way.
RNA Seq library preparation was performed with NebNext Ultra II Directional Kit. Library fragment length was determined with Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and concentration was measured with a Qubit 3.0 Fluorometer (Thermo Scientific, Waltham, MA, USA). Libraries were sequenced with 1 x 75 bp single end reads following the protocols for the NextSeq500 sequencing platform (NextSeq 500 High Output Kit 75bp; NextSeq System Guide; NextSeq Denature and Dilute Libraries Guide; Illumina, San Diego, CA, USA, Document # 15048776 v02, Document # 15046563 v02).

treatment_protocol: Peripheral blood from three healthy male donors was collected into EDTA-Monovettes. Three separate blood samples for each proband and the three investigated irradiation settings were placed into a spine phantom set up in a Dual Source CT scanner (SOMATOM Force, Siemens Medical Solutions, Forchheim, Germany). Exposure was done according to the standard protocol for lumbar spine examinations. This resulted in an administered effective dose of 7.0 +/- 0.08 mSv as calculated in accordance to ICRP 103 report by means of Monte Carlo model-based dose estimation implemented in ImpactDose (CT Imaging GmbH, Erlangen, Germany).

tag: tube setting (80kv/150kv/de/null)

tag: exposure (yes/no)

value: no


title: F_P7_hyperoxia_CD45_2_DC35_M22

tag: sequencing run

tag: gender

value: T cell


title: G3_NULL

description:
rRNA depleted RNA
sham control
G3_80kVvsNULL.xlsx
G3_150kVvsNULL.xlsx
G3_DEvsNULL.xlsx


title: RNA_46: tandem_3

city: New York

first: Eric

middle: Edison

last: Gardner

state: New York

address: 413 East 69th Street, BRB-1352

institute: Weill Cornell Medicine

description: clone 3

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the human reference genome (GRCh38) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version 28) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

growth_protocol: Cells were seeded at 50% confluence in 100mm tissue culture plates. 24 hours following plating, cells were used for experiments

extract_protocol:
Culture media was removed, cells were washed 1X with cold PBS/2% FBS/1mM EDTA and then scraped from plates and immediately frozen on dry ice. Total RNAs were purified using an RNeasy kit with DNAse digestion (Qiagen).
TruSeq Stranded Total RNA library prep kit (poly-A depletion) performed by the WCM Epigenomics or Genomics Resources Core Facility
balanced block design

treatment_protocol: Cells were treated with vehicle (DMSO) or 1uM kinase inhibitor for 12 hours in complete culture media prior to collection

tag: crispr ko

value: vehicle

tag: duration

value: simultaneous KO


title: G3_DE

description:
rRNA depleted RNA
treatment
G3_DEvsNULL.xlsx
G3_80kVvsDE.xlsx
G3_150kVvsDE.xlsx

value: DE

value: yes


title: RNA_45: tandem_2

description: clone 2


title: RNA_44: tandem_1

description: clone 1


title: RNA_42: seq_xeno_osi_1

description: clone 1

source_name: NCI-H1975 xenograft

value: osimertinib

value: continuous


title: PB_luci_poly_3 [RNA-Seq]

tag: developmental stage

value: polychromatic

value: luciferase control


title: M_P7_hyperoxia_CD45_1_DC35_C3

value: M

tag: plate

tag: well

value: hyperoxia

tag: cell type

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_N21

tag: timepoint

tag: treatment

value: immune

tag: cell subtype

value: B cell


title: M_P7_hyperoxia_CD45_2_DC35_K6

value: DC I

tag: mousename

tag: coverage

tag: number of genes


title: G1_NULL

description:
rRNA depleted RNA
sham control
G1_80kVvsNULL.xlsx
G1_150kVvsNULL.xlsx
G1_DEvsNULL.xlsx


title: F_P7_hyperoxia_CD45_2_DC35_O2

value: F

value: Mac V


title: RNA_40: seq_xeno_1

description: clone 1

tag: cell line


title: RNA_41: seq_xeno_2

description: clone 1


title: G3_150kV

description:
rRNA depleted RNA
treatment
G3_150kVvsNULL.xlsx
G3_80kVvs150kV.xlsx
G3_150kVvsDE.xlsx

tag: tube setting (80kv/150kv/de/null)


title: G2_DE

description:
rRNA depleted RNA
treatment
G2_DEvsNULL.xlsx
G2_80kVvsDE.xlsx
G2_150kVvsDE.xlsx

tag: exposure (yes/no)


title: G2_150kV

description:
rRNA depleted RNA
treatment
G2_150kVvsNULL.xlsx
G2_80kVvs150kV.xlsx
G2_150kVvsDE.xlsx


title: M_P7_hyperoxia_CD45_2_DC35_B22

tag: sequencing run

value: Mac II


title: G1_DE

description:
rRNA depleted RNA
treatment
G1_DEvsNULL.xlsx
G1_80kVvsDE.xlsx
G1_150kVvsDE.xlsx


title: RNA_38: safe_xeno_osi_1

description: clone 1

value: SAFE

value: 6 hours


title: G1_150kV

description:
rRNA depleted RNA
treatment
G1_150kVvsNULL.xlsx
G1_80kVvs150kV.xlsx
G1_150kVvsDE.xlsx


title: M_P7_hyperoxia_CD45_1_DC35_F2

tag: gender


title: M_P7_hyperoxia_CD45_2_DC35_D12

value: Mac III


title: G3_80kV

description:
rRNA depleted RNA
treatment
G3_80kVvsNULL.xlsx
G3_80kVvs150kV.xlsx
G3_80kVvsDE.xlsx

value: yes


title: M_P7_hyperoxia_CD45_2_DC35_E15


title: RNA_36: safe_xeno_1

description: clone 1

tag: crispr ko

value: vehicle


title: RNA_39: safe_xeno_osi_2

description: clone 1

value: osimertinib

tag: duration


title: M_P7_hyperoxia_CD45_1_DC35_F13


title: M_P7_hyperoxia_CD45_1_DC35_I21


title: G1_80kV

description:
rRNA depleted RNA
treatment
G1_80kVvsNULL.xlsx
G1_80kVvs150kV.xlsx
G1_80kVvsDE.xlsx


title: RNA_43: seq_xeno_osi_2

description: clone 1

value: continuous


title: F_P7_hyperoxia_CD45_2_DC35_A17

value: mast cell


title: G2_80kV

description:
rRNA depleted RNA
treatment
G2_80kVvsNULL.xlsx
G2_80kVvs150kV.xlsx
G2_80kVvsDE.xlsx


title: RNA_33: safe_osi_6

description: clone 1

value: 12 hours


title: M_P7_hyperoxia_CD45_1_DC35_A15

value: M

value: hyperoxia


title: RNA_34: safe_daco_1

description: clone 1

value: dacomitinib


title: M_P7_hyperoxia_CD45_2_DC35_I19

value: immune


title: RNA_32: safe_osi_5

description: clone 1


title: GCGR-NS19-K27WT_ATAC_rep1

value: Hindbrain derived neural stem cells

tag: genotype

tag: chip antibody


title: GCGR-NS19-K27WT_ATAC_rep2


title: M_P7_hyperoxia_CD45_2_DC35_D6

tag: plate

tag: well

value: Mac IV


title: RNA_31: safe_gef_2

description: clone 1

value: gefitinib


title: F_P7_hyperoxia_CD45_2_DC35_K6

value: F

tag: timepoint

tag: cell type

value: Mac II


title: RNA_30: safe_gef_1

description: clone 1

value: SAFE

tag: treatment


title: RNA_37: safe_xeno_2

description: clone 1

value: 6 hours


title: F_P7_hyperoxia_CD45_2_DC35_H15

tag: cell subtype

value: B cell

tag: mousename


title: RNA_29: safe_erl_2

description: clone 1

value: erlotinib


title: GCGR-NS19-K27M_ATAC_rep2


title: RNA_35: safe_daco_2

description: clone 1


title: M_P7_hyperoxia_CD45_2_DC35_L3

value: Mac III

tag: coverage

tag: number of genes


title: RNA_28: safe_erl_1

description: clone 1

tag: cell line


title: GCGR-NS19-K27M_ATAC_rep1


title: M_P7_hyperoxia_CD45_2_DC35_L21


title: GCGR-NS13-K27WT_ATAC_rep1


title: GCGR-NS13-K27WT_ATAC_rep2


title: GCGR-NS13-K27M_ATAC_rep2


title: F_P7_hyperoxia_CD45_2_DC35_H13


title: GCGR-NS13-K27M_ATAC_rep1


title: RNA_25: seq_osi_2

description: clone 1

value: osimertinib


title: M_P7_hyperoxia_CD45_2_DC35_F22


title: GCGR-NS13-K27WT_RNA-Seq_Rep1

description: counts.tsv


title: RNA_27: seq_daco_2

description: clone 1


title: RNA_23: seq_gef_2

description: clone 1


title: M_P7_hyperoxia_CD45_2_DC35_M15


title: GCGR-NS13-K27M_RNA-Seq_Rep1

description: counts.tsv


title: RNA_26: seq_daco_1

description: clone 1


title: RNA_22: seq_gef_1

description: clone 1


title: WT_4

city: Dunedin

first: Joanna

last: Williams

address: Great King St

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Torrent Suite Software 4.2 used for basecalling
Reads were trimmed for adapter sequences using AdapterRemoval, trimmed for quality using Trimmomatic, then mapped to mm10 genome using STAR v2.5.4b
MiRNA were analysed separately, and mapped to mouse miRNA sequences obtained from mirBase using MirDeep2.
Differential expression analysis was performed using edgeR in R version 4.0.3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of raw read counts for each sample

source_name: Left Hippocampus

extract_protocol:
Left hippocampus were removed and flash frozen on dry ice. Total RNA was extracted using mirVana PARIS RNA isolation kit (Invitrogen) according to manufacturer's instructions.
500ng total RNA was used for library preparation using modifications to the Ion Total RNA-Seq kit v2 (Life Technologies) protocol. The major modifications were as follows: ligation of Ion adapters was performed at 16C for 16 hours; rRNA depletion was achieved by the use of QIASeq FastSelect rRNA removal kit (QIAGen). Samples were pooled into two mixed pools and sequenced on the Ion Proton platform on ion PI v3 chips.

tag: tissue

value: brain

tag: strain

tag: age

value: 15 months

value: wild-type


title: GCGR-NS13-K27WT_RNA-Seq_Rep2

description: counts.tsv


title: M_P7_hyperoxia_CD45_1_DC35_M11

source_name: distal lung

tag: sequencing run

tag: gender

value: M

value: hyperoxia


title: F_P7_hyperoxia_CD45_2_DC35_J19

value: immune


title: M_P7_hyperoxia_CD45_1_DC35_D21

value: DC III


title: GCGR-NS13-K27M_RNA-Seq_Rep2

description: counts.tsv

value: Hindbrain derived neural stem cells

tag: genotype


title: M_P7_hyperoxia_CD45_2_DC35_A15


title: RNA_19: seq_3

description: clone 3

tag: crispr ko

value: vehiicle

tag: duration

value: 12 hours


title: RNA_20: seq_erl_1

description: clone 1


title: TG_4


title: TG_3


title: GCGR-NS19-K27WT_RNA-Seq_Rep2

description: counts.tsv

tag: chip antibody


title: F_P7_hyperoxia_CD45_2_DC35_M13

value: F

tag: plate

tag: well

tag: timepoint


title: RNA_17: seq_1

description: clone 1

tag: treatment

value: vehicle


title: GCGR-NS13-K27WT-V5_ChIP-Seq

tag: cell type


title: GCGR-NS19-K27M_RNA-Seq_Rep2

description: counts.tsv


title: F_P7_hyperoxia_CD45_2_DC35_F22

tag: cell subtype

tag: mousename

tag: coverage


title: RNA_18: seq_2

description: clone 2

tag: cell line


title: GCGR-NS19-K27M_RNA-Seq_Rep1

description: counts.tsv


title: WT_3

tag: tissue

tag: strain


title: M_P7_hyperoxia_CD45_2_DC35_F12

tag: sequencing run

tag: number of genes


title: RNA_21: seq_erl_2

description: clone 1


title: M_P7_hyperoxia_CD45_1_DC35_D4

tag: gender

value: Mac IV


title: GCGR-NS19-K27WT_RNA-Seq_Rep1

description: counts.tsv

tag: genotype


title: RNA_24: seq_osi_1

description: clone 1

tag: crispr ko

tag: duration


title: GCGR-NS19-K27WT-V5_ChIP-Seq

tag: chip antibody


title: TG_1

tag: age


title: WT_2


title: GCGR-NS13-K27M-V5_ChIP-Seq


title: F_P7_hyperoxia_CD45_2_DC35_F14

tag: plate

tag: well

tag: timepoint

value: mast cell


title: RNA_16: rb1_osi_4

description: clone 4

tag: treatment


title: M_P7_hyperoxia_CD45_2_DC35_G22

tag: cell type

tag: cell subtype

tag: mousename


title: LPS+MMS [192]

city: Edinburgh

first: Eamon

last: Fitzgerald

state: Midlothian

address: 47 Little France Cres

country: United Kingdom

institute: University of Edinburgh

description:
192
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

data_processing:
The raw pH files were converted to flow signals and aligned to the mm10 reference genome using a built in automated workflow with the Torrent Suite software (version 5.2.0).
Differential expression was assessed using Degust and the Limma with sample weights method.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

source_name: Cortex

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit as per manufacturer's instructions.
Library was prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit.

tag: tissue

value: Cortex

value: LPS+MMS


title: RNA_15: rb1_osi_3

description: clone 3

tag: cell line

value: osimertinib


title: M_P7_hyperoxia_CD45_1_DC35_O8

tag: sequencing run

value: Mac III

tag: coverage


title: RNA_14: rb1_osi_2

description: clone 2


title: GCGR-NS19-K27M-V5_ChIP-Seq


title: M_P7_hyperoxia_CD45_2_DC35_K9

tag: gender

value: neutrophil

tag: number of genes


title: GCGR-NS13-K27WT-Input_ChIP-RX

description: Mus musculus spike-in

tag: genotype


title: GCGR-NS19-K27WT-Input_ChIP-RX

description: Mus musculus spike-in


title: RNA_12: rb1_4

description: clone 4

tag: crispr ko

tag: duration


title: M_P7_hyperoxia_CD45_2_DC35_B2

value: Mac II


title: MMS [191]

description:
191
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

tag: strain

tag: age

value: MMS


title: M_P7_hyperoxia_CD45_2_DC35_K20

value: M

tag: plate

tag: well

value: hyperoxia


title: RNA_11: rb1_3

description: clone 3

tag: treatment


title: RNA_13: rb1_osi_1

description: clone 1


title: LPS [190]

description:
190
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

value: LPS


title: M_P7_hyperoxia_CD45_1_DC35_H2

tag: timepoint

tag: cell type

value: immune

value: DC I


title: Control [189]

description:
189
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

value: Control


title: WT_1

value: brain

value: 15 months

value: wild-type


title: GCGR-NS19-K27M-Input_ChIP-RX

description: Mus musculus spike-in

value: Hindbrain derived neural stem cells

tag: chip antibody


title: RNA_10: rb1_2

description: clone 2

value: vehicle

value: 12 hours


title: F_P7_hyperoxia_CD45_2_DC35_H3

value: F

tag: cell subtype

tag: mousename


title: F_P7_hyperoxia_CD45_2_DC35_K14

tag: sequencing run

value: Mac III


title: RNA_9: rb1_1

description: clone 1

tag: cell line


title: MMS [171]

description:
171
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

tag: tissue

value: Cortex


title: M_P7_hyperoxia_CD45_1_DC35_A18

tag: gender

tag: coverage

tag: number of genes


title: GCGR-NS13-K27WT-SUZ12_ChIP-RX

description: Mus musculus spike-in

tag: genotype


title: GCGR-NS13-K27M-SUZ12_ChIP-RX

description: Mus musculus spike-in


title: LPS [170]

description:
170
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

tag: strain


title: RNA_8: safe_osi_4

description: clone 4

tag: crispr ko

value: SAFE

value: osimertinib

tag: duration


title: GCGR-NS13-K27M-Input_ChIP-RX

description: Mus musculus spike-in


title: F_P7_hyperoxia_CD45_2_DC35_I21

tag: plate

tag: well

value: B cell


title: GCGR-NS19-K27M-SUZ12_ChIP-RX

description: Mus musculus spike-in


title: F_P7_hyperoxia_CD45_2_DC35_E1

tag: timepoint

tag: treatment

value: hyperoxia


title: LPS+MMS [160]

description:
160
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

tag: age

value: LPS+MMS


title: RNA_6: safe_osi_2

description: clone 2


title: RNA_5: safe_osi_1

description: clone 1


title: RNA_4: safe_4

description: clone 4


title: F_P7_hyperoxia_CD45_2_DC35_H9

tag: cell type

value: immune

tag: cell subtype

value: neutrophil


title: LPS [158]

description:
158
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

value: LPS


title: MMS [159]

description:
159
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

value: MMS


title: GCGR-NS13-K27WT-H3K27ac_ChIP-RX

description: Mus musculus spike-in

tag: chip antibody


title: GCGR-NS13-K27M-H3K27ac_ChIP-RX

description: Mus musculus spike-in


title: F_P7_hyperoxia_CD45_2_DC35_E8

tag: sequencing run

tag: mousename


title: LPS+MMS [172]

description:
172
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

tag: tissue


title: RNA_3: safe_3

description: clone 3

tag: cell line


title: GCGR-NS19-K27WT-H3K27ac_ChIP-RX

description: Mus musculus spike-in


title: Control [157]

description:
157
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt

value: Control


title: GCGR-NS19-K27WT-SUZ12_ChIP-RX

description: Mus musculus spike-in


title: RNA_7: safe_osi_3

description: clone 3


title: GCGR-NS19-K27M-H3K27ac_ChIP-RX

description: Mus musculus spike-in


title: Control [169]

description:
169
3' RNA sequencing
E161606_EF_QuantSeq_Pool1_25OCT18.rpm.bcmatrix.txt


title: RNA_2: safe_2

description: clone 2


title: F_P7_hyperoxia_CD45_2_DC35_N17

tag: gender

value: Mac IV

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_1_DC35_N23

value: M

value: Mac V


title: M_P7_hyperoxia_CD45_1_DC35_I12


title: RNA_1: safe_1

description: clone 1

tag: crispr ko

value: vehicle

value: 12 hours


title: GCGR-NS13-K27M-H3K27me2_ChIP-RX

description: Mus musculus spike-in

value: Hindbrain derived neural stem cells

tag: genotype


title: F_P7_hyperoxia_CD45_2_DC35_B7

value: F

tag: plate


title: GCGR-NS13-K27WT-H3K27me2_ChIP-RX

description: Mus musculus spike-in


title: F_P7_hyperoxia_CD45_2_DC35_F12

tag: well

value: T cell


title: M_P7_hyperoxia_CD45_2_DC35_J22

tag: timepoint

value: DC I


title: ATAC_30: tandem_osi_1

description: clone 1

data_processing:
Alignment and identification of open chromatin regions The data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium, n.d.): Reads were aligned to the human reference genome (version GRCh38) with BWA-backtrack (Heng Li and Durbin 2009). Post-alignment filtering was done with samtools and Picard tools (Li et al. 2009, Broad Institute (2015)) to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin represented by enrichments of reads, peak calling was performed with MACS2 (Liu 2014). For every replicate, the narrowpeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01.
Coverage files Individual coverage files per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --blackListFileName hg38.blacklist --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 -p 1.  Version 1 blacklist files were retrieved from https://sites.google.com/site/anshulkundaje/projects/blacklists.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: BigWig files for each sample

extract_protocol:
Culture media was removed, cells were washed 1X with cold PBS/2% FBS and then removed using TrypLE. Samples were processed using the Omni-ATAC protocol (MR Corces, et al.) by the WCM Epigenomics Core
NEB Nextera kit using the original ATAC-seq library prep protocol (JD Buenrostro, et al.) by the WCM Epigenomics Core
balanced block design

tag: treatment

value: osimertinib

tag: duration


title: MMS 4

data_processing:
Raw pH DAT files were produced directly from the Ion platform, which were then converted to flow signals and aligned to the mm10 reference genome in an automated workflow
Further downstream analysis was done using Galaxy and differential gene expression done with Degust software.
Genome_build: mm10

source_name: Hypothalamus tissue

extract_protocol:
RNA was extracted using the RNA/DNA extraction kit from Qiagen using standard protocols
Library preparation was done using the QuantSeq 3’ RNA-Seq Library Prep Kit

treatment_protocol: RNA was extraction from the P6 hypothalamus after

tag: strain

tag: group


title: Control 6

value: control


title: ATAC_29: tandem_3

description: clone 3


title: GCGR-NS13-K27WT-H3K27me3_ChIP-RX

description: Mus musculus spike-in

tag: cell type

tag: chip antibody


title: ATAC_32: tandem_osi_3

description: clone 3


title: Control 4


title: M_P7_hyperoxia_CD45_1_DC35_B19

tag: sequencing run

value: hyperoxia

tag: cell subtype

value: Mac II

tag: mousename


title: MMS 5


title: GCGR-NS19-K27WT-H3K27me2_ChIP-RX

description: Mus musculus spike-in


title: GCGR-NS19-K27M-H3K27me2_ChIP-RX

description: Mus musculus spike-in


title: ATAC_28: tandem_2

description: clone 2

tag: cell line


title: ATAC_27: tandem_1

description: clone 1


title: M_P7_hyperoxia_CD45_2_DC35_P2

tag: gender

value: immune

value: neutrophil

tag: coverage


title: ATAC_31: tandem_osi_2

description: clone 2

tag: crispr ko


title: Control 5


title: MMS 6

value: MMS


title: GCGR-NS13-K27WT-H3K4me3_ChIP-RX

description: Mus musculus spike-in

tag: genotype


title: GCGR-NS13-K27M-H3K4me3_ChIP-RX

description: Mus musculus spike-in


title: Control 3


title: GCGR-NS19-K27WT-H3K27me3_ChIP-RX

description: Mus musculus spike-in


title: MMS 3


title: GCGR-NS19-K27M-H3K27me3_ChIP-RX

description: Mus musculus spike-in


title: M_P7_hyperoxia_CD45_2_DC35_G6

tag: plate

value: Mac III

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_H5

tag: well

tag: timepoint


title: GCGR-NS19-K27WT-H3K4me3_ChIP-RX

description: Mus musculus spike-in


title: MMS 2


title: ATAC_26: seq_osi_3

description: clone 3

value: RB1, PTEN

tag: treatment

tag: duration


title: M_P7_hyperoxia_CD45_2_DC35_P7

value: M


title: F_P7_hyperoxia_CD45_2_DC35_K22


title: MMS 1

tag: strain

tag: group


title: GCGR-NS13-K27M-H3K27me3_ChIP-RX

description: Mus musculus spike-in

tag: cell type

tag: chip antibody


title: Control 2


title: ATAC_24: seq_osi_1

description: clone 1


title: Day 36 Reporter double negative replicate 3

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
Sequence reads were aligned to a combination of the human genome reference (GRCh38) and GFP reporter sequence, using STAR v.2.5.2b
Counts per gene were summarized using the featureCounts function from the subread package v.1.6.2.
The edgeR package v.3.25.10 was used to import, organize, filter and normalize the data. Genes that were not expressed in at least one of the experimental groups were filtered out (keeping only genes that had at least 0.5 counts per million of mapped reads in at least 3 libraries)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix of fragments per kilobase per million reads mapped

source_name: RUES2 ST15AG4CR8 human ESC line

growth_protocol: To derive distal lung epithelial cells, PSCs were first dissociated into single cells suspension and 1.8-2X106 cells were plated per well of a 6-well tissue culture plate coated with Matrigel for 24 hours in mTeSR media containing ROCK inhibitor (RI) prior to differentiation into definitive endoderm differentiation using the Definitive Endoderm Kit (Stem Cell Technologies, 05110) for 3 days (day 0-3). To drive anteriorization of definitive endoderm, day 3 cells were then passed 1:3-1:6 to a new plate in complete serum free differentiation medium (cSFDM) described in Gouon-Evans et al. (2006) supplemented with 2mM of dorsomorphin (DS, Stemgent, 040024) and 10mM SB431543 (SB, Biotechne, 1614) (together constituting DS/SB media) for 3 days (day 3-6) plus 10mM RI for the first 24 hrs. On day 6, cells were re-fed with cSFDM media supplemented with 3mM CHIR (Biotechne, 4423) 100nM retinoic acid (Sigma-Aldrich, R2625), and 10ng/mL rhBMP4 (BioTechne, 314BP) for specification of lung lineage. On day 15, cells were single-cell dissociated by trypsin for fluorescence activated cell sorting using CD47hi/CD26lo staining strategy detailed in Hawkins et al (2017) to enrich for NKX2-1+ lung primordial progenitors. Following cell sorting, NKX2-1 enriched cells were re-plated in three separate plates (n=3) of 3D Matrigel (Corning, 356231) in the concentration of 400 cells/ml and fed with cSFDM media supplemented with CHIR, KGF, dexamethasone, cyclic AMP and IBMX, constituting the "CK+DCI distal lung differentiation media" described in Jacob et al. (2019, 2020) containing RI for the first 72 hours then subsequently re-fed with CK+DCI medium every other day onward. On day 36, live, SFTPCtdTomato/ABCA3:GFP reporter double positive cells, ABCA3:GFP reporter single positive cells, and reporter double negative cells were sorted for total RNA extraction followed by global transcriptomic analysis (triplicate samples, n=3).

extract_protocol:
Following cell sorting for desired cell population, biological triplicate (n=3) samples of purified RNA was harvested using Qiazol and RNA Sample Preparation Kit v2 (QIAGEN).
Total mRNA was isolated using magnetic beads-based poly(A) selection, fragmented, and randomly fragmented for reverse transcription, followed by synthesis of cDNA fragments. cDNA fragments were then end-paired, and ligated to Illumina Paired-End sequencing adapters. The products were end-paired and PCR-amplified to create the final cDNA library.

tag: developmental stage

value: day 36 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: enriched for reporter negative cells by reporter sorting


title: M_P7_hyperoxia_CD45_2_DC35_A19

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

tag: sequencing run

tag: gender

tag: cell subtype

value: Mac IV

tag: mousename


title: Ci: Control Input MeDIP-seq

data_processing:
Bam files generated by IonTorrent Suite v5.2.0
Peaks were called using MACS2 v2.1
Differential peaks were identified using DiffBind
Peaks were annotated using Homer v4.8
Genome_build: mm11

source_name: Hypothalamus

extract_protocol:
Qiagen RNA/DNA extraction kit
100ng of DNA was used for library preparation using the Ion Xpress Plus Fragment Library Kit. Amplification was carried out for 8 cycles and purified using the Agnecourt AMPure XP PCR clean up kit.

tag: tissue

value: Hypothalamus

tag: antibody

value: BI-MECY

tag: molecule subtype

value: Methylated cytosine


title: M_P7_hyperoxia_CD45_1_DC35_G20

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: plate

tag: well

tag: timepoint

tag: coverage

tag: number of genes


title: Day 36 Reporter double negative replicate 2


title: M_P7_hyperoxia_CD45_1_DC35_D7

tag: treatment

tag: cell type

value: Mac V


title: IgG: IgG MeDIP-seq

tag: strain


title: HT 72 hour DMSO 3

city: London

first: James

last: Heward

state: England

address: Haemato Oncology, Barts Cancer Institute, Charterhouse Square

institute: Barts Cancer Institute

description:
RNA
KDM5i_RNA_seq_DE_data

data_processing:
For ChIP seq analysis - Input FASTQ files were mapped to hg19 using Bowtie, whilst H3K4me3 FASTQ files were mapped to hg19 and dm3. The number of reads mapping to the dm3 genome were used to calculate a scaling factor and sequencing reads were randomly removed from samples requiring normalization using SAMtools (samtools view -b -s <scaling.factor> <filename.bam>  > <scaled.bam>). Peaks were identified using the broad source option in MACS2 (macs2 callpeak -t <filename.bam> -c <input.bam> --broad -n <filename> -g hs --broad-cutoff 0.1 -q 0.05) and regions known to result in poor quality sequencing (https://www.encodeproject.org/annotations/ENCSR636HFF/) removed using BEDtools
For KDM5i RNA-seq analysis - mRNA isolation and strand-specific cDNA libraries were prepared using the Illumina TruSeq stranded mRNA Prep kit according to the manufactures instructions. For SU-DHL-6 and OCI-LY-18, two hundred cycles of sequencing on the Illumina HiSeq 2500 instrument were performed to generate 2x100bp paired-end sequencing reads. HT libraries were sequenced by 300 cycles of sequencing on the HiSeq 4000 to generate 2x150bp paired-end sequencing reads. Raw data was aligned to hg19 using STAMPY and BWA. The number of uniquely aligned reads (quality score q > 10) aligned to the exonic region of each gene were counted using HTSeq based on the Ensembl annotation (version 75). Only genes that achieved at least one read per million reads (CPM) in at least 3 samples were kept. Aligned reads numbers were further normalised using the ‘cqn’ method, accounting for gene length and GC content. Differential expression (DE) analysis was then performed using the edgeR R package, employing the generalised linear model (GLM) approach, for the treated versus control pairwise matched comparisons.
For FL patient RNA-seq analysis - 14 FL RNA samples  with a RIN value > 6 were isolated from fresh frozen biopsies and sequenced on the HiSeq 2000. 100bp reads were aligned to the reference genome hg19 using Tophat2 and analysed as above using the ‘cqn’ method to obtain RPKM values for all filtered genes.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files of ChIP seq data and data matrix of analysed RNA-seq data.

source_name: HT cells

growth_protocol: Cells were cultured in RPMI-1640 media at 37°C 5% CO2

extract_protocol:
mRNA was extracted using QIAGEN Rneasy kits. ChIP was performed using a modied version of the Active Motif ChIP-IT High Sensitivity Kit protocol.
RNA-seq libraries were prepared using the TruSeq stranded mRNA Prep kit and ChIP-seq libraries prepared using the NEBNext Ultra II kit .

treatment_protocol: Cells were treated with DMSO or 1μM GS-701644 for 24 or 72 hours

tag: sample type

value: DMSO

tag: time

value: 72 hours


title: Control 1

tag: group

value: control


title: ATAC_23: seq_3

description: clone 3

tag: cell line

tag: crispr ko

value: vehicle

tag: duration

value: 12 hours


title: GCGR-NS19-K27M-H3K4me3_ChIP-RX

description: Mus musculus spike-in

value: Hindbrain derived neural stem cells

tag: genotype

tag: chip antibody


title: Si: MMS input MeDIP-seq

tag: tissue

tag: antibody

tag: molecule subtype


title: ATAC_22: seq_2

description: clone 2


title: ATAC_25: seq_osi_2

description: clone 2

value: osimertinib


title: HT 24 hour KDM5i 3

description:
RNA
KDM5i_RNA_seq_DE_data

value: 24 hours


title: ATAC_21: seq_1

description: clone 1

value: RB1, PTEN


title: F_P7_hyperoxia_CD45_2_DC35_L1

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

tag: mousename


title: HT 72 hour KDM5i 3

description:
RNA
KDM5i_RNA_seq_DE_data

tag: sample type

tag: time


title: M_P7_hyperoxia_CD45_2_DC35_K10

value: M

tag: treatment

tag: cell type

value: neutrophil

tag: coverage

tag: number of genes


title: Day 36 Reporter double negative replicate 1

tag: developmental stage

value: day 36 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: enriched for reporter negative cells by reporter sorting


title: HT 72 hour KDM5i 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: F_P7_hyperoxia_CD45_2_DC35_C22

value: T cell


title: 6: MMS 3 MeDIP-seq

tag: strain

tag: tissue

value: Hypothalamus

tag: antibody

value: BI-MECY

tag: molecule subtype

value: Methylated cytosine


title: F_P7_hyperoxia_CD45_2_DC35_L13

tag: sequencing run

tag: gender

tag: plate

tag: well

value: basophil


title: Day 36 ABCA3:GFP reporter single positive replicate 3

value: enriched for ABCA3:GFP single positive cells by reporter sorting


title: 5: Control 3 MeDIP-seq


title: Day 36 ABCA3:GFP reporter single positive replicate 2


title: HT 72 hour DMSO 2

description:
RNA
KDM5i_RNA_seq_DE_data

tag: sample type

value: DMSO

value: 72 hours


title: F_P7_hyperoxia_CD45_2_DC35_I17

tag: timepoint

tag: cell subtype

value: Mac III

tag: mousename


title: HT 24 hour DMSO 3

description:
RNA
KDM5i_RNA_seq_DE_data

tag: time

value: 24 hours


title: 4: MMS 2 MeDIP-seq


title: Day 36 ABCA3:GFP reporter single positive replicate 1


title: 3: Control 2 MeDIP-seq


title: Day 36 SFTPCtdTomato/ABCA3:GFP reporter double positive replicate 2

value: enriched for SFTPCtdTomato/ ABCA3:GFP double positive cells by reporter sorting


title: Day 36 SFTPCtdTomato/ABCA3:GFP reporter double positive replicate 3


title: F_P7_hyperoxia_CD45_2_DC35_H6

value: F

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: coverage

tag: number of genes


title: 2: MMS 1 MeDIP-seq

tag: strain


title: F_P7_hyperoxia_CD45_2_DC35_F16

value: mast cell


title: HT 24 hour KDM5i 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: HT 24 hour DMSO 2

description:
RNA
KDM5i_RNA_seq_DE_data


title: M_P7_hyperoxia_CD45_2_DC35_B19

value: M


title: 1: Control 1 MeDIP-seq

tag: tissue


title: HT 72 hour DMSO 1

description:
RNA
KDM5i_RNA_seq_DE_data


title: Day 33 NKX2-1GFP single positive

data_processing:
Raw sequence FASTQ data were demultiplexed using the C1 mRNA Sequencing High Throughput Demultiplexer Perl script (Fluidigm). Read quality was evaluated using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and adapter content was trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Reads were mapped to the reference genome, including human (GRCh38), and reference sequences for spike-in ERCC controls (Jiang et al., 2011) and E.coli for additional quality checks, using the STAR aligner version 2.5.2b (Dobin et al., 2013).
Reads mapped to the exons of a gene were summed at the gene level. Sequencing statistics including mapped counts, uniquely mapping reads and percentage of reads mapping to mitochondrial genes were summarized and checked for outliers.
A total of 365.37 Million read pairs mapped to 800 barcodes, corresponding to a depth of 456,710 reads / cell. Of these, 163.17 Million mapped uniquely, resulting in an average of 203.96K unique reads / cell. Cells with less than 2000 genes detected were flagged as outliers. Cells with a percentage of mitochondrial reads beyond one Median Absolute Deviation Expression of the median were also flagged as outliers.
The package Scran (scran_1.10.1, Lun et al., 2016) was used for computing the size factors to scale the counts on each cell and Scater (scater_1.10.0, McCarthy et al., 2017) was used for normalization. Limma (limma_3.38.3, Law et al., 2016) was used for statistical analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of cell passing QC and mappings of barcode to cell names

source_name: BU3-NGST human iPSC

growth_protocol: To derive distal lung epithelial cells, PSCs were first dissociated into single cells suspension and 1.8-2X106 cells were plated per well of a 6-well tissue culture plate coated with Matrigel for 24 hours in mTeSR media containing ROCK inhibitor (RI) prior to differentiation into definitive endoderm differentiation using the Definitive Endoderm Kit (Stem Cell Technologies, 05110) for 3 days (day 0-3). To drive anteriorization of definitive endoderm, day 3 cells were then passed 1:3-1:6 to a new plate in complete serum free differentiation medium (cSFDM) described in Gouon-Evans et al. (2006) supplemented with 2mM of dorsomorphin (DS, Stemgent, 040024) and 10mM SB431543 (SB, Biotechne, 1614) (together constituting DS/SB media) for 3 days (day 3-6) plus 10mM RI for the first 24 hrs. On day 6, cells were re-fed with cSFDM media supplemented with 3mM CHIR (Biotechne, 4423) 100nM retinoic acid (Sigma-Aldrich, R2625), and 10ng/mL rhBMP4 (BioTechne, 314BP) for specification of lung lineage. On day 15, cells were single-cell dissociated by trypsin for fluorescence activated cell sorting for NKX2-1GFP+ lung primordial progenitors, re-plated in 3D Matrigel (Corning, 356231) in the concentration of 500 cells/ml and fed with cSFDM media supplemented with CHIR, KGF, dexamethasone, cyclic AMP and IBMX, constituting the "CK+DCI distal lung differentiation media" described in Jacob et al. (2019, 2020) containing RI for the first 72 hours then subsequently re-fed with CK+DCI medium every other day onward. On day 33, live, SFTPCtdTomato+/NKX2-1GFP reporter double positive cells and NKX2-1GFP single positive cells were sorted for Fluidigm single cell RNA-sequencing analysis.

extract_protocol: Single cells were captured on the Fluidigm C1 chip with automated microfluidic system followed by cell lysis, reverse transcription, and cell multiplexing in an integrated fluidic circuit chip.

tag: developmental stage

value: day 33 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: enriched for epithelial cells by NKX2-1GFP+ reporter sorting


title: WSU#22 72h KDM5i 6 [WSU22_K6_H3K4me3]

description:
WSU22_K6_H3K4me3
Chromatin

data_processing:
For ChIP-seq analysis - Input FASTQ files were mapped to hg19 using Bowtie, whilst H3K4me1/H3K4me3 FASTQ files were mapped to hg19 and dm3. The number of reads mapping to the dm3 genome were used to calculate a scaling factor and sequencing reads were randomly removed from samples requiring normalization using SAMtools (samtools view -b -s <scaling.factor> <filename.bam> > <scaled.bam>). Peaks were identified using the broad source option in MACS2 (macs2 callpeak -t <filename.bam> -c <input.bam> --broad -n <filename> -g hs --broad-cutoff 0.1 -q 0.05) and regions known to result in poor quality sequencing (https://www.encodeproject.org/annotations/ENCSR636HFF/) removed using BEDtools.
For KDM5i RNA-seq analysis - mRNA isolation and strand-specific cDNA libraries were prepared using the Illumina TruSeq stranded mRNA Prep kit according to the manufacturer's instructions. WSU-DLCL2/WSU#22 cells were sequenced using 2x40bp reads generated on the NextSeq 500. Only genes that achieved at least one read per million reads (CPM) in at least 3 samples were kept. Aligned reads numbers were further normalised using the ‘cqn’ method, accounting for gene length and GC content. Differential expression (DE) analysis was then performed using the edgeR R package, employing the generalised linear model (GLM) approach, for the treated versus control pairwise matched comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files of ChIP-seq data.
Supplementary_files_format_and_content: RNA_analysis.xlsx: Data matrix of log CPM and DE values for RNA-seq analysis.

source_name: WSU#22 KMT2D -/+ mutant cells

growth_protocol: Cells were cultured in RPMI-1640 media at 37°C 5% CO2.

extract_protocol:
mRNA was extracted using QIAGEN RNeasy kits. ChIP was performed using a modified version of the Active Motif ChIP-IT High Sensitivity Kit protocol.
RNA-seq libraries were prepared using the TruSeq stranded mRNA Prep kit and ChIP-seq libraries prepared using the NEBNext Ultra II kit.

treatment_protocol: Cells were treated with DMSO or 1μM KDM5-inh1 for 72 hours.

tag: cell line

tag: genotype/variation

value: KMT2D -/+ mutant

tag: chip antibody


title: F_P7_hyperoxia_CD45_2_DC35_B17

tag: sequencing run

tag: gender

tag: plate

tag: well

value: neutrophil


title: TG_2

value: brain

tag: age

value: 15 months

tag: genotype


title: Day 33 SFTPCtdTomato/NKX2-1GFP double positive

value: enriched for epithelial cells by SFTPCtdTomato+/NKX2-1GFP+ reporter sorting


title: HT 72 hour KDM5i 1

description:
RNA
KDM5i_RNA_seq_DE_data

tag: sample type

tag: time

value: 72 hours


title: M_P7_hyperoxia_CD45_2_DC35_D20

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_N1


title: EG2-poly(I:C) rep2

city: Chengdu

first: zhang

last: yan

state: Sichuan

address: Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Clean reads were mapped to the Oryctolagus cuniculus genome sequence with HISAT2 (v2.0.4).
The mapped reads of each sample were assembled by StringTie (v1.3.1).
Fragments per kilo-base of exon per million fragments mapped (FPKMs) of both lncRNAs and coding genes in each sample were calculate by StringTie (v1.3.1). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group based on the length of the fragments and read count mapped to that fragment.
The Cufflinks (v2.2.0) software was used to splice the Mapped Reads and compare with the original annotation information to find the original unannotated transcriptional area
Differential expression analysis of two groups was performed using the DESeq R package (v1.10.1).
Genome_build: OryCun2.0_NCBI.Oryctolagus_cuniculus.OryCun2.0_NCBI.genome.fa
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample; gff files include chromosome, strand, start, length…

organism: Oryctolagus cuniculus

source_name: Endometrial stromal cells

extract_protocol:
Total RNA was extracted from each sample using trizol reagent.
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextRUltraTM Directional RNA Library Prep Kit for IlluminaR(NEB, Ipswich, MA, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, MA, USA). Then 3 μl USER Enzyme (NEB, Ipswich, MA, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR. The library preparations were sequenced by Illumina Hiseq 2000 platform.

value: Endometrial stromal cells

tag: passages

tag: strain

value: New Zealand white rabbit


title: HT 24 hour KDM5i 1

description:
RNA
KDM5i_RNA_seq_DE_data

value: 24 hours


title: WSU#22 72h KDM5i 4 [WSU22_K4_H3K4me3]

description:
WSU22_K4_H3K4me3
Chromatin

tag: cell line

tag: genotype/variation

tag: chip antibody


title: EG3-poly(I:C) rep3


title: EG1-poly(I:C) rep1


title: WSU#22 72h DMSO 6 [WSU22_D6_H3K4me3]

description:
WSU22_D6_H3K4me3
Chromatin

value: DMSO


title: WSU#22 72h KDM5i 5 [WSU22_K5_H3K4me3]

description:
WSU22_K5_H3K4me3
Chromatin


title: M_P7_hyperoxia_CD45_1_DC35_M21

first: Fabio

last: Zanini

address: High and Botany St

institute: University of New South Wales

tag: sequencing run

tag: gender

tag: plate

tag: well

value: hyperoxia

value: immune

value: Mac III


title: CG3-control rep3


title: HT 24 hour DMSO 1

description:
RNA
KDM5i_RNA_seq_DE_data

tag: sample type

tag: time


title: KDM5i H3K4m3 ChIP 5

description: Chromatin

source_name: SU-DHL-6 cells


title: Day 36 SFTPCtdTomato/ABCA3:GFP reporter double positive replicate 1

tag: developmental stage

value: day 36 distal lung directed differentiation

tag: culture media

tag: isolation method

value: enriched for SFTPCtdTomato/ ABCA3:GFP double positive cells by reporter sorting


title: KDM5i H3K4m3 ChIP 7

description: Chromatin


title: F_P7_hyperoxia_CD45_2_DC35_C1

value: F

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

tag: mousename


title: F_P7_hyperoxia_CD45_2_DC35_E12

value: B cell

tag: coverage

tag: number of genes


title: HEK293T_EmptyVector

type: RNA

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: human embryonic kidney cells + pCDF1 empty vector

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human Gene 2.1 ST arrays according to the standard Affymetrix protocol.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC).  CEL files generated by the Affymetrix AGCC program were normalized using Robust Multi-Array Average (RMA) and log2 transformed using Bioconductor.  Pairwise comparisons were performed to assess for gene transcripts that were greater than two-fold up or down regulated in abundance across experimental conditions.  Ontology analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) version 6.8 (https://david.ncifcrf.gov/).

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA

growth_protocol: Asynchronously proliferating cells cultured in DMEM + 10% fetal bovine serum + 1% penicillin/streptomycin at 37 degrees Celsius in a humidified incubator containing 5% CO2

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Infected with lentivirus expressing either pCDF1 empty vector, TRAF7 wildtype, or TRAF7 G536S mutant.  Stable expression was selected for by culture in puromycin.

value: human embryonic kidney cell line

tag: cell line

tag: genotype/variation

value: pCDF1 empty vector


title: HEK293T_TRAF7wildtype

description: human embryonic kidney cells + pCDF1-TRAF7 wildtype

value: pCDF1-TRAF7 wildtype


title: HEK293T_TRAF7G536Smutant

description: human embryonic kidney cells + pCDF1-TRAF7 G536S mutant

value: pCDF1-TRAF7 G536S mutant


title: KDM5i input 7

description: Chromatin

value: 72 hours


title: KDM5i input 5

description: Chromatin


title: WSU#22 72h DMSO 4 [WSU22_D4_H3K4me3]

description:
WSU22_D4_H3K4me3
Chromatin

value: KMT2D -/+ mutant

tag: chip antibody


title: M_P7_hyperoxia_CD45_2_DC35_I16

city: Kensington

tag: sequencing run

tag: gender

value: M

tag: plate

value: Mac IV


title: DMSO H3K4m3 ChIP 7

description: Chromatin

tag: sample type

tag: time


title: WSU-DLCL2 72h KDM5i 4 [WSU_K4_H3K4me3]

description:
WSU_K4_H3K4me3
Chromatin

source_name: WSU-DLCL2 cells

value: Parental


title: F_P7_hyperoxia_CD45_2_DC35_E14

tag: well


title: M_P7_hyperoxia_CD45_2_DC35_E3


title: Yb_EC50_3

city: Vandoeuvre-les-Nancy

first: Damien

last: Blaudez

address: Faculté des Sciences et Technologies Bld des Aiguillettes, BP 70239

country: France

institute: LIEC UMR 7360 CNRS-Université de Lorraine

data_processing:
Illumina HiSeq 2500 with chemistry v4 applying the high-output run mode, using a 2x100 bp paired-end sequencing
Sequenced reads were trimmed for adaptor sequence Trimmomativ v0.36.1 and FastQC v0.67 used for quality check. Reads passing the quality check were mapped on the reference genome (S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/) of S. cerevisiae using TopHat v2.1.1. Reads that were mapped on the reference genome were quantified using HTSeq-count v0.6.1p1. Finally, differential gene expression analysis between treatments was carried out using DESeq2 v1.14.1. Differentially expressed genes between conditions were obtained and expressed as log2-fold change with adjusted p-values calculated via a Benjamini-Hochberg test. A cut-off adjusted p-value of < 0.01 was applied.
Genome_build: S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/
Supplementary_files_format_and_content: tab-delimited text file include normalized gene count for each sample.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: The wild-type strain was grown in YNB-β-glycerophosphate liquid medium

extract_protocol:
Cells were harvested by centrifugation at 4000 rpm for 1 min at room temperature and snap frozen. After cell disruption by bead-beating, total RNAs were column purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions, and gDNA was removed using DNAse I (Sigma Aldrich). RNA integrity was further assessed using a Bioanalyzer 2100 (Agilent, CA, USA).
Strand-specific cDNA libraries were prepared using the TruSeq-3 library kit

treatment_protocol: Cultures were inoculated at an OD600nm of 0.05 and once the cultures reached an OD600nm of 0.6, cells were exposed for 1 h to 50 or 160 µM lanthanum, or to 6 or 8 µM of ytterbium, corresponding to their EC10 and EC50, respectively

tag: strain

tag: agent

value: ytterbium

tag: concentration

value: Yb EC50 (8 microM)

tag: time point

value: 1 hour


title: DMSO input 7

description: Chromatin

value: DMSO


title: WSU-DLCL2 72h DMSO 5 [WSU_D5_H3K4me3]

description:
WSU_D5_H3K4me3
Chromatin

tag: treatment


title: WSU-DLCL2 72h KDM5i 6 [WSU_K6_H3K4me3]

description:
WSU_K6_H3K4me3
Chromatin


title: CG2-control rep2

tag: cell type

value: Endometrial stromal cells

tag: passages

value: New Zealand white rabbit


title: CG1-control rep1


title: M_P7_hyperoxia_CD45_1_DC35_E9

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: IL cell

tag: mousename

tag: coverage

tag: number of genes


title: WSU-DLCL2 72h KDM5i 5 [WSU_K5_H3K4me3]

description:
WSU_K5_H3K4me3
Chromatin

tag: cell line

tag: genotype/variation

tag: chip antibody


title: M_P7_hyperoxia_CD45_1_DC35_P4

tag: sequencing run

tag: gender

tag: plate


title: Yb_EC50_1

tag: strain

tag: agent


title: WSU-DLCL2 72h DMSO 4 [WSU_D4_H3K4me3]

description:
WSU_D4_H3K4me3
Chromatin


title: F_P7_hyperoxia_CD45_2_DC35_O21

value: F

tag: well

value: B cell


title: DMSO H3K4m3 ChIP 5

description: Chromatin

tag: sample type

tag: time


title: WSU-DLCL2 72h DMSO 6 [WSU_D6_H3K4me3]

description:
WSU_D6_H3K4me3
Chromatin

tag: treatment


title: Yb_EC10_2

tag: concentration

value: Yb EC10 (6 microM)

tag: time point


title: M_P7_hyperoxia_CD45_1_DC35_A8

tag: timepoint

tag: cell type

tag: cell subtype

value: mast cell II

tag: mousename


title: DMSO input 5

description: Chromatin

value: 72 hours


title: Yb_EC50_2


title: WSU#22 72h KDM5i 6 [WSU22_K6_H3K4me1]

description:
WSU22_K6_H3K4me1
Chromatin

tag: cell line

tag: genotype/variation

value: KMT2D -/+ mutant


title: control IP1

city: Regensburg

first: Jan

last: Medenbach

address: Universitaetsstrasse 31

institute: University of Regensburg

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
control IP1

data_processing:
Genome indexing STAR-2.7.3a
Adaptor trimming and demultiplexing iCount (https://github.com/tomazc/iCount.git)  Number of tolerated mismatches when comparing barcodes = 1
Mapping of reads to the genome STAR-2.7.3a
Quantifying cross-linked sites iCount (https://github.com/tomazc/iCount.git)
Peak calling iCount (https://github.com/tomazc/iCount.git) --scores
Identifying clusters of peaks iCount (https://github.com/tomazc/iCount.git)
Extracting FASTA sequences from BED files BEDTOOL v2.29.0
Genome_build: Drosophila melanogaster Ensembl release 98 (DM6 from the Berkeley Drosophila Genome Project) iCount (https://github.com/tomazc/iCount.git)
Supplementary_files_format_and_content: BED. Scores.tsv

organism: Drosophila melanogaster

source_name: SL2 cells

growth_protocol: Drosophila S2R+ cells were propagated at 80% confluency in Express Five SFM (ThermoFisher) supplemented with 10X Glutamax (ThermoFisher).

extract_protocol:
Cell pellets were thawn on ice and iCLIP was performed as described in Buchbender et al. 2019. Briefly, native cell extracts were prepared and subjected to RNase treatment using 10U of RNase I (Ambion). Immunoprecipitation was performed with anti-FLAG antibody (M2, Sigma Aldrich) or control serum on Dynabeads Protein A (Life Technologies) for 2h at 4°C. After washing four times with washing buffer (50mM Tris/Cl pH7.4, 1M NaCl, 0.05% Tween 20), the precipitated RNA-protein complexes were eluted. The co-immunoprecipited RNA was dephosphorylated, ligated to a 3’-RNA linker and 5’-radiolabeled with T4 PNK and [γ-³²P]-ATP. Samples were subjected to neutral SDS-PAGE (NuPAGE, Invitrogen) and transferred to a nitrocellulose membrane. Protein/RNA-complexes were visualized by autoradiography. Mei-P26:RNA-complexes were cut from the membrane, proteins were digested with Proteinase K and RNA was subjected to iCLIP library preparation.
Library preparation occurred as previously described by Buchbender et al., 2019. In brief, after immunoprecipitation, 3' end dephosphorylation occurred, followed by linker ligation to the 3' end of the RNA (see above). After further purification of the ribonucleoprotein complexes and removal of the protein moiety by proteolytic digestion (as described above), reverse transcription occurred using a primer directed against the linker sequence. Purification of the cDNAs occurred via MyONE resin, followed by ligation of an adapter to the 3' end of the cDNA and a second clean-up step employing MyONE resin. 6 cycles of PCR were performed to pre-amplify the library. After size selection via ProNex beads, the final PCR amplification step occurred, introducing Illumina-compatible overhangs for sequencing followed by an additional round of ProNex purification.
iCLIP2 protocol as described in Buchbender et al. 2019.

treatment_protocol: Cells were transfected with plasmids encoding FLAG-tagged versions of full-length Mei-P26 or ist NHL-domain only. Mutated protein versions (R1150A, K1172A and R1175A) that exhibit reduced RNA interaction served as control. Per 15cm dish, 15µg DNA were transfected using Fugene HD (Promega) following the manufacturer’s instructions. After incubation at 25°C for 48h, the cells were extensively washed with PBS and UV-crosslinked (300mJ/cm² at 254nm) using a UV Stratalinker 2400 (Stratagene). Subsequently, the cells were harvested and snap frozen in liquid nitrogen.

value: non-transfected control cells

tag: antibody

value: anti-FLAG M2, mouse monoclonal, RRID:AB_262044

value: Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC CRL-1963)


title: control IP3

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
control IP3


title: F_P7_hyperoxia_CD45_2_DC35_M3

tag: sequencing run

tag: gender

value: basophil

tag: coverage

tag: number of genes


title: Mei-P26-NHL IP3

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
Mei-P26-NHL IP3

value: transfected with plasmid encoding flag-tagged Mei-P26-NHL (pAC5.1-Mei-P26-NHL) encompassing amino acids 908-1206


title: F_P7_hyperoxia_CD45_2_DC35_B13

tag: plate

tag: well

value: Mac III


title: control IP2

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
control IP2


title: Yb_EC10_3

tag: strain

tag: agent

value: ytterbium

value: 1 hour


title: La_EC50_3

value: lanthanum

tag: concentration

value: La EC50 (160 microM)


title: A375-shBMI-1

city: Xi’an

first: Yanting

last: Liu

address: 157 Xiwu Road

department: Dermatology

institute: Northwest Hospital, Xi’an Jiaotong University

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

source_name: A375-shBMI-1 cells

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Human melanoma cell line A375 was cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (GIBCO, USA). All cells were maintained in a 5% CO2 incubator at 37°C.

extract_protocol: The total RNA were extracted by Trizol after harvesting 1X106 cells of A375-vector and A375-shBMI-1 cells according to the manufacturer’s instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The BMI‑1 shRNA lentivirus and empty lentivirus were transfected into A375 cells. BMI-1 was silenced in A375-shBMI-1 cells comparing with A375-vector cells, which was confirmed by real‑time PCR and western blot analysis.

tag: tissue

value: melanoma cell line


title: M_P7_hyperoxia_CD45_1_DC35_F4

value: M

tag: timepoint

tag: treatment

value: hyperoxia

value: immune


title: WSU#22 72h DMSO 5 [WSU22_D5_H3K4me1]

description:
WSU22_D5_H3K4me1
Chromatin

value: DMSO

tag: chip antibody


title: WSU#22 72h DMSO 6 [WSU22_D6_H3K4me1]

description:
WSU22_D6_H3K4me1
Chromatin


title: M_P7_hyperoxia_CD45_1_DC35_L12

tag: cell type

tag: cell subtype

tag: mousename


title: Yb_EC10_1

value: Yb EC10 (6 microM)

tag: time point


title: A375-vector

source_name: A375-vector cells

tag: cell line


title: Mei-P26-NHL IP1

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
Mei-P26-NHL IP1

tag: antibody


title: Mei-P26-NHL IP2

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
Mei-P26-NHL IP2


title: WSU#22 72h DMSO 4 [WSU22_D4_H3K4me1]

description:
WSU22_D4_H3K4me1
Chromatin

tag: genotype/variation

value: KMT2D -/+ mutant


title: M_P7_hyperoxia_CD45_1_DC35_J6

tag: sequencing run

tag: gender

tag: coverage

tag: number of genes


title: La_EC50_2

tag: strain

tag: agent


title: F_P7_hyperoxia_CD45_2_DC35_N3

value: F

tag: plate

tag: well


title: WSU#22 72h KDM5i 4 [WSU22_K4_H3K4me1]

description:
WSU22_K4_H3K4me1
Chromatin

tag: treatment


title: La_EC50_1

tag: concentration


title: F_P7_hyperoxia_mesench_1_DC34_C7

tag: timepoint

tag: cell type

value: mast cell


title: La_EC10_3

value: La EC10 (50 microM)


title: WSU#22 72h KDM5i 5 [WSU22_K5_H3K4me1]

description:
WSU22_K5_H3K4me1
Chromatin

tag: chip antibody


title: full-length Mei-P26 IP3

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
full-length Mei-P26 IP3

value: transfected with plasmid encoding Flag-tagged Mei-P26 full length (pAC5.1-Mei-P26)

value: anti-FLAG M2, mouse monoclonal, RRID:AB_262044

value: Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC CRL-1963)


title: F_P7_hyperoxia_mesench_1_DC34_E10

tag: cell subtype

tag: mousename


title: full-length Mei-P26 IP1

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
full-length Mei-P26 IP1

tag: antibody

tag: cell line


title: F_P7_hyperoxia_mesench_2_DC34_C6

tag: sequencing run

value: DC III


title: WSU-DLCL2 72h KDM5i 4 [WSU_K4_H3K4me1]

description:
WSU_K4_H3K4me1
Chromatin

tag: genotype/variation

value: Parental


title: WSU-DLCL2 72h KDM5i 5 [WSU_K5_H3K4me1]

description:
WSU_K5_H3K4me1
Chromatin


title: F_P7_hyperoxia_mesench_2_DC34_G9

tag: gender

value: neutrophil

tag: coverage


title: WSU-DLCL2 72h DMSO 6 [WSU_D6_H3K4me1]

description:
WSU_D6_H3K4me1
Chromatin


title: F_P7_hyperoxia_mesench_1_DC34_N14

value: Mac V

tag: number of genes


title: Ctrl_3

tag: strain

tag: agent

value: non treated

value: 0 microM

tag: time point

value: 1 hour


title: WSU-DLCL2 72h DMSO 5 [WSU_D5_H3K4me1]

description:
WSU_D5_H3K4me1
Chromatin

tag: treatment


title: WSU-DLCL2 72h DMSO 4 [WSU_D4_H3K4me1]

description:
WSU_D4_H3K4me1
Chromatin


title: WSU-DLCL2 72h KDM5i 6 [WSU_K6_H3K4me1]

description:
WSU_K6_H3K4me1
Chromatin


title: Ctrl_1

tag: concentration


title: Ctrl_2


title: full-length Mei-P26 IP2

description:
Protocol according to Buchbender et al., Methods, 2019: Improved library preparation with the new iCLIP2 protocol (doi: 10.1016/j.ymeth.2019.10.003)
full-length Mei-P26 IP2


title: M_P7_hyperoxia_CD31_1_DC30_K10

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune


title: WSU#22 72h KDM5i 6 [WSU22_K6_input]

description:
WSU22_K6_input
Chromatin

value: KMT2D -/+ mutant

tag: sample type

value: ChIP input

tag: chip antibody


title: WSU#22 72h KDM5i 5 [WSU22_K5_input]

description:
WSU22_K5_input
Chromatin


title: La_EC10_2

value: lanthanum


title: M_P7_hyperoxia_CD31_1_DC30_P6

tag: cell type

tag: cell subtype

value: NK cell

tag: mousename


title: WSU#22 72h KDM5i 4 [WSU22_K4_input]

description:
WSU22_K4_input
Chromatin

tag: cell line

tag: genotype/variation


title: M_P7_hyperoxia_CD31_1_DC30_C11

tag: sequencing run

tag: gender

tag: coverage


title: WSU#22 72h DMSO 6 [WSU22_D6_input]

description:
WSU22_D6_input
Chromatin

value: DMSO


title: met2set25_mRNA_rep1

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

data_processing:
RNAseq reads were mapped to ce10 with WS235 gene annotations using STAR and per gene quantification were generated by featureCounts.
Genome_build: ce10
Supplementary_files_format_and_content: Each tsv contains a gene (row) by replicate (column) table of raw counts.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Wild-type and met-2 set-25 mutant worms were grown at 20°C on NGM plates, harvested at the L3 stage, and flash frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from frozen worms using TriPure (Roche) and purified with the Zymo Research RNA Clean and Concentrator kit (R1013) after DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: met-2 set-25

tag: developmental stage


title: N2_mRNA_rep2


title: met2set25_mRNA_rep2


title: M_P7_hyperoxia_CD31_1_DC30_J22

tag: treatment

value: Mac IV

tag: number of genes


title: WSU#22 72h DMSO 5 [WSU22_D5_input]

description:
WSU22_D5_input
Chromatin


title: F_P7_hyperoxia_mesench_2_DC34_A15

value: F

tag: plate

value: DC III


title: N2_mRNA_rep1


title: F_P7_hyperoxia_CD45_1_DC28_B21

tag: well