title: D7_N_T_3

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

institute: National Research Council of Italy (CNR)

data_processing:
The quality of raw reads in fastq format was analyzed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Adapter contamination in the reads were removed using Trim Galore v. 0.4.0
Paired-end reads were aligned to the human reference genome using STAR v2.4.2a in two pass mode
Expected gene counts were extracted using RSEM v1.3.0
Genome_build: hg38 assembly (Ensembl Build 79)

source_name: Early spinal cord progenitors

extract_protocol:
Total RNA was isolated using using the Norgen Biotek kit-QC before library construction was carried out via: (1) Nanodrop: for RNA purity (OD260/OD280).  (2) Agarose gel electrophoresis: for RNA integrity and potential contamination.  (3) Agilent 2100
Library preparation was done using the  NEB Next® Ultra™ RNA Library Prep Kit. After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
Double stranded cDNA synthesis, end repair, poly A/Adaptor addition, fragment selection, PCR

treatment_protocol: human embryonic stem cells (H9 background) grown in mTESR medium on vitronectin; D3 cells were generated after treatment of hPSCs in CHIR99021 (3 uM) and 20 ng/ml FGF2; D7 cells were generated after treatment fo D3 cells in CHIR99021 (3 uM) and 100 ng/ml FGF2

tag: cell type

value: Early spinal cord progenitors


title: MYH7.SID-10239

status: Public on Mar 09 2021

type: SRA

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description:
MYH7.SID-10239
EMB

library_source: transcriptomic

data_processing:
Bcl2fastq 1.20 used for base-calling and fastq generation
Alignment was performed using STAR, default settings
custom Rscript (as descibed and published in TTN paper) was used to groups samples and generate PCA plot
Genome_build: UCSC Hg38
Supplementary_files_format_and_content: tab delimeted raw reads per RefSeq annotated gene-transcript

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
miRVana
Illumina TruSeq LT stranded, Samples random pooled per 12.

tag: tissue

value: Heart biopsy

tag: genotype


title: D7_N_T_1

country: Italy

molecule: total RNA


title: D7_N_T_2


title: LMNA.SID-10180

description:
LMNA.SID-10180
EMB

value: LMNA-DCM


title: Δamn-1 50mM Isoleucine Biological Replicate 1

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

country: USA

institute: Cornell University

data_processing:
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.1.0 with the parameters --max-intronlen 5000 --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-unstranded -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
FPKMs in the FPKM_Metafile.txt were generated by running all samples through cuffmerge v2.2.1; then cuffquant v2.2.1 with the parameters --library-type fr-unstranded --max-bundle-frags=10000000; then cuffnorm v2.2.1 with the parameters --library-type fr-unstranded.
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample

organism: Neurospora crassa

source_name: Neurospora crassa mycelia

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were washed in media lacking a carbon source (for mannose or carbon starvation) or media lacking a nitrogen source (for all others) and then transferred to 3ml of Vogel's minimal media with thie indicated carbon or nitrogen source and incubated at 25C in constant light with constant shaking at 200rpm for 4h prior to harvesting for RNAseq.

tag: media

value: Vogel's minimal medium with 2% Sucrose and 50mM Isoleucine


title: Δamn-1 50mM Isoleucine Biological Replicate 2


title: Δnit-2 50mM Isoleucine Biological Replicate 1


title: D3_N_T_3

source_name: NMP-like axial progenitors

value: NMP-like axial progenitors


title: RBM20.SID-10168

description:
RBM20.SID-10168
EMB


title: D3_N_T_2


title: Granulocytes_PMF_4

type: RNA

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: Gene expression of granulocytes from PMF peripheral blood

hyb_protocol: Microarray hybridization and staining was performed by means of GeneAtlas™ Hybridization, Wash, and Stain Kit (Affymetrix) using the GeneAtlas System (Affymetrix) following the manufacturer’s recommendations.

scan_protocol: Microarray scanning was performed by means of GeneAtlas™ Hybridization, Wash, and Stain Kit (Affymetrix) using the GeneAtlas System (Affymetrix) following the manufacturer’s recommendations.

data_processing: Partek® Genomics Suite® software, version 7.0 (Partek Inc., St. Louis, MO, USA) was used to normalize the probe level data and convert them into expression values by means of robust multiarray average (RMA). An exploratory principal component analysis (PCA) was performed and existing batch effect was removed by means of the specific tool implemented in Partek® GS®.

label: biotin

source_name: Granulocytes from PMF peripheral blood

label_protocol: Biotin-labeled complementary RNA was synthesized starting from 100 ng total RNA by means of GeneChip™ HT 3' IVT PLUS Reagent Kit (Applied Biosystems) according to the standard protocol supplied.

extract_protocol: Total cellular RNA was isolated from stored frozen granulocyte pellets by means of TrizolTM Reagent (InvitrogenTM, ThermoFisher Scientific) following manufacturer’s instructions. RNA sample concentration was evaluated using NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific) and purity was assessed by means of 260/280 nm and 260/230 ratios. Agilent 2100 Bioanalyzer (Agilent Technologies) was used to determine the integrity of total RNA.

tag: disease

value: Overt-PMF

tag: driver mutation

value: CALR Type 2


title: Granulocytes_PrePMF_5

description: Gene expression of granulocytes from PrePMF peripheral blood

source_name: Granulocytes from PrePMF peripheral blood

value: Pre-PMF


title: Granulocytes_PrePMF_12

value: TN


title: Granulocytes_PrePMF_3


title: Granulocytes_PrePMF_2


title: Granulocytes_PMF_3

value: MPL


title: Wild type 50mM NH4Cl Biological Replicate 2

value: FGSC 2489

value: Vogel's minimal medium with 2% Sucrose and 50mM NH4Cl


title: Granulocytes_PET_2

description: Gene expression of granulocytes from PET peripheral blood

source_name: Granulocytes from PET peripheral blood

value: PET


title: TTN.SID-10152

description:
TTN.SID-10152
EMB

value: TTNtv-DCM


title: Granulocytes_PrePMF_1


title: Wild type 50mM NH4Cl Biological Replicate 1


title: D3_N_T_1


title: hPSC_3

source_name: human embryonic stem cells

value: human embryonic stem cells


title: RBM20.SID-10086

description:
RBM20.SID-10086
EMB


title: hPSC_2


title: Wild type 50mM NaNO3 Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM NaNO3


title: Wild type 50mM NaNO3 Biological Replicate 2


title: TTN.SID-10063

description:
TTN.SID-10063
EMB


title: Wild type 50mM NH4Cl Biological Replicate 3


title: Wild type 50mM NaNO3 Biological Replicate 1


title: TTN.SID-10053

description:
TTN.SID-10053
EMB


title: hPSC_1


title: Wild type 50mM Tryptophan Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM Tryptophan


title: Granulocytes_PMF_2

value: CALR Type 1


title: Complete_KO_Molt4_2 [SJTALL065786_C7]

city: Memphis

first: Timothy

last: Shaw

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using htseq/0.6.1p1 with gencode.v19.annotation.gtf
htseq was used to derive the read counts with parameters -r name -a 0 -s no -m union -t exon
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: 100% KO USP7 in Molt4

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Mini kit.
The total stranded RNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing). RNA sequencing was performed on NovaSeq 6000 system (Illumina).

tag: cell line

value: Jurkat

value: T-ALL Cancer Cell Line

tag: genotype/varaition

value: 100% KO USP7 in Molt4

tag: molecule subtype

value: Ribo-depleted


title: Granulocytes_PPV_2

description: Gene expression of granulocytes from PPV peripheral blood

source_name: Granulocytes from PPV peripheral blood

value: PPV


title: Complete_KO_Molt4_1 [SJTALL065786_C6]


title: Partial_KO_Molt4_2 [SJTALL065786_C4]

source_name: Partial KO USP7 in Molt4

value: Partial KO USP7 in Molt4


title: LMNA.SID-10029

description:
LMNA.SID-10029
EMB

value: Heart biopsy

value: LMNA-DCM


title: TTN.SID-10017

description:
TTN.SID-10017
EMB


title: TTN.SID-10085

description:
TTN.SID-10085
EMB


title: Wild type 50mM Tryptophan Biological Replicate 1


title: Molt4_WT_1 [SJTALL065786_C1]

source_name: Wild-type Jurkat cell line

value: Wild-type


title: LMNA.SID-835

description:
LMNA.SID-835
EMB


title: Granulocytes_PET_1


title: TTN.SID-794

description:
TTN.SID-794
EMB


title: Wild type 50mM Proline Biological Replicate 3

value: FGSC 2489

value: Vogel's minimal medium with 2% Sucrose and 50mM Proline


title: Granulocytes_PPV_3


title: Granulocytes_PMF_1

value: Overt-PMF


title: LMNA.SID-771

description:
LMNA.SID-771
EMB


title: Partial_KO_Molt4_1 [SJTALL065786_C3]


title: TTN.SID-732

description:
TTN.SID-732
EMB

value: TTNtv-DCM


title: Wild type 50mM Proline Biological Replicate 2


title: HSB2_USP7shRNA4058_2 [SJTALL061907_C2]

source_name: Hsb-2 cell line treated with USP7 shRNA-4058

tag: treatment

value: USP7 shRNA-4058


title: Wild type 50mM Proline Biological Replicate 1


title: Wild type 50mM Isoleucine Biological Replicate 3

value: Vogel's minimal medium with 2% Sucrose and 50mM Isoleucine


title: TTN.SID-722

description:
TTN.SID-722
EMB


title: Granulocytes_PPV_1


title: HSB2_USP7shRNA4058_1 [SJTALL061907_C1]


title: Wild type 50mM Tryptophan Biological Replicate 2

value: Vogel's minimal medium with 2% Sucrose and 50mM Tryptophan


title: Wild type 50mM Isoleucine Biological Replicate 2


title: TKO rep3

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

country: China

institute: Zhejiang University School of Medicine

data_processing:
The software hisat2 (version 2.1.0) was used to generate genome indices for mouse reference genome (GRCm38/mm10) and extract splice sites with gencode vM24 annotation.
Next, the high quality paired-end RNA-seq reads were aligned to mouse reference genome, and the consequence of alignment served as the input for featureCounts to quantify raw read counts for protein-coding genes.
We used R package DESeq2 (version 1.38.0) to identify differentially expressed genes (DEGs) between different groups. The raw read count per gene served as the input for DESeq2. Since three samples were collected in either condition, they were treated as biological replicates to improve the reliability of DEGs identification. Statistical tests for differential expression were based on a model using the negative binomial distribution. The reported statistical significances were corrected for multiple testing using the Benjamini-Hochberg procedure with a false discovery rate less than 0.05. In addition, to be called DEGs we required the fold change > 1.5. The up-regulated genes in QKO condition versus KO condition were queried to Gene Ontology Consortium for gene ontology enrichment assessment, with specification of biological process (BP).
Genome_build: GRCm38/mm10, December 2011
Supplementary_files_format_and_content: Count table for each sample

organism: Mus musculus

source_name: CD8+ TILs

extract_protocol:
CD8+ TILs were isolated from B16 tumor-bearing wild-type mice on day 14. Two individual tumors were combined as one biological replicate. CD8+ TILs were stained with antibodies against CD45.2, TCRbeta, CD8. 7-AAD Viability Staining Solution was used to exclude dead cells. The CD45.2+TCRbeta+CD8+ cells were then sorted on a BD Aria. Approximately 30,000~70,000 sorted cells for each biological replicate were directly lysed in 1 ml TRIzol Reagent. After incubation for 5 mins, 0.2 ml chloroform was added and mixed by inverting the tubes several times. Samples were incubated for 2~3 mins and later centrifuged for 15 minutes at 12,000g at 4 °C. The upper aqueous phase containing the RNA was collected and mixed with equal volume of 70% ethanol, which was then loaded into a spin column from a RNeasy Micro Kit and subjected to RNA isolation according to the instruction manual. The on-column DNase digestion was conducted to eliminate DNA contamination.
Purified total RNA was quantified by Qubit (Invitrogen) and used to generate polyA+ enriched RNA. The purified polyA+ RNA was used to generate a directional RNA library with a NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®  and NEBNext® Multiplex Oligos for Illumina® according to the manufacturer’s instructions. Library concentrations and quality were assessed on a Bioanalyzer and by qPCR. The library was sequenced at Novaseq (Illumina) to generate reads from paired-ends (2X150bp).

tag: strain

value: C57BL/6 mice

value: Implanted B16 tumor

value: WT


title: HSB2_USP7shRNA4057_1 [SJTALL061906_C1]

source_name: Hsb-2 cell line treated with USP7 shRNA-4057

value: T-ALL Cancer Cell Line

value: USP7 shRNA-4057


title: TKO rep2


title: Wild type 50mM Isoleucine Biological Replicate 1


title: HSB2_scrambled_2 [SJTALL061905_C2]

source_name: Hsb-2 cell line treated with scrambled siRNA

value: scrambled siRNA

value: Ribo-depleted


title: LMNA.SID-685

description:
LMNA.SID-685
EMB

value: Heart biopsy


title: CASB library for scRNA-seq of a mixture of 16 celltypes from 7 species

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Gene-cell matrices were determined using 10X Genomics Cellranger version 3.1.0 with default parameters (cellranger count).
Genome_build: concatenated genome, ensembl version 102 of 7 species (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Cricetulus griseus, Chlorocebus_sabaeus, Drosophila melanogaster)
Supplementary_files_format_and_content: h5 file produced by cellranger

organism:
Drosophila melanogaster
Homo sapiens
Canis lupus familiaris
Cricetulus griseus
Mus musculus
Rattus norvegicus
Chlorocebus sabaeus

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide and using a custom CASB library preparation protocol.

value: mixture (HEK-293T, RPE-1, Jurkat, K-562, HCT116, HepG2, Hela, 786-0, RAW264.7, CT26, 4T1, REF, MDCK, CHO, Vero, S2)


title: HSB2_scrambled_1 [SJTALL061905_C1]


title: RBM20.SID-616

description:
RBM20.SID-616
EMB


title: scRNA-seq of a mixture of 16 celltypes from 7 species

source_name: HEK-293T, RPE-1, Jurkat, K-562, HCT116, HepG2, Hela, 786-0, RAW264.7, CT26, 4T1, REF, MDCK, CHO, Vero, S2


title: QKO rep3


title: HSB2_WT_2 [SJTALL061904_C2]

source_name: Wild-type Hsb-2 cell line


title: QKO rep2


title: HSB2_USP7shRNA4057_2 [SJTALL061906_C2]


title: HSB2_WT_1 [SJTALL061904_C1]


title: Lsd1 KO rep3


title: MYH7.SID-480

description:
MYH7.SID-480
EMB


title: MYH7.SID-699

description:
MYH7.SID-699
EMB


title: TTN.SID-328

description:
TTN.SID-328
EMB


title: Jurkat_USP7shRNA4057_2 [SJTALL061902_C2]

source_name: Jurkat cell line treated with USP7 shRNA-4057

value: Jurkat


title: Jurkat_USP7shRNA4058_1 [SJTALL061903_C1]

source_name: Jurkat cell line treated with USP7 shRNA-4058


title: SAS tumour spheres, biological replicate 2

city: Kuala Lumpur

first: Chua

last: Eng Wee

state: Kuala Lumpur

address: Jalan Raja Muda Abdul Aziz,

department: Faculty of Pharmacy

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: For the generation of CSCs of SAS, SAS cells were cultured at a low cell density of 2.5 × 104 cells/mL in a 6-well plate coated with a thin layer of 1 % agarose to promote low anchorage-dependent characteristics of the cells. The cells were maintained in a growth medium consisting of serum-free DMEM/F12, 1 % penicillin/streptomycin, 1 % N-2 supplement (Thermo Fisher Scientific, USA), 10 µg/mL heparin sodium salt (Sigma-Aldrich, USA), 20 ng/mL human recombinant basic fibroblast growth factor, and 20 ng/mL epidermal growth factor (Gold Biotechnology Inc., USA). The medium was replenished every other day for 7 days.

hyb_protocol: Hybridization-ready targets were prepared using the GeneChip Hybridization, Wash and Stain Kit (Thermo Fisher Scientific Inc., USA) prior to injection into the array. Hybridization of the arrays was performed on the GeneChip Hybridization Oven 645 (Thermo Fisher Scientific Inc., USA) for 16 h. The hybridized arrays were then washed and stained using the GeneChip Hybridization, Wash and Stain Kit on the GeneChip Fluidic Station 450 (Thermo Fisher Scientific Inc., USA).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Thermo Fisher Scientific Inc., USA).

data_processing: The raw scanned GeneChip images (DAT file) and their converted raw data files (CEL file) were obtained from the GeneChip Command Console Software (Thermo Fisher Scientific, USA). Quality control checks and gene expression analysis were performed using the Transcriptome Analysis Console 4.0 Software (Thermo Fisher Scientific, USA). The gene expression levels were computed using the Robust Multi-array Average (RMA) algorithm whereby the probe signal intensities were background-corrected, quantile-normalized, and log2-transformed. Inter-sample differences in gene expression levels were determined by the one-way analysis of variance (one-way ANOVA). A gene was considered differentially expressed between two samples when the positive or negative fold change exceeded 2, and the p-value was less than 0.05.

label: Biotin

source_name: CSCs derived from OSCC SAS, OSCC tumour stage 2, less responsive to cisplatin treatment, higher IC50 of cisplatin

label_protocol: Biotinylated sense-strand cDNA was prepared using the GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., USA) according to the manufacturer’s instructions.

growth_protocol: SAS cells were cultured in Dulbecco’s Modified Eagle’s Medium/ Ham’s Nutrient Mixture F12 (DMEM/F12; Nacalai Tesque Inc., Japan), supplemented with 10 % fetal bovine serum (GE Healthcare Life Sciences, USA) and 1 % penicillin/streptomycin (Nacalai Tesque Inc., Japan). H103 cells were cultured in a growth medium of a similar composition but with added 0.5 µg/mL sodium hydrocortisone succinate (Sigma-Aldrich, USA). All the cells were maintained in 37 ºC incubator with humidified atmosphere of 5 % CO2.

extract_protocol: Total RNA was isolated using innuPREP RNA Mini Kit (Analytik Jena, Germany). Subsequently, contaminating genomic DNA was removed by DNase 1 treatment using RapidOut DNA Removal Kit (Thermo Fisher Scientific Inc., USA). In brief, 100 ng of purified RNA was prepared for a whole transcriptomic analysis using the Affymetrix GeneChip Human Clariom S Array (Thermo Fisher Scientific Inc., USA).

treatment_protocol: No treatment was performed on the cells prior to the RNA extraction.

tag: tumour stage

value: Stage 2

tag: tissue origin

value: tongue


title: Lsd1 KO rep2


title: SAS tumour spheres, biological replicate 3


title: TTN.SID-386

description:
TTN.SID-386
EMB


title: TKO rep1


title: Lsd1 KO rep1


title: TTN.SID-303

description:
TTN.SID-303
EMB


title: SAS cell, biological replicate 3

source_name: OSCC tumour stage 2, more responsive to cisplatin treatment, lower IC50 of cisplatin


title: SAS tumour spheres, biological replicate 1


title: RBM20.SID-602

description:
RBM20.SID-602
EMB


title: TTN.SID-245

description:
TTN.SID-245
EMB


title: QKO rep1


title: Jurkat_USP7shRNA4058_2 [SJTALL061903_C2]


title: SAS cell, biological replicate 2


title: SAS cell, biological replicate 1


title: Jurkat_scrambled_1 [SJTALL061901_C1]

source_name: Jurkat cell line treated with scrambled siRNA


title: Scram rep3


title: RBM20.SID-236

description:
RBM20.SID-236
EMB


title: Jurkat_WT_2 [SJTALL061900_C2]


title: Scram rep1


title: TTN.SID-131

description:
TTN.SID-131
EMB


title: MYH7.SID-504

description:
MYH7.SID-504
EMB


title: Jurkat_scrambled_2 [SJTALL061901_C2]


title: Jurkat_USP7shRNA4057_1 [SJTALL061902_C1]


title: H103 cell, biological replicate 3

source_name: OSCC tumour stage 1, less responsive to cisplatin treatment, higher IC50 of cisplatin

value: Stage 1


title: Acute myeloid leukemia cell line U937

type: genomic

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

country: Germany

institute: University of Freiburg Medical Center

hyb_protocol: according to manufacturer (Affymetrix)

scan_protocol: according to manufacturer (Affymetrix)

data_processing: CEL files were analysed using the Affymetrix Chromosome Analysis Suite ChAS (USCD-AMl1/ELF-153/KG-1) and the Affymetrix Genoyping Console Software (U937); data was annotated to the reference genome assembly GRCh37(hg19).

molecule: genomic DNA

source_name: Acute myeloid leukemia cell line U937

label_protocol: Samples were labeled using the Affymetrix CytoScan Reagent and the SNP 6.0 Core Reagent Kits (USCD-AML1/ELF-153/KG-1 and U937, respectively)

growth_protocol: KG-1 and U937 were grown in RPMI supplemented with 10 % fetal calf serum and 1 % penicillin/streptomycin. UCSD-AML1 and ELF-153 were grown in RPMI supplemented with 20 % fetal calf serum, 1 % penicillin/streptomycin and 5 ng/ml human GM-CSF.

extract_protocol: Genomic DNA was extracted using the Quiagen DNeasy Blood and Tissue DNA extraction Kit according to manufacturer's protocol.

treatment_protocol: All cell lines were untreated prior to SNP analysis.

value: Acute myeloid leukemia cell line


title: H103 cell, biological replicate 2


title: pdhR ALE-2 Replicate_2

status: Public on Mar 08 2021

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode
Estimated the dispersion of each gene using DESeq2
Transcript per Million (TPM) were calculated by DESeq2
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: csv file includes TPM values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as carbon source. The culture was incubated at 37C overnight with shaking, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with shaking to the mid-log phase (OD600 ≈ 0.5).

extract_protocol: KAPA Stranded RNA-Seq Kit

treatment_protocol: M9 minimal media w/ 4g/L glucose

tag: protocol

value: M9 minimal media w/ 4g/L glucose


title: pdhR ALE-2 Replicate_1


title: pdhR ALE-3 Replicate_1


title: pdhR ALE-1 Replicate_2


title: pdhR ALE-4 Replicate_1


title: pdhR ALE-4 Replicate_2


title: Scram rep2


title: pdhR ALE-3 Replicate_2


title: pdhR ALE-1 Replicate_1


title: H103 cell, biological replicate 1


title: R7941 (10X-TETD #2)

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using Bowtie2 to Mycobacterium tuberculosis complete genome H37Rv
Gene counts were obtained using featureCounts on AL123456.3
Genome_build: H37Rv
Supplementary_files_format_and_content: gene_counts

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacteria

growth_protocol: Early log phase cultures (OD600nm ~ 0.2) of Mycobacterium tuberculosis grown in Middlebrook 7H9 medium were used

extract_protocol:
The TETD tretaed M. tuberculosis cultures were processed for total RNA isolation by TRIzol reagent as per manufacturer’s protocol. Mtb total RNAs were analyzed using an Agilent Bioanalyser for quality assessment with a RNA Integrity Number (RIN) range of 6.2 to 9.7 and a median of 8.1. Ribosomal RNA (rRNA) were depleted from 500ng of bacterial RNA using RiboMinus™ Bacteria Transcriptome Isolation Kit (Invitrogen Thermo Fisher Scientific), according to manufacturer's protocol.
cDNA libraries were prepared from rRNA depleted mRNA using Lexogen SENSE Total RNA-Seq Library Prep Kit according to manufacturer's protocol. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2 x 151 cycles on an Illumina HiSeq 4000 system.

treatment_protocol: M. tuberculosis cultures were either treated with 1x- or 10x-MIC99 concentration of disulfiram (TETD) for 24 h. DMSO tretaed M. tuberculoiss were kept as controls.

tag: treatment group

value: TETD 10x


title: R7942 (10X-TETD #3)


title: R7938 (1X-TETD #4)

value: TETD  1x


title: R7939 (1X-TETD #5)


title: R7936 (1X-TETD #2)


title: R7934_R (DMSO #4)

value: DMSO control


title: R7937 (1X-TETD #3)


title: R7943 (10X-TETD #4)


title: Jurkat_WT_1 [SJTALL061900_C1]


title: R7933 (DMSO #3)


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 167

city: Olsztyn

first: Maciej

last: Florczyk

address: Słoneczna 45G

country: Poland

institute: University of Warmia and Mazury in Olsztyn

data_processing:
To remove adapter sequences and low-quality bases, the reads were processed using Trimmomatic, version 0.36
After quality trimming, every 6th read (starting from the 6th) was selected for downstream analysis.
Genome_build: Selected reads were assembled into a reference genome using Trinity, version 2.5.1
Trinity de novo assembled genome was filtered for redundant transcripts using the cd-hit-est algorithm of CD-HIT, with a sequence identity threshold of 0.9.
Filtering by expression was executed with RSEM implemented by the Trinity-provided perl script ‘align_and_estimate_abundance’.
Next, the transcripts were searched for open reading frames (ORFs) by Transdecoder, version 2.0.1.
To identify protein coding transcripts, ORFs and transcripts were searched against the UniProt-Swiss-Prot and Atlantic salmon proteins reference databases (GCF_000233375.1) using blastp and blastx from the BLAST+ suite with a threshold E-value of 1 × 10−3
Protein family searches were performed with the Pfam 32.0 database [78] using the ORF protein sequences in HMMER, version 3.2.1.
Finally, the top BLAST hit based on the bit score, E-value and percent alignment, and all HMMER hits were loaded into Trinotate, version 3.2.1, to generate an annotation report. Based on the report, transcripts that were not coding were then filtered against the RFAM database, version 12.0, by the cmscan algorithm implemented by Infernal, version 1.1.3.
Any hit that Infernal considered significant using the default parameters was filtered out (and labeled as a known ncRNA).
All remaining putative novel NCTs were further validated by calculating coding potential using Coding Potential Calculator (CPC)
To further verify that the remaining contigs were completely separated from mRNAs, putative novel non-coding transcripts were subjected to a blastn search against the Reference RNA Sequences database (NCBI, refseq_rna).
At this point, all transcripts that were considered to be putative novel ncRNAs, were counted in each sequenced sample using samtools idxstats
Contigs that were differentially expressed in the MC-LR-treated and the control (PBS) groups were indicated using the DESeq2 package, version 1.28.0 for R, version 3.6.3. Adjusted p-values were calculated with Benjamini and Hochberg’s method.
Supplementary_files_format_and_content: CSV files (comma separated) includes the output of the DESeq2 analysis as well as transcripts raw count for each sample.

organism: Coregonus lavaretus

source_name: liver

extract_protocol:
Total RNA was extracted from the RNAlater-preserved liver fragments (approximately 20 mg) using a PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. To remove the genomic DNA residue, the extracted samples were incubated with TURBO DNAse (Invitrogen, Carlsbad, CA, USA) and then purified using the PureLink RNA Mini Kit. RNA integrity was evaluated with an Agilent Bioanalyzer 2100 with an Agilent 6000 Nano Kit and the samples with mean RNA integrity number (RIN) > 8 were taken for library preparation with the Illumina TruSeq Stranded mRNA Library Prep protocol. The libraries were sequenced with an Illumina HiSeq4000 sequencer (250–300 bp insert cDNA size, PE150, 50 M reads, 15 Gb).
Illumina TruSeq Stranded mRNA Library Prep

tag: agent

value: MC-LR

tag: time point

value: Rutki-strain


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 166


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 108


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 168


title: R7932 (DMSO #2)


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 46


title: R7944 (10X-TETD #5)


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 102


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 43


title: RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 59

value: PBS


title: RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 55


title: RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 58


title: RNA-Seq of Coregonus lavaretus after PBS injection – individual no. 52


title: 5.SBP.24b

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

description:
RD89
mRNA

data_processing:
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the A. niger NRRL 3 genome (Aguilar‐Pontes et al., 2018) using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Genome_build: Aspergillus niger NRRL 3 genome (Aguilar‐Pontes et al., 2018).
Supplementary_files_format_and_content: .txt files represent number of raw read counts mapping to each gene.

organism: Aspergillus niger

source_name: Aspergillus niger N593 delta-kusA

growth_protocol: The strains were grown at 30°C using Minimal Medium (MM, pH 6) or Complete Medium (CM, pH 6) with the appropriate carbon source. When required, media of auxotrophic strains were supplemented with 1.22 g/L uridine. All liquid cultures were incubated in an orbital shaker at 250 rpm and 30°C.

extract_protocol:
Total RNA was extracted from ground mycelial samples using TRIzol® reagent (Invitrogen) and purified with the NucleoSpin® RNA Clean-up Kit (Macherey-Nagel), while contaminant gDNA was removed by rDNase treatment directly on the silica membrane. The RNA quality and quantity were analysed with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA‐Seq, the TruSeq stranded mRNA (cat#20020594) was used to generate cDNA library for Illumina NextSeq550 platform according to the manufacturer protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).

treatment_protocol: The pre-cultures containing 250 ml CM with 2% D-fructose in 1 L Erlenmeyer flasks were inoculated with 10e6 spores/ml and incubated for 16 h. Subsequently, the mycelia were harvested by filtration on sterile cheesecloth, washed with MM and ~0.5 g (dry weight) was transferred to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 1% WB or 1% SBP. All cultures were performed in triplicate. After 2, 8 and 24 h of incubation, the mycelia were harvested by vacuum filtration, dried between tissue paper and frozen in liquid nitrogen.

value: lxrA/lxrB

value: mycelia

tag: medium

value: 1xMM + 1% sugar beet pulp

value: 24 hr


title: 5.SBP.24c

description:
RD90
mRNA

tag: tissue


title: 5.WB.24c

description:
RD81
mRNA

tag: genotype

value: 1xMM +1% wheat bran


title: 5.SBP.2a

description:
RD82
mRNA

value: 2 hr


title: 5.SBP.8b

description:
RD86
mRNA

value: 8 hr


title: 5.SBP.2b

description:
RD83
mRNA


title: 5.SBP.8c

description:
RD87
mRNA


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 47


title: 5.WB.8c

description:
RD78
mRNA


title: 5.WB.24a

description:
RD79
mRNA


title: 5.SBP.24a

description:
RD88
mRNA


title: RNA-Seq of Coregonus lavaretus after MC-LR injection – individual no. 110


title: 5.SBP.2c

description:
RD84
mRNA


title: 5.WB.24b

description:
RD80
mRNA


title: 5.SBP.8a

description:
RD85
mRNA


title: 5.WB.2c

description:
RD75
mRNA


title: 5.WB.2b

description:
RD74
mRNA


title: 5.WB.8a

description:
RD76
mRNA


title: 5.WB.2a

description:
RD73
mRNA


title: 4.SBP.24c

description:
RD72
mRNA

value: ladA/xdhA/sdhA


title: 4.SBP.24a

description:
RD70
mRNA


title: 5.WB.8b

description:
RD77
mRNA


title: 4.SBP.8c

description:
RD69
mRNA


title: 4.SBP.24b

description:
RD71
mRNA


title: 4.SBP.8a

description:
RD67
mRNA


title: 4.SBP.8b

description:
RD68
mRNA


title: 4.SBP.2b

description:
RD65
mRNA


title: 4.SBP.2c

description:
RD66
mRNA


title: 4.SBP.2a

description:
RD64
mRNA


title: 4.WB.24c

description:
RD63
mRNA


title: 4.WB.24b

description:
RD62
mRNA


title: 4.WB.24a

description:
RD61
mRNA


title: 4.WB.8c

description:
RD60
mRNA


title: 4.WB.2c

description:
RD57
mRNA


title: 4.WB.8b

description:
RD59
mRNA


title: 3.SBP.24c

description:
RD54
mRNA

value: larA/larB/xyrA


title: 3.SBP.24b

description:
RD53
mRNA


title: 4.WB.2a

description:
RD55
mRNA


title: 3.SBP.24a

description:
RD52
mRNA


title: 3.SBP.8c

description:
RD51
mRNA


title: 3.SBP.8b

description:
RD50
mRNA


title: 3.SBP.8a

description:
RD49
mRNA


title: 3.SBP.2c

description:
RD48
mRNA


title: 3.SBP.2b

description:
RD47
mRNA


title: 3.WB.24c

description:
RD45
mRNA


title: 3.SBP.2a

description:
RD46
mRNA


title: 3.WB.24b

description:
RD44
mRNA


title: 3.WB.8c

description:
RD42
mRNA


title: 3.WB.8b

description:
RD41
mRNA


title: 3.WB.24a

description:
RD43
mRNA


title: 3.WB.2b

description:
RD38
mRNA


title: 3.WB.2c

description:
RD39
mRNA


title: 3.WB.8a

description:
RD40
mRNA


title: 4.WB.8a

description:
RD58
mRNA


title: 4.WB.2b

description:
RD56
mRNA


title: 2.SBP.24b

description:
RD35
mRNA

value: xkiA


title: 2.SBP.24c

description:
RD36
mRNA


title: 2.SBP.24a

description:
RD34
mRNA


title: EPCAM

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
FASTQ files were generated using the Cell Ranger v3.0.2 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic human reference using Cell Ranger v3.0.2 (10X Genomics) to generate count matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 gene count matrices

source_name: lung explant

extract_protocol: Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit v2 following the manufacturer’s user guide.

tag: cell type

value: EPCAM+

value: lung

value: IPF


title: SSc_Digest_060

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie v4.2.2 against the GENCODE Basic gene model on the human genome assembly GRCh38.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV count matrices

source_name: Digest

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

tag: disease

value: SSc-ILD


title: SSc_Digest_051


title: SSc_Digest_039


title: SSc_Biopsy_059

source_name: Biopsy


title: 2.SBP.8a

description:
RD31
mRNA


title: 2.SBP.8b

description:
RD32
mRNA


title: 2.SBP.8c

description:
RD33
mRNA


title: SSc_Biopsy_050


title: 2.SBP.2b

description:
RD29
mRNA


title: 2.SBP.2c

description:
RD30
mRNA


title: CD90


title: SSc_BAL_052

source_name: Bronchoalveolar lavage


title: 3.WB.2a

description:
RD37
mRNA


title: Normal_Digest_079

value: Normal


title: SSc_Biopsy_038


title: Normal_Digest_066


title: 2.SBP.2a

description:
RD28
mRNA


title: 2.WB.24b

description:
RD26
mRNA


title: Primary microglial culture exposed to hypoxia (1% O2, 6h), biological rep1

city: Seville

first: Clara

last: Ortega-de San Luis

address: Av. Manuel Siurot S/N

country: Spain

institute: Instituto de Biomedicina de Sevilla (IBiS); Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data from the extraction software Expression Console was imported to the R statistical processing environment using the LIMMA/Bioconductor package. Quality of the data was assessed using Array Quality Metrics package. Data were normalized using Robust Multi-Array (RMA) method using LIMMA/Bioconductor package.
MTA-1_0 data
MTA-1_0.na34.mm10.transcript.csv

source_name: Primary microglial culture 3, hypoxia

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Primary microglial culture from P0 CD1 mouse pups. 5 mice were used and pooled.

extract_protocol: RNA was extracted with TRIZOL reagent following the recommended protocol

treatment_protocol: Exposition to either Normoxia (21% oxygen) or Hypoxia (1% oxygen) for 6 h in a Hypoxia chamber (InvivO2 300; Ruskinn)

tag: oxygen concentration

value: Hypoxia

value: Microglia


title: Primary microglial culture exposed to hypoxia (1% O2, 6h), biological rep2

source_name: Primary microglial culture 4, hypoxia


title: Primary microglial culture, biological rep3

source_name: Primary microglial culture 6, normoxia

value: Normoxia


title: Primary microglial culture exposed to hypoxia (1% O2, 6h), biological rep3

source_name: Primary microglial culture 6, hypoxia


title: 2.WB.24a

description:
RD25
mRNA

value: mycelia


title: Primary microglial culture, biological rep1

source_name: Primary microglial culture 3, normoxia


title: 2.WB.8c

description:
RD24
mRNA


title: 2.WB.8a

description:
RD22
mRNA


title: Primary microglial culture, biological rep2

source_name: Primary microglial culture 4, normoxia


title: Normal_Digest_045


title: 2.WB.2c

description:
RD21
mRNA


title: Normal_BAL_067


title: SSc_BAL_061


title: 2.WB.24c

description:
RD27
mRNA


title: Normal_Biopsy_078


title: 1.SBP.24c

description:
RD18
mRNA

value: parent

value: 1xMM + 1% sugar beet pulp


title: Normal_Biopsy_065


title: 2.WB.2b

description:
RD20
mRNA

value: 1xMM +1% wheat bran


title: Normal_Biopsy_062


title: 1.SBP.24b

description:
RD17
mRNA

value: 24 hr


title: 2.WB.2a

description:
RD19
mRNA

value: 2 hr


title: Normal_BAL_064


title: 2.WB.8b

description:
RD23
mRNA

value: 8 hr


title: Normal_Digest_033


title: Normal_BAL_046


title: Normal_Digest_063


title: 1.SBP.24a

description:
RD16
mRNA


title: Normal_BAL_034


title: 1.SBP.8b

description:
RD14
mRNA


title: 1.SBP.8a

description:
RD13
mRNA


title: IPF_Digest_069


title: IPF_Digest_191


title: IPF_Digest_074


title: IPF_Digest_077


title: 1.SBP.2b

description:
RD11
mRNA


title: 1.SBP.2a

description:
RD10
mRNA


title: 1.SBP.2c

description:
RD12
mRNA


title: 1.WB.24c

description:
RD9
mRNA


title: IPF_Digest_048


title: 1.WB.24a

description:
RD7
mRNA


title: IPF_Digest_054


title: IPF_Digest_057


title: 1.WB.8c

description:
RD6
mRNA


title: 1.WB.24b

description:
RD8
mRNA


title: 1.WB.2c

description:
RD3
mRNA


title: IPF_Digest_042


title: 1.SBP.8c

description:
RD15
mRNA


title: IPF_Biopsy_190


title: 1.WB.2b

description:
RD2
mRNA


title: 1.WB.8a

description:
RD4
mRNA


title: IPF_Biopsy_076


title: IPF_Digest_036


title: 1.WB.2a

description:
RD1
mRNA


title: IPF_Biopsy_071


title: 1.WB.8b

description:
RD5
mRNA


title: IPF_Digest_072


title: IPF_Biopsy_073


title: mutant_glucose_B

city: Claremont

first: Daniel

last: Stoebel

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

data_processing:
Fastq files were mapped to the V. cholerae biovar El Tor str. N16961 genome (NCBI accession GCA_000006745.1) using the bwa-mem algorithm in BWA version 0.7.12
Aligned reads were counted with htseq-count version 0.11.2 with the intersection-strict argument
Counts were imported into R version 3.6.2 and differential expression was assessed with DEseq2 version 1.26.0
Genome_build: GenBank assembly accession: GCA_000006745.1
Supplementary_files_format_and_content: counts

organism: Vibrio cholerae

source_name: Bacterial culture

growth_protocol: Cells from LB-agar plates were used to inoculate 2 mL of 1X M9 minimal medium supplementedwith 0.1% (wt/vol) trace metals (5% MgSO4, 0.5% MnCl2, 0.5% FeCl3, 0.4% nitrilotriacetic acid) and 0.4% glucose or fructose (w/v). Overnight cultures were diluted into 2 mL fresh 1X M9 medium (+ trace metals) with 0.4% glucose or fructose (starting OD600 ~ 0.05) and grown to an OD600 ~0.30.

extract_protocol: The entire culture was harvested (8,000 x g, 5 min, 4 °C) and the RNA was purified from the cells using the Direct-zol RNA Miniprep kit (Zymo Research) following the manufacturer’s instructions. Eluted samples were treated with DNase at 37 °C for 30 minutes, twice, using Turbo DNA-free (Ambion), according to the manufacturer’s protocol. RNA integrity was initially analyzed by agarose gel electrophoresis.

value: O1 biovar El Tor 484  N16961 deltatcpA

value: deltacra mutant

tag: carbon source

value: glucose


title: IPF_Biopsy_068

value: lung


title: mutant_glucose_A


title: wildtype_glucose_B

value: wildtype


title: IPF_Biopsy_056

value: IPF


title: mutant_fructose_B

value: fructose


title: IPF_Biopsy_053


title: IPF_Biopsy_041


title: wildtype_glucose_A


title: IPF_Biopsy_035


title: Normal_Biopsy_044

value: Normal


title: mutant_fructose_A


title: IPF_BAL_192


title: wildtype_fructose_A


title: IPF_BAL_070


title: IPF_BAL_058


title: IPF_BAL_075


title: Low3

city: Shanghai

first: donghong

last: Cai

address: Yueyang Street

institute: PICB, CAS

description: DNA-seq

library_source: genomic

data_processing:
Library strategy: DNA-seq
First, we generated the read counts for all samples and merged into the matrix from the public pgRNA screening dataset
Then normalized the data by “median ratio normalization” and estimated the significant pgRNA by the negative binomial distribution. For estimating the essential lncRNAs, MAGeCK was applied α-Robust rank aggregation for 20 pgRNA to target each lncRNA to calculate the RRA score.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

growth_protocol: 293T cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin/Streptomycin.

extract_protocol:
The genomic DNA of every replicate from 4 X 106 live cells was isolated using QIAamp DNA mini kit (Qiagen).
The genomic DNA was subjected to 2 step PCR. For the first PCR, the amount of input gDNA was more than 200X coverage of designed gRNA library (assuming 106 cells have 6.6 ug genome DNA), which calculated as 20ug for genomic DNA PCR. For each sample, at least 5 independent PCR reactions were done, then all the amplicons were pooled together. gRNAs were amplified by PCR (NEB Q5 hot start DNA polymerase) with 28 cycles of reaction using primers targeting U6 promoter and linker between two guide RNAs of each pair. Then the PCR products were second amplified with the Illumina adapter and index sequence. The PCR products were purified with QIAquick PCR purification kit (Qiagen), followed by Illumina deep sequencing.

treatment_protocol: After stimulated by 10ng/ml TNF, the cells were selected for GFP high and GFP low by FACS

value: GFP low

tag: cell line


title: Low2

description: DNA-seq


title: wildtype_fructose_B


title: High3

description: DNA-seq

value: GFP high


title: IPF_BAL_043


title: IPF_BAL_055


title: High1

description: DNA-seq


title: Low1

description: DNA-seq


title: IPF_BAL_049


title: Input, 293T

description: DNA-seq

value: total sgRNAs


title: IPF_BAL_037


title: SAEC_Plastic_Senescent_Day12_331

source_name: Small airway epithelial cells

value: SAEC

value: Plastic Senescent Day 12


title: IPF_Biopsy_047


title: A375-KD-EZH2

city: Beijing

first: Lin

last: Shan

address: 10 You’anmen Outer West 1st Street

institute: Capital Medical University

data_processing:
ChIP-seq reads quality control performed using FastQC v0.11.5 and  cutadapt v1.8.3
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2
ChIP-seq peaks were called using macs2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq  bed files were generated using macs2

source_name: A375 cells

growth_protocol: A375 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Approximately 5X107 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by polyclonal antibodies against USP7, EZH2, H3K27me3 or H2BK120ub1. The DNA samples were purified with the Qiagen PCR purification kit before in-depth whole genome DNA sequencing was performed by CapitalBio Corporation (Beijing, China).
The raw sequencing image data were examined by the Illumina analysis pipeline, aligned to the unmasked human reference genome (hg19) using Bowtie2, and further analyzed by MACS (Model-based Analysis for ChIP-seq).

treatment_protocol: Infection with shRNA against USP7 were performed using polybrene reagent according to the manufacturer's insturctions.

value: knockdown of USP7

tag: chip antibody


title: SAEC_Plastic_Senescent_Day12_330

tag: treatment


title: A375-KD-USP7


title: A375-KD-input


title: SAEC_Plastic_Senescent_Day12_329


title: SAEC_Plastic_Senescent_Day5_327

value: Plastic Senescent Day 5


title: A375-NC-EZH2

value: untreated


title: SAEC_Plastic_Senescent_Day5_326


title: A375-NC-input


title: High2

description: DNA-seq


title: A375-KD-H2BK120ub1


title: A375-KD-input-H2BK120ub1


title: SAEC_Plastic_Control_Day5_324

value: Plastic Control Day 5


title: A375-A-Input-H2BK120ub1


title: SAEC_Matrigel_Senescent_Day5_322

value: Matrigel Senescent Day 5


title: SAEC_Plastic_Control_Day5_323


title: SAEC_Matrigel_Senescent_Day5_321


title: SAEC_Matrigel_Senescent_Day5_320


title: A375-A-H2BK120ub1


title: A375-KD-input-H3K27me3


title: A375-KD-H3K27me3


title: SAEC_Plastic_Senescent_Day5_328


title: SAEC_Matrigel_Control_Day5_319

value: Matrigel Control Day 5


title: A375-A-Input-H3K27me3


title: SAEC_Matrigel_Control_Day5_317


title: SAEC_Matrigel_Control_Day5_318


title: A375-A-H3K27me3


title: SAEC_H2O2_50uM_442

value: H2O2 50uM


title: SAEC_H2O2_100uM_441


title: SAEC_H2O2_100uM_440


title: SAEC_Doxorubicin_500nM_439

value: Doxorubicin 500nM


title: SAEC_DMSO_437

value: DMSO


title: SAEC_DMSO_436


title: BEC_Doxorubicin_250nM_447

source_name: Basal epithelial cells

value: BEC

value: Doxorubicin 250nM


title: BEC_Doxorubicin_250nM_449


title: BEC_Doxorubicin_250nM_448


title: BEC_DMSO_446


title: SAEC_H2O2_50uM_443


title: BEC_DMSO_445


title: BEC_DMSO_444


title: Doxorubicin_927

source_name: Normal human bronchial epithelial cells

value: NHBE

value: lung

value: Doxorubicin 500 nM


title: SAEC_Doxorubicin_500nM_438


title: Doxorubicin_925


title: miR-378a mimic + IL-17A, biological rep4

city: Solna

first: Enikö

last: Sonkoly

state: Stockholm

address: Visionsgatan 18

department: Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from primary human keratinocytes transfected with miR-378a mimic and treated with IL-17A

hyb_protocol: Affymetrix GeneChip Human Gene 2.0 ST arrays were hybridized to 6ug of biotin labeled cDNA, washed and stained according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G (GCS 3000 7G)

data_processing: The data were analyzed with Trancriptome Analysis Console 4.0 (TAC 4.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: miR-378a mimic + IL-17A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary human keratinocytes (NHEK, Thermo Fisher Scientific, Catalog# C0055C) were cultured at 37 °C in 5% CO2 in EpiLife serum-free medium (Thermo Fisher Scientific) containing Human Keratinocyte Growth Supplement (HKGS) (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) antibiotics. For RNA extraction and quantitative real-time PCR experiments, cells were seeded in 24-well plates at a density of 40,000 cells/well.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Keratinocytes in monolayer cultures were transfected with 1 nM mirVana™ miRNA Mimic miR-378a or Negative Control #1 (Thermo Fisher Scientific) using Lipofectamine 2000 (Thermo Fisher Scientific). Upon transfection, cells were treated with IL-17A (100 ng/ml) (R&D Systems) for the indicated time points.

value: primary human keratinocytes


title: miR-378a mimic + IL-17A, biological rep1


title: Mimic control + IL-17A, biological rep3

description: Gene expression data from primary human keratinocytes transfected with mimic control and treated with IL-17A

source_name: Mimic control + IL-17A


title: miR-378a mimic + IL-17A, biological rep3


title: miR-378a mimic + IL-17A, biological rep2


title: Mimic control + IL-17A, biological rep4


title: miR-378a mimic, biological rep4

description: Gene expression data from primary human keratinocytes transfected with miR-378a mimic

source_name: miR-378a mimic


title: Mimic control + IL-17A, biological rep2


title: Mimic control, biological rep4

description: Gene expression data from primary human keratinocytes transfected with mimic control

source_name: Mimic control


title: miR-378a mimic, biological rep2


title: miR-378a mimic, biological rep1


title: miR-378a mimic, biological rep3


title: Mimic control, biological rep1


title: Doxorubicin_923


title: Mimic control, biological rep2


title: GFP-positive_TAAR5-Cre&L10-GFP_H3K9me3_Input

first: Qian

address: 280 South Chongqing Road, Building No.5, Room 408

department: Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were mapped to the mouse reference genome (mm10) with Bowtie 2 (version 2.2.9) using the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: GFP-positive cells sorted from TAAR5-Cre&L10-GFP mice

extract_protocol:
ULI-ChIP-seq of H3K9me3 was performed as previously described (Brind'Amour, J. et al. An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat Commun 6, 6033, 2015.) except for the library preparation portion. For each reaction, 1,000–10,000 cells and 0.25 ug of antibody (ABclonal, A2360) were used.
Libraries were prepared with an NEBNext Ultra kit (NEB) and 12–15 PCR cycles.

tag: strain

tag: age

value: Adult

tag: antibody

value: input


title: Mimic control, biological rep3


title: Mimic control + IL-17A, biological rep1


title: GFP-negative_TAAR5-Cre&L10-GFP_H3K9me3_Input

source_name: GFP-negative cells sorted from TAAR5-Cre&L10-GFP mice


title: Doxorubicin_921


title: Doxorubicin_919


title: DMSO_926


title: GFP-negative_TAAR5-Cre&L10-GFP_H3K9me3_ChIPseq


title: H3K27ac - HFFc6-R4

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street, AS5-1049

department: Program in Systems Biology

institute: University of Massachusetts Medical School

description:
Subclone c6 of HFF-hTERT
HFFc6_H3K27ac.bigWig

data_processing:
Library strategy: Cut&Tag
All datasets proseed uning nf-core  ATAC Seq pipeline  ( https://nf-co.re/atacseq )
BWA is used for mapping the fastq files to hg38 reference genome
MACS2 with default parameters is used to find the enriched peaks
BEDtools intersect is used to find the loop anchors that have MACS2 peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bw files  for genome wide read coverage, bed files for peaks

growth_protocol: 4DN Protocols are  used to culture the cells. Protocols can be found here: https://data.4dnucleome.org/resources/experimental-resources/cell-lines

extract_protocol:
The  referenced protocols are used to generate these datasets. Cut&Tag: Kaya-Okur et al. 2020, Cut&Run:  Janssens et al. 2019, ATAC-Seq:Buenrostro JD et al. 2013.
Libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: Cut&Run

tag: enzyme

value: MNase


title: GFP-positive_TAAR5-Cre&L10-GFP_H3K9me3_ChIPseq


title: DMSO_924


title: H3K27ac - HFFc6-R1


title: H3K27ac - HFFc6-R2


title: H3K4me3 - HFFc6-R4

description:
Subclone c6 of HFF-hTERT
HFFc6_H3K4me3.bigWig


title: DMSO_920


title: DMSO_918


title: H3K4me3 - HFFc6-R3


title: H3K4me3 - HFFc6-R2


title: U54-HFFc6-NS-AT-R2-T2

description:
Subclone c6 of HFF-hTERT
HFFc6_Atacseq.mRp.clN_peaks.narrowPeak
HFFc6_Atacseq.mRp.clN.bigWig

data_processing:
All datasets proseed uning nf-core  ATAC Seq pipeline  ( https://nf-co.re/atacseq )
BWA is used for mapping the fastq files to hg38 reference genome
MACS2 with default parameters is used to find the enriched peaks
BEDtools intersect is used to find the loop anchors that have MACS2 peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bw files  for genome wide read coverage, bed files for peaks

value: ATAC-Seq


title: U54-HFFc6-NS-AT-R2-T1


title: U54-HFFc6-NS-AT-R2-T3


title: U54-HFFc6-NS-AT-R2-T4


title: U54-HFFc6-NS-AT-R1-T2


title: U54-HFF-plate-FA-MNase-20190509-R2-T1

description: Micro-C on HFF cells with 1% Formaldehyde

data_processing:
Distiller (https://github.com/mirnylab/distiller-nf) pipeline is used to process Hi-C and Micro-C datasets.
Sequencing reads were mapped to hg38 using bwa mem with flags-SP.
Mapped reads were parsed and classified using the pairtools package  (https://github.com/mirnylab/pairtools ) to get 4DN-compliant pairs files.
PCR and/optical duplicates removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ >  30)  on each side of aligned chimeric read, binned into multiple resolutions and low coverage bins are removed.
Multiresolution cooler files are created using cooler package (https://github.com/mirnylab/cooler.git)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Compartment Calls (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Insulation Boundaries (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Loop Calls (https://github.com/open2c/cooltools)

source_name: Human Foreskin Fibroblasts

growth_protocol: 4DN Protocols are  used to culture the cells. Protocols can be found here: https://data.4dnucleome.org/resources/experimental-resources/cell-lines, https://data.4dnucleome.org/biosources/4DNSRGTEEYSL/?redirected_from=%2F4DNSRGTEEYSL. Hela S3 syncronization protocols are adopted from Abramo et al.2019. Nat Cell Biol.

extract_protocol:
Nuclei was extracted by lyse cells in lysis buffer containing NP40 and protease inhibitor.
DNA library was generated by biotin fill-in followed blunt end ligation. Then removal of biotin from un-ligated ends, sonication, end repair, biotin pull-down, Illumina adaptor ligation and paired end PCR.
Hi-C library generated Hi-C 2.0 protocol. Belaghzal et at.2017.

value: Micro-C

value: HFF


title: U54-HFFc6-NS-AT-R1-T4


title: H3K27ac - HFFc6-R3


title: U54-HFFc6-NS-AT-R1-T1


title: U54-HFFc6-NS-AT-R1-T3


title: U54-HFF-plate-EGS-MNase-20190509-R2-T1

description: Micro-C on HFF cells with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HFF-plate-EGS-HindIII-20190718-R2-T1

description: In situ Hi-C with HindIII on HFF cells with 1% Formaldehyde and 3mM EGS crosslinking

value: in situ Hi-C

value: HindIII


title: U54-HFF-plate-DSG-MNase-20190509-R2-T1

description: Micro-C on HFF cells with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HFF-plate-FA-DpnII-20180904-R1-T1

description: In situ Hi-C with DpnII on HFF cells with 1% Formaldehyde

value: DpnII


title: U54-ESC-FA-DdeI-20190711-R2-T1

description: In situ Hi-C with DdeI on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde

source_name: Human Emriyonic stem cells

value: DdeI


title: U54-HFF-plate-FA-DdeI-20170119

description: In situ Hi-C with DdeI on HFF cells with 1% Formaldehyde


title: DMSO_922

value: DMSO


title: U54-HFF-plate-EGS-DpnII-20160902-R1-T1

description: In situ Hi-C with DpnII on HFF cells with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-ESC-DSG-microC-20170508-GTGAAA

description: Micro-C on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-END-DSG-DpnII-20190711-R2-T1

description: In situ Hi-C with DpnII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM DSG crosslinking

source_name: Endoderm

value: Endoderm


title: H3K4me3 - HFFc6-R1


title: U54-HFF-plate-DSG-DpnII-20170119

description: In situ Hi-C with DpnII on HFF cells with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HFF-plate-DSG-DdeI-20160812-R1-T1

description: In situ Hi-C with DdeI on HFF cells with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HelaS3-M-FA-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (mitotic) with 1% Formaldehyde

source_name: Hela S3

value: Hela S3


title: U54-HelaS3-NS-FA-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (non synchronized) with 1% Formaldehyde


title: U54-HelaS3-NS-EGS-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (non synchronized) with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HelaS3-NS-EGS-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (non synchronized) with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HelaS3-NS-FA-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (non synchronized) with 1% Formaldehyde


title: U54-HelaS3-NS-EGS-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (non synchronized) with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HFF-plate-FA-HindIIII-20160226-R2-T1

description: In situ Hi-C with HindIII on HFF cells 1% Formaldehyde


title: U54-HelaS3-NS-FA-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (non synchronized) with 1% Formaldehyde


title: U54-HFF-plate-DSG-HindIII-20160226-R1-T1


title: U54-HFF-plate-EGS-DdeI-20161031-R1-T1

description: In situ Hi-C with DdeI on HFF cells with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HelaS3-NS-DSG-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (non synchronized) with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HelaS3-NS-DSG-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (non synchronized) with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HelaS3-NS-DSG-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (non synchronized) with 1% Formaldehyde and 3mM DSG crosslinking


title: D7_MC943_EGFP

city: Isehara

first: Masahiro

last: Okabe

address: 143 Shimokasuya

country: Japan

institute: Tokai University School of Medicine

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC943 7 days after LMB2 injection

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized using Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D SG13164306) using one color scan setting for 8x60k array slides using scan protocol AgilentG3_HiSen_GX_1Color.

data_processing: The scanned images were analyzed with Feature Extraction Software11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: EGFP(+) podocytes, Day 7, Pod-hCD25T/G mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop.

extract_protocol: Podocytes were isolated from Pod-hCD25T/G mouse and sorted with FACSAria (BD Biosciences), and RNA was prepared using TRIzol LS Reagent (Thermo Fisher Scientific).

treatment_protocol: Heminephrectomy followed by 25 ng/gBW LMB2 injection

value: Kidney podocytes

tag: gender

value: male

tag: genetic background

tag: cell marker

value: EGFP

tag: time (day)


title: D7_MC824_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC824 7 days after LMB2 injection


title: D7_MC221_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC221 7 days after LMB2 injection

source_name: TdTomato(+) podocytes, Day 7, Pod-hCD25T/G mouse

value: TdTomato


title: D7_MC791_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC791 7 days after LMB2 injection


title: D7_MC791_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC791 7 days after LMB2 injection


title: D7_MC221_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC221 7 days after LMB2 injection


title: D4_MC822_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC822 4 days after LMB2 injection

source_name: EGFP(+) podocytes, Day 4, Pod-hCD25T/G mouse


title: D4_MC823_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC823 4 days after LMB2 injection

source_name: TdTomato(+) podocytes, Day 4, Pod-hCD25T/G mouse


title: D4_MC823_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC823 4 days after LMB2 injection


title: U54-HelaS3-M-EGS-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM EGS crosslinking


title: D4_MC822_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC822 4 days after LMB2 injection


title: U54-HelaS3-M-DSG-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HelaS3-M-EGS-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM EGS crosslinking


title: D4_MC692_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC692 4 days after LMB2 injection


title: D4_MC692_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC692 4 days after LMB2 injection


title: D4_MC151_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC151 4 days after LMB2 injection


title: D4_MC151_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC151 4 days after LMB2 injection


title: D1_MC542_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC542 1 day after LMB2 injection

source_name: TdTomato(+) podocytes, Day 1, Pod-hCD25T/G mouse


title: D1_MC831_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC831 1 day after LMB2 injection


title: U54-HelaS3-M-DSG-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM DSG crosslinking


title: U54-HelaS3-M-DSG-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (mitotic) with 1% Formaldehyde and 3mM DSG crosslinking


title: D1_MC541_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC541 1 day after LMB2 injection

source_name: EGFP(+) podocytes, Day 1, Pod-hCD25T/G mouse


title: U54-HelaS3-M-FA-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (mitotic) with 1% Formaldehyde


title: U54-HelaS3-G1-FA-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (G1 phase) with 1% Formaldehyde


title: U54-HelaS3-G1-FA-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (G1 phase) with 1% Formaldehyde


title: U54-HelaS3-G1-EGS-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HelaS3-M-FA-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (mitotic) with 1% Formaldehyde


title: D1_MC541_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC541 1 day after LMB2 injection


title: U54-HelaS3-G1-FA-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (G1 phase) with 1% Formaldehyde


title: D1_MC125_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC125 1 day after LMB2 injection


title: U54-HelaS3-G1-EGS-HindIII-20180730-R1-T1

description: In situ Hi-C with HindIII on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-HelaS3-G1-EGS-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM EGS crosslinking


title: D1_MC125_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC125 1 day after LMB2 injection


title: U54-ESC-FA-MNase-20170508-R1-T1

description: Micro-C on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde

value: Mnase


title: U54-ESC-FA-HindIII-20160311-R1-T1

description: In situ Hi-C on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde


title: SAEC_Plastic_Control_Day5_325

source_name: Small airway epithelial cells

value: SAEC

value: Plastic Control Day 5


title: D0_MC753_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC753 before LMB2 injection

source_name: TdTomato(+) podocytes, Day 0, Pod-hCD25T/G mouse


title: D0_MC742_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC742 before LMB2 injection


title: D0_MC753_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC753 before LMB2 injection

source_name: EGFP(+) podocytes, Day 0, Pod-hCD25T/G mouse


title: D0_MC731_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC731 before LMB2 injection


title: U54-ESC-FA-DpnII-20170119-R2-T1


title: D0_MC742_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC742 before LMB2 injection


title: D1_MC542_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC542 1 day after LMB2 injection


title: D0_MC731_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC731 before LMB2 injection


title: D0_MC122_EGFP

description: Gene expression in EGFP(+) podocytes sorted from a Pod-hCD25T/G mouse MC122 before LMB2 injection


title: D0_MC122_TdTomato

description: Gene expression in TdTomato(+) podocytes sorted from a Pod-hCD25T/G mouse MC122 before LMB2 injection


title: P10 whole lung input rep 1

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
Fastqc was run on the raw Fastq files to determine initial quality of reads.
Trimmomatic was performed to remove barcodes and poor quality bases.
Fastqc was run for quality control.
Bowtie alignment to the mm10 genomic with -m1 -k1 -v1 parameters and filtered for unmapped reads with sam file output
After alignment, sam files were converted to bam files and filtered for unmapped reads, chimeric alignments, low quality alignments, and PCR duplicates using Picard59 MarkDuplicates and samtools60 settings: -b -h -F 4 -F 1024 -F 2048 -q 30.
Peaks were then called using MACS263,64 with the default settings for NKX2-1, H3K4me3, and H3K27ac, and the –broad setting for the broad histone mark H3K4me1.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph
Supplementary_files_format_and_content: peaks.narrowPeak

source_name: Lung tissue

extract_protocol:
Whole lung ChIP-seq were performed as described in the associated paper and cell type specific ChIp-seqs were performed on chromatin from sorted nulcei based on a SunGFP reporter induced by recombination undercontrol of cell type specific Cre or CreERs.
ChIP DNA quantity was measured using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851). 2-5ng of sample DNA was used to generate sequencing libraries using the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Step 3.1 in the NEB protocol was skipped to improve sample retention per manufacturer’s recommendation. Samples were PCR amplified for 12 cycles and barcoded using indexing primers (New England BioLabs, E7335s or E7500S) followed by a final (.65 x -1 x bead volume) size selection and purification step using a SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size by gel electrophoresis and concentration measured using the Qubit HS dsDNA assay. Samples were then sequenced on the Illumina NextSeq500.

treatment_protocol: YT Sox9 mutants were induced at E15.5 with 3mg of Tamoxifen, GFP labeling of AT2 cells was carried out by 250ug of Tamoxifen at P4 for P7 AT2 cells and 3mg of Tamoxifen at 10 wks, 3 days prior harvest the adult.

value: whole lung

tag: replicate


title: U54-ESC-EGS-MNase-20170508-R1-T1

description: Micro-C on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM EGS crosslinking

value: Micro-C


title: 10wk AT2 cell input rep 1

value: 10 wk

tag: cell type


title: 10wk AT2 cell input rep 2


title: P7 AT2 cell input rep 2


title: U54-ESC-EGS-DdeI-20161118

description: In situ Hi-C with DdeI on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM EGS crosslinking

value: in situ Hi-C


title: U54-ESC-DSG-HindIII-20161206

description: In situ Hi-C with HindIII on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM DSG crosslinking

value: HindIII


title: P7 AT2 cell input rep 1


title: U54-HelaS3-G1-DSG-DpnII-20180709-R1-T1

description: In situ Hi-C with DpnII on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM DSG crosslinking

value: DpnII


title: U54-ESC-EGS-DpnII-20170119

description: In situ Hi-C with DpnII on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-ESC-DSG-DdeI-20161014

description: In situ Hi-C with DdeI on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM DSG crosslinking

value: DdeI


title: P15 YT Wnt3a AT1 cell input rep 2


title: 10wk AT1 cell input rep 2


title: P15 AT1 cell input rep 2


title: 10wk AT1 cell input rep 1


title: U54-ESC-DSG-20160722-DpnII

description: In situ Hi-C with DpnII on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM DSG crosslinking


title: P15 YT Wnt3a AT1 cell input rep 1


title: U54-HelaS3-G1-DSG-MNase-08072018-R1-T1

description: Micro-C on HeLa-S3 (G1 phase) with 1% Formaldehyde and 3mM DSG crosslinking

value: MNase


title: U54-ESC-EGS-HindIII-20161206

description: In situ Hi-C with HindIII on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-END-FA-Mnase-20170508-R1-T1

description: Micro-C on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde

value: Endoderm


title: E18-5 YT Sox9 CreER whole lung input rep 2


title: P7 AT1 cell NKX2-1 input rep 1


title: E18-5 YT Sox9 CreER whole lung input rep 1


title: P7 AT1 cell NKX2-1 input rep 2


title: U54-END-FA-DpnII-20170119

description: In situ Hi-C with DpnII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde


title: U54-END-EGS-Mnase-20170508-R1-T1

description: Micro-C on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM EGS crosslinking


title: E18-5 whole lung input rep 2


title: U54-END-EGS-DpnII-20170119

description: In situ Hi-C with DpnII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM EGS crosslinking


title: U54-END-FA-DdeI-20161118

description: In situ Hi-C with DdeI on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde


title: U54-END-EGS-HindIII-20161219

description: In situ Hi-C with HindIII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM EGS crosslinking


title: E18-5 whole lung input rep 1


title: U54-END-EGS-DdeI-20161219

description: In situ Hi-C with DdeI on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM EGS crosslinking


title: E14-5 whole lung input rep 1


title: E14-5 whole lung input rep 2


title: U54-END-DSG-Mnase-20170508-R1-T1

description: Micro-C on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM DSG crosslinking


title: 10wk AT2 cell H3K4me1 ChIP-seq rep 2

value: H3K4me1 (ab8895, Abcam)


title: U54-HFFc64DN-FA-DSG-MNase-R3-T2

description:
Micro-C on HFF cells with 1% Formaldehyde and 3mM DSG crosslinking
U54-HFFc6-FA-DSG-MNase-R1-R3.hg38.mapq.cis.100000.txt.gz
U54-HFFc6-FA-DSG-MNase-R1-R3.hg38.mapq.cis.100000.bw
U54-HFFc6-FA-DSG-MNase-R1-R3_hg38.txt.gz
U54-HFFc6-FA-DSG-MNase-R1-R3_hg38.mapq_30.1000.mcool
U54-HFFc6-FA-DSG-MNase-R1-R3.hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: 10wk AT2 cell H3K4me1 ChIP-seq rep 1


title: U54-END-DSG-HindIII-20161206

description: In situ Hi-C with HindIII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM DSG crosslinking


title: 10wk AT2 cell H3K27ac ChIP-seq rep 1

value: H3K27ac (ab4729, Abcam)


title: U54-HFFc64DN-FA-DSG-MNase-R3-T1


title: 10wk AT2 cell H3K4me3 ChIP-seq rep 1

value: H3K4me3 (ab4729, Abcam)


title: 10wk AT2 cell H3K27ac ChIP-seq rep 2


title: U54-END-FA-HindIII-031116-R1-T1

description: In situ Hi-C with HindIII on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde


title: U54-END-DSG-DdeI-20161031-R1-T1

description: In situ Hi-C with DdeI on definitive endoderm derived from H1 embryonic stem cells (Maehr lab protocol) with 1% Formaldehyde and 3mM DSG crosslinking


title: P15 AT1 cell input rep 1


title: U54-HFFc64DN-FA-DSG-MNase-R3-T5


title: 10wk AT2 cell H3K4me3 ChIP-seq rep 2


title: 10wk AT1 cell H3K4me1 ChIP-seq rep 2


title: U54-HFFc64DN-FA-DSG-MNase-R3-T7


title: U54-HFFc64DN-FA-DSG-MNase-R3-T6


title: 10wk AT1 cell H3K27ac ChIP-seq rep 1


title: 10wk AT1 cell H3K27ac ChIP-seq rep 2


title: U54-HFFc64DN-FA-DSG-MNase-R1-T3


title: 10wk AT1 cell H3K4me3 ChIP-seq rep 2


title: U54-HFFc64DN-FA-DSG-MNase-R1-T4


title: 10wk AT1 cell H3K4me3 ChIP-seq rep 1


title: P7 AT2 cell H3K4me3 ChIP-seq rep 2


title: U54-HFFc64DN-FA-DSG-MNase-R1-T5


title: U54-HFFc6-p22-FA-DpnII-20170327

description:
In  situ Hi-C with DpnII on Subclone c6 of HFF-hTERT cells with 1% Formaldehyde
U54-HFFc6-FA-DpnII-R1-R2.cis.100000.txt.gz
U54-HFFc6-FA-DpnII-R1-R2.cis.100000.bw
U54-HFFc6-FA-DpnII-R1-R2_hg38.txt.gz
U54-HFFc6-FA-DpnII-R1-R2_hg38.mapq_30.1000.mcool
U54-HFFc6-FA-DpnII-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: P7 AT2 cell H3K4me3 ChIP-seq rep 1


title: U54-HFFc64DN-FA-DSG-MNase-R1-T6


title: P7 AT1 cell H3K4me3 ChIP-seq rep 2


title: P7 AT1 cell H3K4me3 ChIP-seq rep 1


title: P10 whole lung H3K4me3 ChIP-seq


title: 10wk AT2 cell NKX2-1 ChIP-seq rep 2


title: U54-HFFc6-DSG-DpnII-20180319-R1-T1

description:
In situ Hi-C with DpnII on Subclone c6 of HFF-hTERT cells with 1% Formaldehyde and 3mM DSG crosslinking
U54-HFFc6-DSG-DpnII-R1-R2.cis.100000.txt.gz
U54-HFFc6-DSG-DpnII-R1-R2.cis.100000.bw
U54-HFFc6-DSG-DpnII-R1-R2_hg38.txt.gz
U54-HFFc6-DSG-DpnII-R1-R2_hg38.mapq_30.1000.mcool
U54-HFFc6-DSG-DpnII-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: U54-HFFc6-DSG-DpnII-20190102-R2-T1

description:
In  situ Hi-C with DpnII on Subclone c6 of HFF-hTERT cells with 1% Formaldehyde and 3mM DSG crosslinking
U54-HFFc6-DSG-DpnII-R1-R2.cis.100000.txt.gz
U54-HFFc6-DSG-DpnII-R1-R2.cis.100000.bw
U54-HFFc6-DSG-DpnII-R1-R2_hg38.txt.gz
U54-HFFc6-DSG-DpnII-R1-R2_hg38.mapq_30.1000.mcool
U54-HFFc6-DSG-DpnII-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: 10wk AT2 cell NKX2-1 ChIP-seq rep 1


title: U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1

description:
In situ Hi-C with DdeI-DpnII on Subclone c6 of HFF-hTERT cells with 1% Formaldehyde and 3mM DSG crosslinking
U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-R3.cis.100000.txt.gz
U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-R3.cis.100000.bw
U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-R3_hg38.txt.gz
U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-R3_hg38.mapq_30.1000.mcool
U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-R3_hg38.mapq_30.1000.mcool.combined.bedpe.gz

value: DdeI-DpnII


title: 10wk AT1 cell H3K4me1 ChIP-seq rep 1


title: U54-HFFc6-p17-FA-DpnII-20170327


title: P7 AT2 cell NKX2-1 ChIP-seq rep 1


title: U54-HFFc6-DSG-DdeI-DpnII-20191219-R3-T1


title: U54-HFFc64DN-FA-DSG-MNase-R1-T1


title: U54-HFFc6-DSG-DdeI-20181023-R2-T1

description:
In situ Hi-C with DdeI on Subclone c6 of HFF-hTERT cells with 1% Formaldehyde and 3mM DSG crosslinking
U54-HFFc6-DSG-DdeI-R1-R2.cis.100000.txt.gz
U54-HFFc6-DSG-DdeI-R1-R2.cis.100000.bw
U54-HFFc6-DSG-DdeI-R1-R2_hg38.txt.gz
U54-HFFc6-DSG-DdeI-R1-R2_hg38.mapq_30.1000.mcool
U54-HFFc6-DSG-DdeI-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: U54-HFFc64DN-FA-DSG-MNase-R1-T2


title: U54-HFFc64DN-FA-DSG-MNase-R3-T8


title: P7 AT2 cell NKX2-1 ChIP-seq rep 2


title: 10wk AT1 cell NKX2-1 ChIP-seq rep 2


title: U54-HFFc6-DSG-DdeI-20180319-R1-T1


title: U54-H1ESC4DN-FA-DSG-MNase-R2-T1

description:
Micro-C on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM DSG crosslinking
U54-H1ESC4DN-FA-DSG-MNase-R1-R2.cis.100000.txt.gz
U54-H1ESC4DN-FA-DSG-MNase-R1-R2.cis.100000.bw
U54-H1ESC4DN-FA-DSG-MNase-R1-R2_hg38.txt.gz
U54-H1ESC4DN-FA-DSG-MNase-R1-R2_hg38.mapq_30.1000.mcool
U54-H1ESC4DN-FA-DSG-MNase-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz

source_name: Human Embryonic stem cells


title: 10wk AT1 cell NKX2-1 ChIP-seq rep 1


title: U54-H1ESC4DN-FA-DSG-MNase-R2-T2


title: U54-H1ESC4DN-FA-DSG-MNase-R2-T3


title: P15 YT Wnt3a AT1 cell NKX2-1 ChIP-seq rep 2


title: P15 AT1 cell NKX2-1 ChIP-seq rep 2


title: P15 YT Wnt3a AT1 cell NKX2-1 ChIP-seq rep 1


title: P7 AT1 cell NKX2-1 ChIP-seq rep 2


title: U54-H1ESC4DN-FA-DSG-MNase-R1-T1


title: U54-H1ESC4DN-FA-DSG-MNase-R2-T4


title: P7 AT1 cell NKX2-1 ChIP-seq rep 1


title: U54-H1ESC4DN-FA-DSG-MNase-R2-T5


title: U54-H1ESC4DN-FA-DSG-MNase-R1-T2


title: E18-5 YT Sox9 CreER whole lung NKX2-1 ChIP-seq rep 2


title: U54-H1ESC4DN-FA-DSG-MNase-R1-T3


title: U54-H1ESC4DN-FA-DSG-MNase-R1-T4


title: U54-ESC4DN-FA-DpnII-2017524-R1-T2

description:
In situ Hi-C with DpnII on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde
U54-ESC4DN-FA-DpnII-R1-R2.cis.100000.txt.gz
U54-ESC4DN-FA-DpnII-R1-R2.cis.100000.bw
U54-ESC4DN-FA-DpnII-R1-R2_hg38.txt.gz
U54-ESC4DN-FA-DpnII-R1-R2_hg38.mapq_30.1000.mcool
U54-ESC4DN-FA-DpnII-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: U54-ESC4DN-FA-DpnII-2017524-R1-T1


title: E18-5 whole lung NKX2-1 ChIP-seq rep 2


title: U54-ESC4DN-DSG-DpnII-20190530-R2-T1

description:
In situ Hi-C with DpnII on H1 embryonic stem cells from Maehr lab with 1% Formaldehyde and 3mM DSG crosslinking
U54-ESC4DN-DSG-DpnII-R1-R2.cis.100000.txt.gz
U54-ESC4DN-DSG-DpnII-R1-R2.cis.100000.bw
U54-ESC4DN-DSG-DpnII-R1-R2_hg38.txt.gz
U54-ESC4DN-DSG-DpnII-R1-R2_hg38.mapq_30.1000.mcool
U54-ESC4DN-DSG-DpnII-R1-R2_hg38.mapq_30.1000.mcool.combined.bedpe.gz


title: E18-5 whole lung NKX2-1 ChIP-seq rep 1


title: Control 15-wk scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
15wk-control

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Trajectory analysis was carried out using Monocle 2.8
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files can be opened with Seurat (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.

source_name: Lung epithelial, immune, endothelial, and mesenchymal cells

extract_protocol:
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
FACS-purified lung epithelial, immune, endothelial, and mesenchymal cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

tag: developmental stage

tag: genotype

value: control


title: E14-5 whole lung NKX2-1 ChIP-seq rep 2


title: U54-ESC4DN-DSG-DpnII-20190530-R1-T1


title: E14-5 whole lung NKX2-1 ChIP-seq rep 1


title: RML998 (Lung 3 D21)

data_processing:
FASTQ files were mapped using STAR to  GRCm38 genome build
Gene counts were obtained using featureCounts on GENCODE vM16 annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_counts

growth_protocol: Female C57BL/6 mice (6 to 8 weeks old), were anesthetized then infected intratracheally with Mtb at a dose of ~1000 CFU.

extract_protocol:
Total RNA from lung tissue samples from different groups was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction followed by a Qiagen RNeasy Micro clean-up procedure.
Total RNAs were analyzed on Agilent Bioanalyser for quality assessment with RNA Integrity Number (RIN) range from 4.2 to 6.7 and median of RIN 5.1. Ribosomal RNA (rRNA) were depleted from 500ng of RNA using Ribo-Zero™ Gold (Human/Mouse/Rat) according to manufacturer's protocol. cDNA libraries were prepared from the resultant rRNA depleted RNA using Lexogen SENSE Total RNA-Seq Library Prep Kit according to manufacturer's protocol for degraded RNA except with 21 PCR cycles and an additional cleanup with 0.9X Ampure XP beads. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system.

treatment_protocol: Disulfiram treatment was initiated 7 days after infection, and mice were orally administered with the drug once a day, 6 days a week, for 4 wk. Two treatment groups: (i) infected mice receiving DIS (160 mg/kg), diluted in poly-ethylene glycol (PEG); (ii) infected mice receiving vehicle only (PEG).

tag: Sex

value: Female

tag: tissue

value: lung

value: infected

value: untreated

tag: timepoint


title: RML999 (Lung 4 D21)

tag: treatment


title: RML996 (Lung 1 D21)

tag: strain


title: RML997 (Lung 2 D21)


title: Control P10 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
P10-control

value: epithelial, immune, endothelial, and mesenchymal cells

value: Postnatal day 10


title: RML995 (Lung 4 D0)

value: uninfected


title: P15 AT1 cell NKX2-1 ChIP-seq rep 1

tag: chip antibody

tag: age


title: Control P8 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
P8-Normoxia-control

value: Postnatal day 8


title: Control P7 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
P7-control

value: Postnatal day 7


title: E18-5 YT Sox9 CreER whole lung NKX2-1 ChIP-seq rep 1

value: whole lung


title: Control P6 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
P6-control

value: Postnatal day 6


title: RML994 (Lung 3 D0)


title: RML993 (Lung 2 D0)


title: RML992 (Lung 1 D0)


title: Control E16.5 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
E16-5-control

value: Embryonic day 16.5


title: Control P4 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
P4-Normoxia-control

value: Postnatal day 4


title: Control E14.5 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
E14-5-Control

value: Embryonic day 14.5


title: RML1010 (Lung 12 D35)

value: disulfiram


title: RML1009 (Lung 11 D35)


title: Control P15 scRNAseq

description:
control lungs
Aggregate_P15_YT_Wnt3a_scRNAseq_barcodes.tsv
Aggregate_P15_YT_Wnt3a_scRNAseq_genes.tsv
Aggregate_P15_YT_Wnt3a_scRNAseq_matrix.mtx
Aggregate_P15_YT_Wnt3a_scRNAseq_cloupe_processed.cloupe
P15_control

source_name: Lung epithelial

value: epithelial

value: Postnatal day 15


title: Control 10-wk scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
10wk-control

value: control


title: Mutant P15 YT Wnt3a scRNAseq

description:
Deletion of Yap and Taz in developing AT1 cells resulting in a shift in cell fate from AT1 -> AT2
Aggregate_P15_YT_Wnt3a_scRNAseq_barcodes.tsv
Aggregate_P15_YT_Wnt3a_scRNAseq_genes.tsv
Aggregate_P15_YT_Wnt3a_scRNAseq_matrix.mtx
Aggregate_P15_YT_Wnt3a_scRNAseq_cloupe_processed.cloupe
P15_YT_Wnt3a

value: Yap/Taz CKO/CKO; Wnt3a Cre


title: Control E18.5 scRNAseq

description:
control lungs
Aggregate_E185_YT_Sox9_scRNAseq_barcodes.tsv
Aggregate_E185_YT_Sox9_scRNAseq_genes.tsv
Aggregate_E185_YT_Sox9_scRNAseq_matrix.mtx
Aggregate_E185_YT_Sox9_scRNAseq_cloupe_processed.cloupe
E18-5-control

value: Embryonic day 18.5

value: 3 mg Tamoxifen at E15.5 harvested at E18.5


title: RML1011 (Lung 13 D35)

value: Female

value: lung

value: infected


title: RML1008 (Lung 10 D35)


title: Control P20 scRNAseq

description:
control lungs
Aggregate12files_control_scRNAseq_barcodes.tsv
Aggregate12files_control_scRNAseq_genes.tsv
Aggregate12files_control_scRNAseq_matrix.mtx
Aggregate12files_control_scRNAseq_cloupe_processed.cloupe
P20-contro

value: epithelial, immune, endothelial, and mesenchymal cells

value: Postnatal day 20


title: RML1007 (Lung 4 D35)

value: untreated


title: RML1005 (Lung 2 D35)


title: RML1006 (Lung 3 D35)


title: Mutant E18.5 YT Sox9 scRNAseq

description:
Deletion of Yap and Taz in Sox9 prognenitors resulting in specification of predominantly AT2 cells not AT1 cells
Aggregate_E185_YT_Sox9_scRNAseq_barcodes.tsv
Aggregate_E185_YT_Sox9_scRNAseq_genes.tsv
Aggregate_E185_YT_Sox9_scRNAseq_matrix.mtx
Aggregate_E185_YT_Sox9_scRNAseq_cloupe_processed.cloupe
E18-5-YT_Sox9

value: Yap/Taz CKO/CKO; Sox9 CreER


title: 2_NKX2-1_Sftpc_AT2_M

data_processing:
Fastqc was run on the raw Fastq files to determine initial quality of reads.
Trimmomatic was performed to remove barcodes and poor quality bases.
Fastqc was run for quality control.
Bowtie alignment to the mm10 genomic with -m1 -k1 -v1 parameters and filtered for unmapped reads with sam file output
Convert sam to bam using samtools, then sort file
Picard mark duplicates
index bam file
Filter bam files: samtools  -b –f 3 –F 4 –F 256 –F 1024 –F 2048 –q 30
quality control run SPP
Call peaks using MACs2
Genome_build: mm10
Supplementary_files_format_and_content: peaks.broadPeak
Supplementary_files_format_and_content: bedgraph

source_name: AT2 cells

extract_protocol:
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
The OMNI-ATAC protocol68 was followed with minor modifications. 60,000-100,000 sorted GFP cells were centrifuged at 384 rcf for 5 min at 4 °C. The cell pellet was then resuspended by pipetting three times in 50 µl of cold ATAC-RSB lysis buffer (0.1% NP-40, 0.1% Tween, 0.01% Digitonin, 10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2) and incubated for 3 min. Then 1 mL of cold ATAC-RSB + Tween (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween) was added. The sample tube was then inverted three times and centrifuged at 384 rcf for 10 min at 4 °C. After discarding the supernatant, the pellet was resuspended in transposition mixture composed of 22.5 µl of Reaction Mix (PBS, 2.2% Digitonin, 2.2% Tween 20), 25 µl of transposase buffer (10 mM MgCl2, 20mM Tris- HCl, 20% Dimethyl Formamide), and 2.5 µl of Tn5 enzyme (NX#-TDE1, Tagment DNA Enzyme,15027865, Illumina) and incubated at 37 °C for 30 min in a thermocycler. Samples were then purified using the MinElute PCR Purification kit (Qiagen, 29004) and eluted with 10 µL of H2O. Amplification and barcoding of ATAC libraries was carried out using the Greenleaf primers for 12 cycles of PCR enrichment following the standard OMNI-ATAC amplification PCR program. A volume of 5 µL was taken after amplification to examine amplification efficiency prior to size selection. A double-sided size selection was then performed (.5 x -1.8 x volume) using the SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size and absence of primer dimers by gel electrophoresis and concentration was measured using the Qubit HS dsDNA assay (ThermoFisher Scientific, Q32851).

treatment_protocol: 2 doses of 3 mg of Tamoxifen 2 days apart, lungs were harvested 5 days after the 1st dose.

value: AT2 cells

tag: days post tamoxifen

tag: dose of tamoxifen

value: 6 mg

value: Nkx2-1 CKO/CKO; Rosa Sun1GFP/+; Sftpc CreER/+


title: RML1004 (Lung 1 D35)


title: 1_NKX2-1_Sftpc_AT2_M


title: RML1003 (Lung 8 D21)

value: disulfiram


title: 2_Sftpc_AT2_C

value: Rosa Sun1GFP/+; Sftpc CreER/+


title: RML1002 (Lung 7 D21)


title: 1_Sftpc_AT2_C


title: RML1001 (Lung 6 D21)


title: 3_NKX2-1_Rtkn2_AT1_M

source_name: AT1 cells

value: AT1 cells

value: Nkx2-1 CKO/CKO; Rosa Sun1GFP/+; Rtkn2 CreER/+


title: 2_NKX2-1_Rtkn2_AT1_M


title: RML1000 (Lung 5 D21)