title: 958_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_138h-pae_set3_flask2_958

description: Library name: NW_846


title: Day7.organoid.Rep4_Cell_264

status: Public on Apr 07 2026

type: SRA

city: Galveston

first: Marie

last: Kubota

state: TX

address: 301 University Blvd

department: Otolaryngology

country: USA

institute: University of Texas Medical Branch

description: Library name: Cell_264

library_source: transcriptomic single cell

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: mm10 (GRCm38)
Supplementary files format and content: text file with raw read counts

molecule: total RNA

organism: Mus musculus

source_name: organoid

growth_protocol: Greater epithelial ridge cells, enriched by flow cytometry, were cultured in DMEM/F12-based proliferation medium to induce organoid formation for 1, 3, and 7 days.

extract_protocol:
Harvested organoids were rinsed in PBS and incubated in 0.25% Trypsin-EDTA at 37°C and 5% CO2 for 10-20 min. After the addition of soybean trypsin inhibitor, the samples were mechanically dissociated. Single cells were manually collected using a glass micropipette (50-60µm inner diameter) and transferred into 96-well plates.
SmartSeq2 protocol

treatment_protocol: The growth medium consisted of DMEM/F-12 supplemented with 1x N-2 Supplement, 1x B-27 Supplement, 100 µg/mL ampicillin, growth factors (20 ng/mL EGF, 10 ng/mL FGF2, and 50 ng/mL IGF1), and small molecules (3µM CHIR99021, 500 µM valproic acid, 100 µg/mL 2-phospho-L-ascorbic acid, and 2 µM TGFß receptor inhibitor 616452).

tag: strain

tag: cell source

value: P2 mouse cochlear greater epithelial ridge cells

tag: cell type

value: organoid

tag: timepoint

tag: replicate


title: Day7.organoid.Rep4_Cell_242

description: Library name: Cell_242


title: 907_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_0h-pae-PreWash_set4_flask2_907

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

institute: University of Colorado

description: Library name: NW_839

library_source: transcriptomic

data_processing:
After sequencing, bacterial reads were trimmed by Skewer v0.2.2 using an adapter sequence of 5’- CTGTCTCTTATACACATCT-3’, a length of 50-175 bases, and an end quality of 20.
Individual reads were reunited with their mate pair using PairFQ lite v0.17.0.
Paired-end reads were then aligned to the 2016 Mtb Erdman reference assembly using Bowtie2 v2.5.0 with default parameters.
Mapped sequences were counted using HtSeq v1.0 with the default parameters.
The SEARCH-TB panel amplifies Mtb 3,568 genes. In this experiment, 12 genes had high incidences of 0 expression values, so our analysis included 3,552 genes.
Assembly: 2016 Mtb Erdman reference assembly
Supplementary files format and content: Read counts per Mtb Erdman gene are providedin .txt format

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

source_name: Erdman

growth_protocol: Mtb Erdman cells were inoculated into 7H9 media and grown to mid-log. At mid-log, starter cultures were split into separate sterile 125 ml Erlenmeyer flasks, one each for no drug control, 6-hour and 48-hour drug exposure arms each adjusted to an OD600 of 0.05 in 50 ml fresh 7H9. Cultures were then outgrown for 18 h at 37C prior to drug addition. Following drug wash out, cultures were returned to the incubator and grown at 37C until cultures reached an OD600 of 2.0 or exceeded 15 days.

extract_protocol:
RNA was isolated with Precellys Evolution in RLT-TCEP buffer followed by RNA purification with the Maxwell Simply RNA cell kit from Promega.
Extracted RNA was reverse transcribed and prepared for sequencing with Illumina AmpliSeq custom panel library preparation protocol.

treatment_protocol: For drug exposed cultures, a 50 µl drug suspension was added from a 1000X sterile stock solution containing the following: 0.05 mg/ml isoniazid (Sigma-Aldrich), 0.05 mg/ml rifampicin (Chem-Impex-Int’l), 1.6 mg/ml pyrazinamide (MP Biomedicals), 2.0 mg/ml ethambutol (MP Biomedicals). Drugs were suspended in DMSO at the indicated concentrations, sterilized using a 0.22 µm nylon syringe filter, and stored at -80C prior to use. Control non-drug exposed cultures were collected by centrifugation for 5 min at 3220 x g, washed 2 times with 50 ml 7H9 and then resuspended in 50 ml fresh 7H9 to an OD600 of 0.05. Cultures were returned to the incubator and grown at 37C for the pre-defined drug exposure period. At the end of the defined drug exposure period, cultures were collected by centrifugation, washed 2 times with 50 ml 7H9 to remove residual drug and then resuspended in 50 ml fresh 7H9 to an OD600 of 0.05.

tag: cell line

value: Erdman

tag: treatment

value: HRZE

tag: batch


title: Day7.organoid.Rep4_Cell_240

description: Library name: Cell_240


title: 939_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_72h-pae_set4_flask1_939

description: Library name: NW_837


title: Day7.organoid.Rep4_Cell_246

description: Library name: Cell_246


title: Day7.organoid.Rep4_Cell_245

description: Library name: Cell_245


title: 919_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_18h-pae_set4_flask2_919

description: Library name: NW_841


title: Day7.organoid.Rep4_Cell_241

description: Library name: Cell_241


title: Day7.organoid.Rep4_Cell_244

description: Library name: Cell_244


title: Day7.organoid.Rep4_Cell_243

description: Library name: Cell_243


title: 918_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_18h-pae_set3_flask2_918

description: Library name: NW_840


title: 926_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_42h-pae_set3_flask2_926

description: Library name: NW_842


title: 930_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_48h-pae_set3_flask1_930

description: Library name: NW_834


title: 906_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_0h-pae-PreWash_set3_flask2_906

description: Library name: NW_838


title: Day7.organoid.Rep4_Cell_238

description: Library name: Cell_238


title: Day7.organoid.Rep4_Cell_239

description: Library name: Cell_239


title: 938_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_72h-pae_set3_flask1_938

description: Library name: NW_836


title: 923_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_24h-pae_set4_flask1_923

description: Library name: NW_833


title: 922_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_24h-pae_set3_flask1_922

description: Library name: NW_832


title: Day7.organoid.Rep4_Cell_237

description: Library name: Cell_237


title: Day7.organoid.Rep4_Cell_235

description: Library name: Cell_235


title: 931_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_48h-pae_set4_flask1_931

description: Library name: NW_835


title: 898_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_PreRx_set3_flask1_898

description: Library name: NW_830


title: 1156_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_96h-pae_set2_flask3_1156

description: Library name: NW_826


title: Day7.organoid.Rep4_Cell_231

description: Library name: Cell_231


title: Day7.organoid.Rep4_Cell_233

description: Library name: Cell_233


title: Day7.organoid.Rep4_Cell_232

description: Library name: Cell_232


title: Day7.organoid.Rep4_Cell_230

description: Library name: Cell_230


title: Day7.organoid.Rep4_Cell_236

description: Library name: Cell_236


title: 1155_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_96h-pae_set1_flask3_1155

description: Library name: NW_825


title: 1144_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_24h-pae_set2_flask3_1144

description: Library name: NW_822


title: 899_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_PreRx_set4_flask1_899

description: Library name: NW_831


title: 1148_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_48h-pae_set2_flask3_1148

description: Library name: NW_824


title: 1135_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_0h-pae-PreWash_set1_flask3_1135

description: Library name: NW_819


title: Day7.organoid.Rep4_Cell_229

description: Library name: Cell_229


title: Day7.organoid.Rep4_Cell_228

description: Library name: Cell_228


title: 1143_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_24h-pae_set1_flask3_1143

description: Library name: NW_821


title: Day7.organoid.Rep4_Cell_234

description: Library name: Cell_234


title: Day7.organoid.Rep4_Cell_227

description: Library name: Cell_227


title: 957_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_138h-pae_set2_flask2_957

description: Library name: NW_818


title: Day7.organoid.Rep4_Cell_226

description: Library name: Cell_226


title: 1136_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_0h-pae-PreWash_set2_flask3_1136

description: Library name: NW_820


title: 956_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_138h-pae_set1_flask2_956

description: Library name: NW_817


title: Day7.organoid.Rep4_Cell_223

description: Library name: Cell_223


title: 1147_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_48h-pae_set1_flask3_1147

description: Library name: NW_823


title: Day7.organoid.Rep4_Cell_225

description: Library name: Cell_225


title: Day7.organoid.Rep4_Cell_221

description: Library name: Cell_221


title: Day7.organoid.Rep4_Cell_222

description: Library name: Cell_222


title: Day7.organoid.Rep4_Cell_224

description: Library name: Cell_224


title: 924_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_42h-pae_set1_flask2_924

description: Library name: NW_813


title: Day7.organoid.Rep4_Cell_220

description: Library name: Cell_220


title: 941_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_90h-pae_set2_flask2_941

description: Library name: NW_816


title: 940_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_90h-pae_set1_flask2_940

description: Library name: NW_815


title: Day7.organoid.Rep4_Cell_219

description: Library name: Cell_219


title: 905_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_0h-pae-PreWash_set2_flask2_905

description: Library name: NW_810


title: Day7.organoid.Rep4_Cell_217

description: Library name: Cell_217


title: 917_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_18h-pae_set2_flask2_917

description: Library name: NW_812


title: 937_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_72h-pae_set2_flask1_937

description: Library name: NW_808


title: 936_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_72h-pae_set1_flask1_936

description: Library name: NW_807


title: 921_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_24h-pae_set2_flask1_921

description: Library name: NW_804


title: 925_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_42h-pae_set2_flask2_925

description: Library name: NW_814


title: Day1.organoid.Rep1_Cell_214

description: Library name: Cell_214


title: 916_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_18h-pae_set1_flask2_916

description: Library name: NW_811


title: Day1.organoid.Rep1_Cell_210

description: Library name: Cell_210


title: Day1.organoid.Rep1_Cell_216

description: Library name: Cell_216


title: Day1.organoid.Rep1_Cell_208

description: Library name: Cell_208


title: Day1.organoid.Rep1_Cell_209

description: Library name: Cell_209


title: 896_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_PreRx_set1_flask1_896

description: Library name: NW_801


title: 928_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_48h-pae_set1_flask1_928

description: Library name: NW_805


title: Day7.organoid.Rep4_Cell_218

description: Library name: Cell_218


title: Day1.organoid.Rep1_Cell_215

description: Library name: Cell_215


title: 929_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_48h-pae_set2_flask1_929

description: Library name: NW_806


title: 897_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_PreRx_set2_flask1_897

description: Library name: NW_802


title: 904_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_0h-pae-PreWash_set1_flask2_904

description: Library name: NW_809


title: Day1.organoid.Rep1_Cell_213

description: Library name: Cell_213


title: 920_In vitro PAE_NodrugControl_in-vitro-PAE_erdman_7H9Tw_no-drug-control_24h-pae_set1_flask1_920

description: Library name: NW_803


title: bacterial powder was vacuum packed and stored at 4 ℃ for 2 weeks

city: qingdao

first: Liang

last: Liu

country: China

institute: Ocean University of China

description: Library name: FD2w

data_processing:
After standardisation using the SCT method, 3000 cells were randomly sampled from each sample, and the normal cultivation group and rifampicin induced dormancy group were merged using the Harmony method. Monocle2 used the DDRTree method in reverse graph embedding to perform cells clustering and construct pseudotemporal trajectories. After selecting the top 100 pseudotemporally differential genes ranked by qval from smallest to largest, a heatmap was generated to visualize the expression levels of these genes, and the genes were clustered based on their expression patterns.
Assembly: ATCC11842
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

organism: Lactobacillus delbrueckii subsp. bulgaricus

source_name: bacteria

extract_protocol:
bacterial cells were fixed with the same volume of 4% (v/v) paraformaldehyde at 4 ℃ rotation for more than 8 h and no more than 12 h. Then washed twice with 1×PBS containing RNase inhibitor (Vazyme), samples were cryopreserved in 20% (v/v) glycerol at -80℃. Single cell suspensions were prepared using the M20 Genomics VITA platform, involving cell fixation/permeabilization, intracellular random primer hybridization, and reverse transcription to generate tagged RNA fragments. Libraries were constructed via GelBead-in-emulsion (GEM) technology, integrating sequence-barcoded GelBeads, reagents, and oil-phase partitioning for cellular indexing. Amplified cDNA libraries were sequenced on an Illumina platform (2×150 bp) by Majorbio BioPharm Technology Co., Ltd. and M20 Genomics (Hangzhou Yuezhen Biotech)
Amplified cDNA libraries were sequenced on an Illumina platform (2×150 bp) by Majorbio BioPharm Technology Co., Ltd. and M20 Genomics (Hangzhou Yuezhen Biotech)

value: bacteria


title: Day1.organoid.Rep1_Cell_207

description: Library name: Cell_207


title: Day1.organoid.Rep1_Cell_203

description: Library name: Cell_203


title: freeze-dried at -60 ℃ for 48 h

description: Library name: FD


title: cell-free DNA from CTRL patient 32161056

type: other

city: Granada

first: Cristobal

last: Fresno

state: Andalucia

address: Avda. de la Ilustración 114

department: Centre for Genomics and Oncological Research

country: Spain

institute: Pfizer/University of Granada/Andalusian Regional Government (GENyO)

hyb_protocol: Bisulphite converted was amplified, fragmented and hybridized to human Infinium MethylationEPIC Beadchip (Illumina) following standard instructions

scan_protocol: Microarrays were scanned using iScan platform (Illumina)

data_processing:
ChAMP R package was used to read the beta intensities from the .idat files with the default parameters, filters and normalization.
Multivariate batch effect removal was applied using ARSyN R package based on the gold sample labels and back to the beta scale.

label: Cy3 and Cy5

molecule: other

organism: Homo sapiens

source_name: Whole blood cell-free DNA

label_protocol: Standard Illumina protocol

extract_protocol: cfDNA was extracted following the instructions from DNeasy Blood & Tissue Kit (Qiagen)

tag: tissue

value: Whole blood cell-free DNA

tag: age

tag: Sex

value: Female

tag: group

value: CTRL

tag: gold

tag: smoking

tag: obesity

tag: exacerbations

tag: mmrc


title: cell-free DNA from CTRL patient 32170461


title: Day1.organoid.Rep1_Cell_211

description: Library name: Cell_211

tag: strain


title: Day1.organoid.Rep1_Cell_206

description: Library name: Cell_206

tag: cell source


title: Day1.organoid.Rep1_Cell_212

description: Library name: Cell_212

tag: cell type


title: Day1.organoid.Rep1_Cell_201

description: Library name: Cell_201

tag: timepoint


title: the normal state bacterial suspension

description: Library name: CT


title: Day1.organoid.Rep1_Cell_200

description: Library name: Cell_200

tag: replicate


title: cell-free DNA from CTRL patient 32161274


title: cell-free DNA from CTRL patient 32170463


title: cell-free DNA from CTRL patient 32161055


title: Day1.organoid.Rep1_Cell_205

description: Library name: Cell_205


title: Day1.organoid.Rep1_Cell_202

description: Library name: Cell_202


title: cell-free DNA from CTRL patient 32160841

value: Man


title: cell-free DNA from CTRL patient 32160637


title: cell-free DNA from CTRL patient 32161273


title: Day1.organoid.Rep1_Cell_198

description: Library name: Cell_198


title: Day1.organoid.Rep1_Cell_204

description: Library name: Cell_204


title: cell-free DNA from CTRL patient 32160621


title: cell-free DNA from CTRL patient 32160609


title: Day1.organoid.Rep1_Cell_196

description: Library name: Cell_196


title: Day1.organoid.Rep1_Cell_197

description: Library name: Cell_197


title: Day1.organoid.Rep1_Cell_195

description: Library name: Cell_195


title: cell-free DNA from CTRL patient 32160624


title: cell-free DNA from CTRL patient 32160170


title: Day1.organoid.Rep1_Cell_192

description: Library name: Cell_192


title: cell-free DNA from CTRL patient 32160182


title: Day1.organoid.Rep1_Cell_187

description: Library name: Cell_187


title: Day1.organoid.Rep1_Cell_188

description: Library name: Cell_188


title: Day1.organoid.Rep1_Cell_191

description: Library name: Cell_191


title: Day1.organoid.Rep1_Cell_194

description: Library name: Cell_194


title: Day1.organoid.Rep1_Cell_193

description: Library name: Cell_193


title: cell-free DNA from CTRL patient 32160167


title: cell-free DNA from CTRL patient 32160101


title: cell-free DNA from CTRL patient 32160140


title: cell-free DNA from CTRL patient 32160100


title: Day1.organoid.Rep1_Cell_199

description: Library name: Cell_199


title: cell-free DNA from CTRL patient 32160422


title: Day1.organoid.Rep1_Cell_190

description: Library name: Cell_190


title: Day1.organoid.Rep1_Cell_186

description: Library name: Cell_186


title: cell-free DNA from CTRL patient 32160608


title: Day1.organoid.Rep1_Cell_189

description: Library name: Cell_189


title: HUDEP2 cells; Washout 24h_re2

status: Public on Apr 10 2026

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

description: Library name: Wash24_2

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: hg19
Supplementary files format and content: Count file

source_name: Blood

extract_protocol:
RNA samples of two biological replicates were extracted from cultured cells, using TRIzol (Ambion by Life technologies, 343,911), following the manufacturer’s instructions. RNA was then sent out for library preparation and next-generation sequencing to a commercial company, Novogene (CA, USA).
According to the manufacturer's instructions, three biologically duplicated RNA samples were extracted from cultured cells using TRIZOL (Ambion by Life technologies, 343911). RNA sample quality was analyzed, and library were prepared and next-generation sequenced by a commercial company, Novogene (California, USA).

value: Blood

tag: cell line

value: Human blood


title: Day1.organoid.Rep1_Cell_185

description: Library name: Cell_185


title: cell-free DNA from CTRL patient 32160094


title: Day1.organoid.Rep1_Cell_184

description: Library name: Cell_184


title: cell-free DNA from CTRL patient 32160007


title: cell-free DNA from CTRL patient 32160061


title: Day1.organoid.Rep1_Cell_183

description: Library name: Cell_183


title: cell-free DNA from CTRL patient 32160006


title: cell-free DNA from CTRL patient 32160058


title: cell-free DNA from CTRL patient 32160003


title: Day1.organoid.Rep1_Cell_181

description: Library name: Cell_181


title: Day1.organoid.Rep1_Cell_179

description: Library name: Cell_179


title: Day1.organoid.Rep1_Cell_180

description: Library name: Cell_180


title: cell-free DNA from CTRL patient 32160008


title: Day1.organoid.Rep1_Cell_182

description: Library name: Cell_182


title: cell-free DNA from CTRL patient 32152297


title: Day1.organoid.Rep1_Cell_177

description: Library name: Cell_177


title: S2-9: H9/NL4-3 cells, 24hr, 7B2-PNU

city: Bozeman

first: SETH

middle: H.

last: PINCUS

state: Montana

address: 103 Chemistry and Biochemistry Building

department: Chemistry

institute: Montana State University

description:
Library name: S2-9
Column name in SHP_all_data.csv: S2-9

data_processing:
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genomes using the STAR aligner v.2.5.2b. The STAR aligner is a splice aware aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 Only unique reads within exon regions were counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: The processed data are in a CSV format. The numbers represent HIT counts, ie the number of transcripts mapped to each  gene. Individual genes are in the rows identified by the Ensembl gene ID, the columns represent individual samples.

source_name: H9/NL4-3 cells, 24hr, 7B2-PNU

growth_protocol: Cells grown in RPMI 1640 medium plus 10% fetal calf serum, penicillin, streptomycin

extract_protocol:
RNeasy plus Mini Kits (Qiagen)
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Cells were treated for 6 or 24 hr as follows: no treatment, 7B2-dgA (an immunotoxin)  62.5 ng/mL + CD4-IgG2  (enhances immunotoxin or ADC) 500 ng/mL, or 7B2-PNU 250 ng/mL + CD4-IgG2 500 ng/mL

value: HIV-infected CD4+ lymphoma cell line

value: CD4+ Lymphoma cell line

tag: genotype

value: HIV infected

tag: treatment

tag: time

value: 24 hours


title: Day1.organoid.Rep1_Cell_176

description: Library name: Cell_176


title: Day1.organoid.Rep1_Cell_175

description: Library name: Cell_175


title: Day1.organoid.Rep1_Cell_178

description: Library name: Cell_178


title: cell-free DNA from CTRL patient 32152295

tag: tissue

tag: age


title: cell-free DNA from CTRL patient 32152296

tag: Sex

tag: group


title: S2-8: H9/NL4-3 cells, 24hr, 7B2-dgA

description:
Library name: S2-8
Column name in SHP_all_data.csv: S2-8

source_name: H9/NL4-3 cells, 24hr, 7B2-dgA


title: S2-7: H9/NL4-3 cells, 24hr, untreated

description:
Library name: S2-7
Column name in SHP_all_data.csv: S2-7

source_name: H9/NL4-3 cells, 24hr, untreated

value: untreated


title: cell-free DNA from CTRL patient 32152039

tag: gold

tag: smoking


title: Day1.organoid.Rep1_Cell_168

description: Library name: Cell_168


title: Day1.organoid.Rep1_Cell_170

description: Library name: Cell_170


title: cell-free DNA from CTRL patient 32152251

tag: obesity

tag: exacerbations


title: Day1.organoid.Rep1_Cell_173

description: Library name: Cell_173

tag: strain


title: Day1.organoid.Rep1_Cell_171

description: Library name: Cell_171

tag: cell source


title: cell-free DNA from CTRL patient 32152034

tag: mmrc


title: cell-free DNA from CTRL patient 32152040


title: cell-free DNA from CTRL patient 32152122


title: S2-6: H9/NL4-3 cells, 24hr, 7B2-PNU

description:
Library name: S2-6
Column name in SHP_all_data.csv: S2-6

tag: cell type


title: Day1.organoid.Rep1_Cell_169

description: Library name: Cell_169

tag: timepoint

tag: replicate


title: Day1.organoid.Rep1_Cell_172

description: Library name: Cell_172


title: Day1.organoid.Rep1_Cell_174

description: Library name: Cell_174


title: Day1.organoid.Rep1_Cell_165

description: Library name: Cell_165


title: S2-5: H9/NL4-3 cells, 24hr, 7B2-dgA

description:
Library name: S2-5
Column name in SHP_all_data.csv: S2-5

tag: cell line

tag: genotype


title: S2-3: H9/NL4-3 cells, 24hr, 7B2-PNU

description:
Library name: S2-3
Column name in SHP_all_data.csv: S2-3

tag: treatment

tag: time


title: Day1.organoid.Rep1_Cell_167

description: Library name: Cell_167


title: S2-4: H9/NL4-3 cells, 24hr, untreated

description:
Library name: S2-4
Column name in SHP_all_data.csv: S2-4

tag: tissue


title: Day1.organoid.Rep1_Cell_166

description: Library name: Cell_166


title: cell-free DNA from CTRL patient 32152033

tag: age

tag: Sex


title: Day7.organoid.Rep3_Cell_161

description: Library name: Cell_161


title: Day7.organoid.Rep3_Cell_160

description: Library name: Cell_160


title: Day1.organoid.Rep1_Cell_164

description: Library name: Cell_164


title: S2-2: H9/NL4-3 cells, 24hr, 7B2-dgA

description:
Library name: S2-2
Column name in SHP_all_data.csv: S2-2


title: Day1.organoid.Rep1_Cell_163

description: Library name: Cell_163


title: cell-free DNA from CTRL patient 32151886

tag: group

tag: gold


title: S2-1: H9/NL4-3 cells, 24hr, untreated

description:
Library name: S2-1
Column name in SHP_all_data.csv: S2-1


title: cell-free DNA from CTRL patient 32151687

tag: smoking

tag: obesity


title: S1-8: H9/NL4-3 cells, 6hr, 7B2-dgA

description:
Library name: S1-8
Column name in SHP_all_data.csv: S1-8

source_name: H9/NL4-3 cells, 6hr, 7B2-dgA

value: 6 hours


title: Day7.organoid.Rep3_Cell_157

description: Library name: Cell_157

tag: strain

value: P2 mouse cochlear greater epithelial ridge cells


title: cell-free DNA from CTRL patient 32152032

tag: exacerbations


title: Day1.organoid.Rep1_Cell_162

description: Library name: Cell_162

tag: cell source

value: organoid


title: Day7.organoid.Rep3_Cell_159

description: Library name: Cell_159

tag: cell type


title: Day7.organoid.Rep3_Cell_153

description: Library name: Cell_153

tag: timepoint


title: Day7.organoid.Rep3_Cell_152

description: Library name: Cell_152

tag: replicate


title: Day7.organoid.Rep3_Cell_156

description: Library name: Cell_156


title: S1-9: H9/NL4-3 cells, 6hr, 7B2-PNU

description:
Library name: S1-9
Column name in SHP_all_data.csv: S1-9

source_name: H9/NL4-3 cells, 6hr, 7B2-PNU

tag: cell line


title: Day7.organoid.Rep3_Cell_158

description: Library name: Cell_158


title: Day7.organoid.Rep3_Cell_155

description: Library name: Cell_155


title: cell-free DNA from CTRL patient 32151637

tag: mmrc


title: Day7.organoid.Rep3_Cell_151

description: Library name: Cell_151


title: Day7.organoid.Rep3_Cell_154

description: Library name: Cell_154


title: S1-7: H9/NL4-3 cells, 6hr, untreated

description:
Library name: S1-7
Column name in SHP_all_data.csv: S1-7

source_name: H9/NL4-3 cells, 6hr, untreated

tag: genotype

tag: treatment


title: cell-free DNA from CTRL patient 32151627

tag: tissue


title: cell-free DNA from CTRL patient 32151697

tag: age


title: Day7.organoid.Rep3_Cell_148

description: Library name: Cell_148


title: cell-free DNA from CTRL patient 32151636

tag: Sex


title: Day7.organoid.Rep3_Cell_146

description: Library name: Cell_146


title: Day7.organoid.Rep3_Cell_147

description: Library name: Cell_147


title: S1-6: H9/NL4-3 cells, 6hr, 7B2-PNU

description:
Library name: S1-6
Column name in SHP_all_data.csv: S1-6

tag: time


title: S1-4: H9/NL4-3 cells, 6hr, untreated

description:
Library name: S1-4
Column name in SHP_all_data.csv: S1-4


title: S1-5: H9/NL4-3 cells, 6hr, 7B2-dgA

description:
Library name: S1-5
Column name in SHP_all_data.csv: S1-5


title: cell-free DNA from CTRL patient 32151549

tag: group

tag: gold


title: Day7.organoid.Rep3_Cell_145

description: Library name: Cell_145


title: Day7.organoid.Rep3_Cell_149

description: Library name: Cell_149


title: Day7.organoid.Rep3_Cell_150

description: Library name: Cell_150


title: Day7.organoid.Rep3_Cell_143

description: Library name: Cell_143


title: S1-2: H9/NL4-3 cells, 6hr, 7B2-dgA

description:
Library name: S1-2
Column name in SHP_all_data.csv: S1-2


title: Day7.organoid.Rep3_Cell_144

description: Library name: Cell_144


title: Day7.organoid.Rep3_Cell_140

description: Library name: Cell_140


title: S1-1: H9/NL4-3 cells, 6hr, untreated

description:
Library name: S1-1
Column name in SHP_all_data.csv: S1-1


title: Day7.organoid.Rep3_Cell_142

description: Library name: Cell_142


title: cell-free DNA from CTRL patient 32151623

tag: smoking

tag: obesity


title: S1-3: H9/NL4-3 cells, 6hr, 7B2-PNU

description:
Library name: S1-3
Column name in SHP_all_data.csv: S1-3


title: Day7.organoid.Rep3_Cell_141

description: Library name: Cell_141

tag: strain


title: cell-free DNA from CTRL patient 32151464

tag: exacerbations


title: cell-free DNA from CTRL patient 32151554


title: cell-free DNA from CTRL patient 32151546


title: yeast_PR_dLBD_2

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Library name: yeast_PR_dLBD_2
ChEC-seq in yeast

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d) for yeast and deeptools bamtoBigWig for mammalian samples
Assembly: Yeast-GCA_000146045.2 (R64), Mouse-mm10, Human-hg38
Supplementary files format and content: Yeast - .out file contains  genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Supplementary files format and content: Mammalian- bw files contain averaged between repeats BigWIg files using CPM and bin size of 1 bp

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast - Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose; Mammalian- cells were deluted and grown until ~1.4 M cells

extract_protocol:
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021

value: permeabilization followed by 30 sec of Ca2+ incubation


title: yeast_PR_dLBD_1

description:
Library name: yeast_PR_dLBD_1
ChEC-seq in yeast


title: cell-free DNA from CTRL patient 32151379


title: Day7.organoid.Rep3_Cell_139

description: Library name: Cell_139

tag: cell source

tag: cell type


title: Day7.organoid.Rep3_Cell_138

description: Library name: Cell_138

tag: timepoint

tag: replicate


title: Day7.organoid.Rep3_Cell_136

description: Library name: Cell_136


title: cell-free DNA from CTRL patient 32151378

tag: mmrc


title: Day7.organoid.Rep3_Cell_137

description: Library name: Cell_137


title: Day7.organoid.Rep3_Cell_134

description: Library name: Cell_134


title: Day7.organoid.Rep3_Cell_135

description: Library name: Cell_135


title: yeast_PR_DBD_1

description:
Library name: yeast_PR_DBD_1
ChEC-seq in yeast

tag: cell line


title: yeast_GR_dLBD_4

description:
Library name: yeast_GR_dLBD_4
ChEC-seq in yeast

tag: treatment


title: Day7.organoid.Rep3_Cell_129

description: Library name: Cell_129


title: yeast_GR_dLBD_2

description:
Library name: yeast_GR_dLBD_2
ChEC-seq in yeast


title: yeast_GR_dLBD_3

description:
Library name: yeast_GR_dLBD_3
ChEC-seq in yeast


title: cell-free DNA from CTRL patient 32151364

tag: tissue


title: Day7.organoid.Rep3_Cell_130

description: Library name: Cell_130


title: Day7.organoid.Rep3_Cell_132

description: Library name: Cell_132


title: cell-free DNA from CTRL patient 32151083

tag: age


title: Day7.organoid.Rep3_Cell_133

description: Library name: Cell_133


title: yeast_PR_DBD_2

description:
Library name: yeast_PR_DBD_2
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_127

description: Library name: Cell_127


title: Day7.organoid.Rep3_Cell_131

description: Library name: Cell_131


title: Day7.organoid.Rep3_Cell_123

description: Library name: Cell_123


title: Day7.organoid.Rep3_Cell_128

description: Library name: Cell_128


title: Day7.organoid.Rep3_Cell_125

description: Library name: Cell_125


title: cell-free DNA from CTRL patient 32151043

tag: Sex


title: yeast_GR_dLBD_1

description:
Library name: yeast_GR_dLBD_1
ChEC-seq in yeast


title: cell-free DNA from CTRL patient 32151071


title: cell-free DNA from CTRL patient 32151369


title: Day7.organoid.Rep3_Cell_124

description: Library name: Cell_124


title: cell-free DNA from CTRL patient 32151159


title: yeast_GR_IDR_4

description:
Library name: yeast_GR_IDR_4
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_126

description: Library name: Cell_126


title: yeast_GR_IDR_3

description:
Library name: yeast_GR_IDR_3
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_122

description: Library name: Cell_122


title: yeast_GR_IDR_2

description:
Library name: yeast_GR_IDR_2
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_120

description: Library name: Cell_120


title: cell-free DNA from CTRL patient 32150124


title: cell-free DNA from CTRL patient 32150041


title: Day7.organoid.Rep3_Cell_119

description: Library name: Cell_119


title: cell-free DNA from CTRL patient 32150036


title: Day7.organoid.Rep3_Cell_117

description: Library name: Cell_117


title: yeast_GR_IDR_1

description:
Library name: yeast_GR_IDR_1
ChEC-seq in yeast


title: cell-free DNA from CTRL patient 32150032


title: Day7.organoid.Rep3_Cell_121

description: Library name: Cell_121


title: cell-free DNA from CTRL patient 32150045


title: cell-free DNA from CTRL patient 32150214


title: yeast_GR_DBD_2

description:
Library name: yeast_GR_DBD_2
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_118

description: Library name: Cell_118


title: 7251 OS retina

city: Philadelphia

first: Jon

middle: E

last: Chatterton

state: PA

address: 3025 Market St

institute: Roche Therapeutics

description:
Library name: GTSAMPLE3983
Four technical replicates -1, -2, -3, -4 each representing a 10X lane

data_processing:
The snRNA-seq data was aligned to a custom reference containing both the pig genome and the EGFP transgene.
Gene expression counts were quantified using Cellranger version 8.0.0, from the Chromium Single Cell Software Suite by 10x Genomics.
Assembly: Sscrofa11.1 release 113 (GCA_000003025.6)
Supplementary files format and content: *_matrix.mtx.gz: A sparse count matrix in Matrix Market format, derived from filtered_feature_bc_matrix from Cellranger output
Supplementary files format and content: *_features.tsv.gz: Gene names and identifiers to be used as indices for the count matrix
Supplementary files format and content: *_barcodes.tsv.gz: Cell barcodes to be used as indices for the count matrix

molecule: nuclear RNA

organism: Sus scrofa

source_name: Retina

extract_protocol:
Two eyes per condition (vehicle and AAV2.7m8/CAG-GFP at weeks 2 and 4) were individually processed for single-nuclei RNA sequencing. After collecting aqueous and vitreous humor samples, whole globes were flash-frozen in liquid nitrogen, followed by retinal dissection and freezing. Nuclei were isolated using the 10x Genomics Nuclei Isolation Kit with modifications, including tissue homogenization in ice-cold lysis buffer and 10-minute incubation on ice. The nuclear suspension was stained with DAPI (5µM) during the first wash step and incubated for 20 minutes at 4°C with rotation. Finally, nuclei were purified using fluorescence-activated nuclear sorting based on DAPI fluorescence and collected in wash and resuspension buffer containing PBS, BSA, and RNase inhibitor.
Sorted nuclei event count and final volume was used to inform sample loading volume, and the nuclei were immediately loaded onto 10x Chromium GEM-X Single Cell 3’ Chip Kit v4, at ~20k nuclei per sample (this loading concentration was optimized based on sorter nuclear count and 10x nuclear recovery). Four lanes per sample were loaded to maximize cell recovery. Libraries were generated following the manufacturer’s protocol and were sequenced using the Illumina NextSeq 2000.

treatment_protocol: Animals received bilateral intravitreal injections of Vitrase two weeks before AAV treatment to enhance vector diffusion, followed by weekly methylprednisolone pre-treatment starting two days prior to AAV dosing. On day 0, animals received bilateral intravitreal injections of either AAV2.7m8/CAG-GFP (n=7) or vehicle control (n=5) at 5e11 vg/eye. Aqueous and vitreous humor samples were collected at multiple timepoints, with animals sacrificed in week 2, 3, or 4 depending on inflammatory responses. A separate cohort received AAV2.7m8/CAG-FIX (n=3) or vehicle (n=1) and was sacrificed in week 4, with collected tissues used for various analyses including single-nuclei RNAseq, immunofluorescence, MACSima imaging, and flow cytometry.

value: Retina

value: Vehicle

tag: batch

value: Vehicle week 4


title: Day7.organoid.Rep3_Cell_116

description: Library name: Cell_116


title: yeast_GR_dN380_2

description:
Library name: yeast_GR_dN380_2
ChEC-seq in yeast


title: 7250 OS retina

description:
Library name: GTSAMPLE3982
Four technical replicates -1, -2, -3, -4 each representing a 10X lane


title: Day7.organoid.Rep3_Cell_115

description: Library name: Cell_115


title: 7248 OS retina

description:
Library name: GTSAMPLE3980
Four technical replicates -1, -2, -3, -4 each representing a 10X lane

value: AAV

value: AAV week 4


title: 7249 OS retina

description:
Library name: GTSAMPLE3981
Four technical replicates -1, -2, -3, -4 each representing a 10X lane


title: cell-free DNA from CTRL patient 32140237

value: Whole blood cell-free DNA

value: Man

tag: group

value: CTRL


title: yeast_GR_dN380_3

description:
Library name: yeast_GR_dN380_3
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_114

description: Library name: Cell_114


title: yeast_GR_DBD_1

description:
Library name: yeast_GR_DBD_1
ChEC-seq in yeast


title: yeast_GR_dN380_1

description:
Library name: yeast_GR_dN380_1
ChEC-seq in yeast


title: cell-free DNA from CTRL patient 32140236

tag: gold


title: cell-free DNA from CTRL patient 32140221

tag: smoking


title: Day7.organoid.Rep3_Cell_112

description: Library name: Cell_112


title: 7222 OD retina

description:
Library name: GTSAMPLE3979
Four technical replicates -1, -2, -3, -4 each representing a 10X lane

value: Vehicle week 2


title: yeast_GR_dN300_1

description:
Library name: yeast_GR_dN300_1
ChEC-seq in yeast


title: 7221 OD retina

description:
Library name: GTSAMPLE3977
Four technical replicates -1, -2, -3, -4 each representing a 10X lane

value: AAV week 2


title: Day7.organoid.Rep3_Cell_111

description: Library name: Cell_111


title: cell-free DNA from EPOC patient Loja-057

value: EPOC

value: d

value: Former

tag: obesity

value: Sharpening with Bronchoconstriction


title: Day7.organoid.Rep3_Cell_113

description: Library name: Cell_113

tag: strain

value: P2 mouse cochlear greater epithelial ridge cells


title: yeast_GR_dN260_2

description:
Library name: yeast_GR_dN260_2
ChEC-seq in yeast


title: nmumg_pd_dbd_lbd_3

description:
Library name: nmumg_pd_dbd_lbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d) for yeast and deeptools bamtoBigWig for mammalian samples
Assembly: Yeast-GCA_000146045.2 (R64), Mouse-mm10, Human-hg38
Supplementary files format and content: Yeast - .out file contains  genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Supplementary files format and content: Mammalian- bw files contain averaged between repeats BigWIg files using CPM and bin size of 1 bp
Library strategy: ChEC-seq

source_name: NMuMG

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: yeast_GR_dN300_2

description:
Library name: yeast_GR_dN300_2
ChEC-seq in yeast

value: permeabilization followed by 30 sec of Ca2+ incubation


title: cell-free DNA from EPOC patient Loja-056

value: a

value: Active

value: Not sharpening

tag: exacerbations


title: cell-free DNA from EPOC patient Loja-054

value: c


title: Day7.organoid.Rep3_Cell_110

description: Library name: Cell_110

tag: cell source

value: organoid


title: 7222 OS retina

description:
Library name: GTSAMPLE3978
Four technical replicates -1, -2, -3, -4 each representing a 10X lane

value: Retina

value: Vehicle


title: yeast_GR_dN60_3

description:
Library name: yeast_GR_dN60_3
ChEC-seq in yeast


title: 7221 OS retina

description:
Library name: GTSAMPLE3976
Four technical replicates -1, -2, -3, -4 each representing a 10X lane

value: AAV


title: cell-free DNA from EPOC patient Loja-051

value: Whole blood cell-free DNA

value: Man


title: nmumg_pd_dbd_lbd_2

description:
Library name: nmumg_pd_dbd_lbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep3_Cell_108

description: Library name: Cell_108

tag: cell type


title: Day7.organoid.Rep3_Cell_109

description: Library name: Cell_109

tag: timepoint


title: yeast_GR_dN60_2

description:
Library name: yeast_GR_dN60_2
ChEC-seq in yeast


title: cell-free DNA from EPOC patient Loja-050

value: EPOC

value: b


title: yeast_GR_dN260_1

description:
Library name: yeast_GR_dN260_1
ChEC-seq in yeast


title: nmumg_pd_dbd_lbd_1

description:
Library name: nmumg_pd_dbd_lbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep3_Cell_106

description: Library name: Cell_106

tag: replicate


title: yeast_GR_dN240_2

description:
Library name: yeast_GR_dN240_2
ChEC-seq in yeast


title: yeast_GR_dN60_1

description:
Library name: yeast_GR_dN60_1
ChEC-seq in yeast


title: nmumg_gr_dbd_lbd3

description:
Library name: nmumg_gr_dbd_lbd3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_gr_dbd_lbd2

description:
Library name: nmumg_gr_dbd_lbd2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient Loja-048

value: Former

value: Sharpening with emphysema

tag: mmrc


title: Day7.organoid.Rep3_Cell_107

description: Library name: Cell_107

value: P2 mouse cochlear greater epithelial ridge cells


title: cell-free DNA from EPOC patient Loja-045


title: nmumg_gr_dbd_lbd1

description:
Library name: nmumg_gr_dbd_lbd1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: yeast_GR_dN240_1

description:
Library name: yeast_GR_dN240_1
ChEC-seq in yeast

tag: treatment

value: permeabilization followed by 30 sec of Ca2+ incubation


title: Day7.organoid.Rep3_Cell_105

description: Library name: Cell_105


title: cell-free DNA from EPOC patient Loja-044

tag: tissue

value: a


title: Day7.organoid.Rep3_Cell_104

description: Library name: Cell_104


title: Day7.organoid.Rep3_Cell_103

description: Library name: Cell_103


title: cell-free DNA from EPOC patient Loja-042

tag: age

value: Active

value: Not sharpening


title: yeast_AR_dLBD_1

description:
Library name: yeast_AR_dLBD_1
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_100

description: Library name: Cell_100

value: organoid


title: Uninfected liver

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
Library name: uninf_ctr
10x Genomics

data_processing:
Sequencing data was demultiplexed using Cell Ranger 7.0.0 multi (10x GENOMICS) and FASTQ files were generated. Reads were aligned to UCSC mm10 reference genome (GRCm38) followed by quantification of gene expressions and generation of gene-barcode matrix. Transcripts were quantified using CellRanger software suite (v7.1.0; 10x Genomics)
Assembly: Mouse mm10
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz containing CellRanger pipeline output
Supplementary files format and content: molecule_info.h5 from CellRanger output

source_name: Liver

extract_protocol:
Mice were euthanized by CO2 asphyxiation and the liver was perfused with ice cold PBS by inserting a cannula through the portal vein. The liver was removed after perfusion, cut in small pieces and incubated in digestion solution (10% FCS, DNase1 1mg per 10ml, 10mg collagenase IV per 10ml) in a thermostatic bath at 37°C for 45min, stirring (100 rpm). Medium containing 10% FCS was then added to stop the enzymatic activity and the liver was smashed through 70 µm filter. The digested tissue was pelleted by centrifugation at 300g for 5min. Red blood cells (RBC) were lysed using RBC lysis buffer at room temperature for 5min. The pellets were suspended in 33% percoll and gently overlaid with phosphate buffered saline (PBS) and centrifuged at 300g for 20min without breaks. The cells were collected from the bottom of the tube.
Liver cell suspensions isolated from 5 uninfected and 5 S. aureus-infected mice (24 h of infection) were pooled and loaded onto the 10x Chromium Single Cell instrument (10x Genomics). Libraries were prepared from single-cell suspensions using sc 3’GEM-X v4 1-plex 20k according to the 10x Genomics protocol and sequenced using an Illumina NovaSeq X 1,5B 300 cycle sequencer (Illumina) with a sequencing depth of 200 million reads per sample

treatment_protocol: Staphylococcus aureus infection

value: Liver

value: Liver cells

tag: genotype

value: WT

value: Control

value: Batch 1


title: Infected liver (24h of infection)

description:
Library name: inf_24h
10x Genomics

value: Intravenous infection with S. aureus for 24 h

tag: batch


title: nmumg_smad1_bmp_high_2

description:
Library name: nmumg_smad1_bmp_high_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: incubation in 48ng/ml BMP4 for 30 min followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: cell-free DNA from EPOC patient Loja-039

value: Whole blood cell-free DNA

tag: Sex

value: Man

tag: group

value: EPOC


title: yeast_AR_dLBD_3

description:
Library name: yeast_AR_dLBD_3
ChEC-seq in yeast


title: yeast_AR_dLBD_4

description:
Library name: yeast_AR_dLBD_4
ChEC-seq in yeast


title: Infected liver (4h of infection)

description:
Library name: inf_4h
10x Genomics

value: Intravenous infection with S. aureus for 4 h


title: cell-free DNA from EPOC patient Loja-041

tag: gold

tag: smoking


title: Day7.organoid.Rep3_Cell_101

description: Library name: Cell_101

tag: strain

value: P2 mouse cochlear greater epithelial ridge cells


title: nmumg_smad1_bmp_high_3

description:
Library name: nmumg_smad1_bmp_high_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG


title: cell-free DNA from EPOC patient Loja-036

value: Female

value: d

value: Former

tag: obesity

value: Sharpening with emphysema

tag: exacerbations


title: Day7.organoid.Rep3_Cell_102

description: Library name: Cell_102

tag: cell source

tag: cell type

value: organoid


title: cell-free DNA from EPOC patient Loja-040

value: Sharpening with Bronchoconstriction


title: yeast_AR_DBD_4

description:
Library name: yeast_AR_DBD_4
ChEC-seq in yeast

value: permeabilization followed by 30 sec of Ca2+ incubation


title: Day7.organoid.Rep3_Cell_99

description: Library name: Cell_99

tag: timepoint

tag: replicate


title: nmumg_smad1_bmp_high_1

description:
Library name: nmumg_smad1_bmp_high_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line


title: nmumg_smad1_3

description:
Library name: nmumg_smad1_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: treatment

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: yeast_AR_DBD_3

description:
Library name: yeast_AR_DBD_3
ChEC-seq in yeast


title: yeast_AR_dLBD_2

description:
Library name: yeast_AR_dLBD_2
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_98

description: Library name: Cell_98


title: cell-free DNA from EPOC patient Loja-035

tag: tissue

value: a

value: ACO

tag: mmrc


title: yeast_AR_DBD_1

description:
Library name: yeast_AR_DBD_1
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_97

description: Library name: Cell_97


title: cell-free DNA from EPOC patient Loja-030

tag: age


title: nmumg_smad1_2

description:
Library name: nmumg_smad1_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_smad1_1

description:
Library name: nmumg_smad1_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: yeast_AR_DBD_2

description:
Library name: yeast_AR_DBD_2
ChEC-seq in yeast


title: Day7.organoid.Rep3_Cell_95

description: Library name: Cell_95


title: cell-free DNA from EPOC patient Loja-034

value: Active

value: Not sharpening


title: cell-free DNA from EPOC patient Loja-031

value: Whole blood cell-free DNA

value: Man


title: pmel-1 CD8, CpG anti CD2, D7 rep 5

city: Atlanta

first: Ayana

middle: T

last: Ruffin

state: Georgia

address: 1365 Clifton Rd NE,

department: Surgery

institute: Emory University

description:
Library name: A18
HCKTNDSX7_s1_1_IDT8_UDI_008_i7-IDT8_UDI_008_i5_7382-EE-0012.fastq.gz

data_processing:
Rosalind Bio was used.Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC. Reads were aligned to the Mus musculus genome build mm10 using STAR3
Assembly: mm10
Supplementary files format and content: tab delimited txt file includes normalized  counts for each sample

source_name: spleen

extract_protocol:
RNA was extracted using miRNeasy Mini Kit for RNA Extraction from Cells
RNA libraries were constucted using NEB Ultra II RNA Library Preparation

value: spleen

value: CD8 T cells


title: Day7.organoid.Rep3_Cell_96

description: Library name: Cell_96

value: P2 mouse cochlear greater epithelial ridge cells


title: nmumg_mar_wt_lig_3

description:
Library name: nmumg_mar_wt_lig_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG

value: incubation in 100nM of DHT (Dihydrotestosterone) for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep3_Cell_94

description: Library name: Cell_94


title: pmel-1 CD8, CpG anti CD2, D7 rep 3

description:
Library name: A14
HCKTNDSX7_s1_1_IDT8_UDI_079_i7-IDT8_UDI_079_i5_7382-EE-0010.fastq.gz


title: Day7.organoid.Rep3_Cell_93

description: Library name: Cell_93


title: cell-free DNA from EPOC patient Loja-025

value: Female

value: EPOC

value: d

value: Former


title: cell-free DNA from EPOC patient Loja-029

value: b

value: Sharpening with emphysema


title: pmel-1 CD8, CpG anti CD2, D7 rep 2

description:
Library name: A12
HCKTNDSX7_s1_1_IDT8_UDI_067_i7-IDT8_UDI_067_i5_7382-EE-0009.fastq.gz


title: cell-free DNA from EPOC patient Loja-019

value: a


title: nmumg_mar_wt_2

description:
Library name: nmumg_mar_wt_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep3_Cell_91

description: Library name: Cell_91

value: organoid


title: pmel-1 CD8, CpG anti CD2, D7 rep 1

description:
Library name: A8
HCKTNDSX7_s1_1_IDT8_UDI_055_i7-IDT8_UDI_055_i5_7382-EE-0008.fastq.gz


title: Day7.organoid.Rep3_Cell_90

description: Library name: Cell_90


title: pmel-1 CD8, CpG, D7 rep4

description:
Library name: A13
HCKTNDSX7_s1_1_IDT8_UDI_007_i7-IDT8_UDI_007_i5_7382-EE-0004.fastq.gz


title: cell-free DNA from EPOC patient Loja-017

value: Active

value: Not sharpening


title: nmumg_mar_dlbd_dn450_3

description:
Library name: nmumg_mar_dlbd_dn450_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_mar_wt_lig_1

description:
Library name: nmumg_mar_wt_lig_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_mar_wt_1

description:
Library name: nmumg_mar_wt_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_mar_wt_lig_2

description:
Library name: nmumg_mar_wt_lig_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient Loja-027

value: Whole blood cell-free DNA


title: nmumg_mar_wt_3

description:
Library name: nmumg_mar_wt_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: pmel-1 CD8, CpG anti CD2, D7 rep 4

description:
Library name: A16
HCKTNDSX7_s1_1_IDT8_UDI_091_i7-IDT8_UDI_091_i5_7382-EE-0011.fastq.gz

value: spleen


title: nmumg_mar_dlbd_dn450_4

description:
Library name: nmumg_mar_dlbd_dn450_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep3_Cell_92

description: Library name: Cell_92


title: pmel-1 CD8, CpG, D7 rep5

description:
Library name: A15
HCKTNDSX7_s1_1_IDT8_UDI_019_i7-IDT8_UDI_019_i5_7382-EE-0005.fastq.gz

value: CD8 T cells


title: pmel-1 CD8, CpG, D7 rep 6

description:
Library name: A17
HCKTNDSX7_s1_1_IDT8_UDI_031_i7-IDT8_UDI_031_i5_7382-EE-0006.fastq.gz


title: Day7.organoid.Rep3_Cell_89

description: Library name: Cell_89

value: P2 mouse cochlear greater epithelial ridge cells


title: cell-free DNA from EPOC patient Loja-015

value: Man


title: cell-free DNA from EPOC patient Loja-016

value: Sharpening with Bronchoconstriction


title: Day7.organoid.Rep3_Cell_88

description: Library name: Cell_88


title: pmel-1 CD8, CpG, D7 rep3

description:
Library name: A11
HCKTNDSX7_s1_1_IDT8_UDI_090_i7-IDT8_UDI_090_i5_7382-EE-0003.fastq.gz


title: cell-free DNA from EPOC patient Loja-014


title: Day7.organoid.Rep3_Cell_86

description: Library name: Cell_86


title: pmel-1 CD8, CpG, D7 rep2

description:
Library name: A7
HCKTNDSX7_s1_1_IDT8_UDI_078_i7-IDT8_UDI_078_i5_7382-EE-0002.fastq.gz


title: cell-free DNA from EPOC patient Loja-010


title: nmumg_mar_dlbd_dn400_2

description:
Library name: nmumg_mar_dlbd_dn400_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG


title: nmumg_mar_dlbd_dn450_2

description:
Library name: nmumg_mar_dlbd_dn450_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: pmel-1 CD8, CpG, D7 rep1

description:
Library name: A3
HCKTNDSX7_s1_1_IDT8_UDI_066_i7-IDT8_UDI_066_i5_7382-EE-0001.fastq.gz


title: small cell lung cancer tissue, sgScr

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

description: Library name: Insitu_sgScr

data_processing:
Single-cell RNA sequencing libraries were generated using the Chromium Single Cell 5′ Reagent Kits v3 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina NovaSeq 6000 or NovaSeq X Plus platform. To distinguish tumor cells from non-tumor cells, exogenous sequences, including sgRNA and Myc expression constructs, were added to the reference genome. Cleaned reads were then aligned to the mm10 mouse reference genome using Cell Ranger (v7.0.1).
Assembly: mm10
Supplementary files format and content: mtx files and tsv files

source_name: small cell lung cancer tissue

extract_protocol:
Tumor tissues were dissected into 5 mm3 pieces and incubated in a digestion buffer containing 1.0 mg/ml collagenase I (Gibco, 17100–017) and 0.5 mg/ml collagenase IV (Gibco, 17104–019) in DMEM/F12 (Gibco, C11330500BT). The tissues were mechanically pipetted at 10-minute intervals and gently agitated at 37°C for 30 minutes. Subsequently, the resulting mixture was filtered through 100 µm cell strainers. Following red blood cell lysis with ammonium-chloride-potassium (ACK) lysis buffer, cells were collected for subsequent single-cell RNA-seq library preparation.
Single-cell RNA libraries were constructed using the Chromium Single Cell 5′ Reagent Kits v3 according to the manufacturer’s instructions (10x Genomics).

value: small cell lung cancer tissue

value: sgScr


title: nmumg_mar_dlbd_dn450_1

description:
Library name: nmumg_mar_dlbd_dn450_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_mar_dlbd_dn400_3

description:
Library name: nmumg_mar_dlbd_dn400_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep3_Cell_87

description: Library name: Cell_87


title: Day7.organoid.Rep3_Cell_85

description: Library name: Cell_85


title: cell-free DNA from EPOC patient Loja-007

value: Female

value: EPOC

value: d

value: Former


title: Day7.organoid.Rep3_Cell_83

description: Library name: Cell_83


title: nmumg_mar_dlbd_dn400_1

description:
Library name: nmumg_mar_dlbd_dn400_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: cell-free DNA from EPOC patient Loja-006


title: small cell lung cancer tissue, sgIgfbp5, rep2

description: Library name: Insitu_sgIGFBP5_rep2


title: small cell lung cancer tissue, sgIgfbp5, rep1

description: Library name: Insitu_sgIGFBP5_rep1


title: nmumg_mar_dlbd_dn350_4

description:
Library name: nmumg_mar_dlbd_dn350_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient Loja-002

value: c


title: cell-free DNA from EPOC patient Loja-008

value: b

value: Active


title: Day7.organoid.Rep3_Cell_84

description: Library name: Cell_84

value: organoid


title: Delipidated Embryos replicate 3

city: Teramo

first: Domenico

last: Iuso

address: Via Balzarini 1

country: Italy

institute: Universisty of Teramo

description:
Library name: Delipidated 3
3 embryos pooled

data_processing:
The NovaSeq Control Software conducted image analysis and base calling. Raw sequence data (. bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq v.2.20 software. One mismatch was allowed for index sequence identification. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Sub read package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Supplementary files format and content: for each sample: processed sample.counts.txt and raw data sample.fastq.gz
Assembly: Mouse mm10

source_name: embryos derived from delipidated zygote

growth_protocol: Zygotes were cultured in fatty acid-free KSOM previously under Mineral oil at 37.5 °C in a humidified atmosphere of 5% CO₂ and atmospheric O2 from 0.5dpc to 2.0 dpc (zygote to 2-cell embryos).

extract_protocol:
Nine embryos fro each group were randomly selected for RNA-seq analysis and distributed into three independent samples, each consisting of three embryos per Eppendorf tube as experimental replicates. Embryo pools were transferred into 3.5µL of sterile RNase-free PBS and stored at −80°C until processing. Library preparations and sequencing reactions were conducted at GENEWIZ, LLC. /Azenta US, Inc (South Plainfield, NJ, USA). The SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian, 48 rxn (Takara Bio, Cat. ID: 634412) was used to prepare cDNA libraries with embryo samples processed directly without prior RNA extraction.
The protocol included ribosomal RNA depletion, strand-specific cDNA synthesis based on SMART technology. The samples were sequenced using a 2x150 paired-end (PE) configuration, targeting ~10 M read-pairs per sample. Samples were sequenced with 30% Phi-X spike-in.

treatment_protocol: Lipids were removed from zygote-stage embryos. The entire experiment was performed on a pre-warmed plate to maintain physiological conditions. Thirty zygotes were initially placed into a 1.5 mL microcentrifuge tube containing 500 µL M2 medium supplemented with cytochalasin B at a final concentration of 50 µg/mL. A first centrifugation was applied at 4200 × g for 10 minutes to polarize LDs within the blastomere. After the first centrifugation, 250 µL of pre-warmed hyperosmotic solution (M2 medium supplemented with cytochalasin B and 50 µg/mL sucrose) was added to the microcentrifuge tube. The embryos were then subjected to a second centrifugation at 9500 × g for 10 minutes to move the LD aggregates into the perivitelline (PV) space. Then, embryos were transferred to fresh M2 medium containing cytochalasin B 50 µg/mL under the micromanipulation chamber. A small opening was created in the zona pellucida using laser-assisted manipulation, after which the biopsy was mechanically performed by aspirating the LD into a pipette with a 12 µm inner diameter. All manipulations were performed under an Inverted microscope Nikon Eclipse Integra Ti (Nikon Corporation, Japan) using an Eppendorf Micromanipulator 5176 (Eppendorf AG, Germany). Following manipulation, embryos were thoroughly washed in M2 medium and returned to culture in free fatty acid KSOM under standard conditions.

value: F1 (C57Bl/10 X CBA/H)

value: 2-cell embryos

value: embryos derived from delipidated zygote

tag: genotype

value: wt

value: in vitro culture from zygotes

tag: time

value: day 2


title: Day7.organoid.Rep3_Cell_82

description: Library name: Cell_82

source_name: organoid

value: P2 mouse cochlear greater epithelial ridge cells


title: cell-free DNA from EPOC patient GR-040

value: Whole blood cell-free DNA

tag: Sex

value: Man

tag: group

value: a

value: Sharpening with Bronchoconstriction


title: Day7.organoid.Rep2_Cell_81

description: Library name: Cell_81


title: Day7.organoid.Rep2_Cell_79

description: Library name: Cell_79


title: Delipidated Embryos replicate 1

description:
Library name: Delipidated 1
3 embryos pooled


title: nmumg_mar_dlbd_dn350_1

description:
Library name: nmumg_mar_dlbd_dn350_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG


title: cell-free DNA from EPOC patient GR-037

value: EPOC

tag: gold

tag: smoking

value: Not sharpening


title: Delipidated Embryos replicate 2

description:
Library name: Delipidated 2
3 embryos pooled

tag: strain


title: Day7.organoid.Rep2_Cell_80

description: Library name: Cell_80


title: nmumg_mar_dlbd_dn350_2

description:
Library name: nmumg_mar_dlbd_dn350_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: cell-free DNA from EPOC patient GR-036

value: b

value: Active

tag: obesity

tag: exacerbations


title: Control Embryos replicate 2

description:
Library name: Control 2
3 embryos pooled

source_name: embryos derived from control zygote

value: F1 (C57Bl/10 X CBA/H)

tag: cell type

value: embryos derived from control zygote


title: Control Embryos replicate 3

description:
Library name: Control 3
3 embryos pooled

value: 2-cell embryos


title: cell-free DNA from EPOC patient GR-033

value: Female

value: Former


title: nmumg_mar_dlbd_dn300_2

description:
Library name: nmumg_mar_dlbd_dn300_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_78

description: Library name: Cell_78

tag: cell source

value: organoid

tag: timepoint


title: Day7.organoid.Rep2_Cell_77

description: Library name: Cell_77

value: P2 mouse cochlear greater epithelial ridge cells

tag: replicate


title: Control Embryos replicate 1

description:
Library name: Control 1
3 embryos pooled

value: wt

tag: treatment

value: in vitro culture from zygotes

value: day 2


title: cell-free DNA from EPOC patient GR-030

tag: tissue

value: Whole blood cell-free DNA

value: Man

value: d

value: Sharpening with Bronchoconstriction


title: nmumg_mar_dlbd_dn300_3

description:
Library name: nmumg_mar_dlbd_dn300_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: nmumg_mar_dlbd_dn350_3

description:
Library name: nmumg_mar_dlbd_dn350_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient GR-032

tag: age

value: EPOC

value: b

value: Not sharpening

tag: mmrc


title: Day7.organoid.Rep2_Cell_76

description: Library name: Cell_76


title: nmumg_mar_dlbd_4

description:
Library name: nmumg_mar_dlbd_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient GR-029

value: a

value: Active


title: cell-free DNA from EPOC patient GR-026

value: Female

value: Former


title: KO E14.5 palatal shelf replicate 3

city: Fukuoka-shi

first: TAO

last: HAN

address: Maidashi 3-1-1

country: Japan

institute: Faculty of Dental Science, Kyushu University

description: Library name: RNA1095

data_processing:
DESeq2 R package (version 1.5.2)
Assembly: mm10
Supplementary files format and content: Tab-delimited matrix file containing gene-level FPKM values for all genes across all six samples.
Supplementary files format and content: txt files include FPKM values of each samples.

source_name: E14.5 mouse embyos palatal shelves tissue

extract_protocol:
Total RNA was extracted from the palatal shelves or cells using a ReliaPrep RNA Miniprep System (Promega, Madison, WI)
RNA-seq libraries were constructed from total RNA isolated from E14.5 mouse palatal shelf tissues using a standard Illumina-compatible library preparation protocol performed by the sequencing provider.

tag: genotype

value: p130Casfl/fl; CAG-Cre


title: KO E14.5 palatal shelf replicate 2

description: Library name: RNA1091

value: E14.5 mouse embyos palatal shelves tissue


title: Day7.organoid.Rep2_Cell_75

description: Library name: Cell_75

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid


title: nmumg_mar_dlbd_3

description:
Library name: nmumg_mar_dlbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_mar_dlbd_dn300_1

description:
Library name: nmumg_mar_dlbd_dn300_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_74

description: Library name: Cell_74


title: KO E14.5 palatal shelf replicate 1

description: Library name: RNA1065


title: Day7.organoid.Rep2_Cell_72

description: Library name: Cell_72


title: cell-free DNA from EPOC patient GR-025

source_name: Whole blood cell-free DNA

value: Whole blood cell-free DNA

tag: Sex

value: Sharpening with emphysema


title: nmumg_mar_dlbd_1

description:
Library name: nmumg_mar_dlbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient GR-027

value: Man

tag: group


title: WT E14.5 palatal shelf replicate 2

description: Library name: RNA1094


title: nmumg_mar_dlbd_2

description:
Library name: nmumg_mar_dlbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_mar_dbd_3

description:
Library name: nmumg_mar_dbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_73

description: Library name: Cell_73


title: cell-free DNA from EPOC patient GR-023

tag: gold

value: d


title: WT E14.5 palatal shelf replicate 3

description: Library name: RNA1098


title: Day7.organoid.Rep2_Cell_71

description: Library name: Cell_71


title: cell-free DNA from EPOC patient GR-022

tag: smoking


title: nmumg_mar_dbd_2

description:
Library name: nmumg_mar_dbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG


title: Day7.organoid.Rep2_Cell_70

description: Library name: Cell_70

tag: strain


title: nmumg_mar_dbd_1

description:
Library name: nmumg_mar_dbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Thymus DN3_3

city: Oklahoma City

first: Aneta

last: Pankow

state: Oklahoma

address: 825 NE 13th St

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

description:
Library name: 10.17_Thy_DN3_3__S120
gene_names_counts_ILC2_DN3.csv

data_processing:
Data were normalized using DESEq2
Assembly: GRCm39.112
Supplementary files format and content: Count matrix table with raw gene counts for each population

source_name: Thymus

extract_protocol:
PicoPureTM RNA Isolation Kit (ThermoFisher Scientific).
Watchmaker Genomics mRNA kit

value: Thymus

value: CD4 and CD8 double negative 3 (DN3)

value: No treatment

tag: batch


title: WT E14.5 palatal shelf replicate 1

description: Library name: RNA1093


title: cell-free DNA from EPOC patient GR-017

value: EPOC

tag: obesity

tag: exacerbations


title: Day7.organoid.Rep2_Cell_69

description: Library name: Cell_69

tag: cell source

tag: cell type


title: Day7.organoid.Rep2_Cell_68

description: Library name: Cell_68

tag: timepoint

tag: replicate


title: cell-free DNA from EPOC patient GR-015

tag: tissue

value: a

value: Sharpening with Bronchoconstriction


title: Day7.organoid.Rep2_Cell_67

description: Library name: Cell_67


title: Thymus DN3_1

description:
Library name: 10.17_Thy_DN3_1__S118
gene_names_counts_ILC2_DN3.csv

tag: treatment


title: Lung ILC2 ZSgreen_pos_3

description:
Library name: 04.08_P10_S37
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv

source_name: Lung

value: Lung

value: Group 2 innate lymphoid cell (ILC2)

tag: cell subtype

value: pos


title: nmumg_hpr_wt_lig_3

description:
Library name: nmumg_hpr_wt_lig_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line

value: incubation in 100nM of Progesterone for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: nmumg_hpr_wt_lig_1

description:
Library name: nmumg_hpr_wt_lig_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_hpr_wt_lig_2

description:
Library name: nmumg_hpr_wt_lig_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Thymus DN3_2

description:
Library name: 10.17_Thy_DN3_2__S119
gene_names_counts_ILC2_DN3.csv

tag: genotype


title: Day7.organoid.Rep2_Cell_66

description: Library name: Cell_66

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid


title: cell-free DNA from EPOC patient GR-014

value: Whole blood cell-free DNA

tag: age

tag: Sex

value: b

value: Former

value: Sharpening with emphysema

tag: mmrc


title: cell-free DNA from EPOC patient GR-012

value: Man

tag: group

tag: gold

tag: smoking

value: Active


title: nmumg_hpr_wt_3

description:
Library name: nmumg_hpr_wt_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Lung ILC2 ZSgreen_pos_2

description:
Library name: 6_S95
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv

value: No treatment

tag: batch


title: Lung ILC2 ZSgreen_pos_1

description:
Library name: 3_S92
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv


title: Day7.organoid.Rep2_Cell_65

description: Library name: Cell_65

tag: strain


title: Day7.organoid.Rep2_Cell_64

description: Library name: Cell_64

tag: cell source


title: nmumg_hpr_wt_2

description:
Library name: nmumg_hpr_wt_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient GR-010

value: EPOC

tag: obesity

value: Not sharpening

tag: exacerbations


title: Lung ILC2 ZSgreen_neg_5

description:
Library name: 04.08_P9_S36
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv

value: Lung

tag: cell type

value: neg


title: nmumg_hpr_wt_1

description:
Library name: nmumg_hpr_wt_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_63

description: Library name: Cell_63

tag: timepoint

tag: replicate


title: Day7.organoid.Rep2_Cell_62

description: Library name: Cell_62


title: cell-free DNA from EPOC patient GR-009

tag: tissue

value: Female

value: a


title: Lung ILC2 ZSgreen_neg_4

description:
Library name: 5_S94
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv

value: Group 2 innate lymphoid cell (ILC2)

tag: cell subtype

tag: treatment


title: cell-free DNA from EPOC patient GR-007

tag: age


title: nmumg_hpr_dlbd_dn450_1

description:
Library name: nmumg_hpr_dlbd_dn450_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line


title: Day7.organoid.Rep2_Cell_60

description: Library name: Cell_60

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid


title: Lung ILC2 ZSgreen_neg_1

description:
Library name: 1_S90
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv

tag: genotype


title: Lung ILC2 ZSgreen_neg_2

description:
Library name: 2_S91
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv


title: Day7.organoid.Rep2_Cell_61

description: Library name: Cell_61


title: nmumg_hpr_dlbd_dn450_2

description:
Library name: nmumg_hpr_dlbd_dn450_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient GR-016

value: Whole blood cell-free DNA

tag: Sex

tag: group

value: d

tag: mmrc


title: cell-free DNA from EPOC patient GR-008

tag: gold

value: b

tag: smoking

value: Former


title: Clonally traced olfactory and forebrain region and surrounding tissue 1, embryonic day (E) 11.5

city: Solna

first: Felix

middle: Robert Nicodemus

last: Waern

state: Uppland

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Library name: exp2_olfac1

data_processing:
Alignment of reads was performed using 10x Genomics Cell Ranger v.70.01 with chimeric mm39 and FP genome refrence.
TREX v.0.4dev402 was used for extraction of clonal barcodes.
Assembly: chimeric mm39
Supplementary files format and content: filtered_feature_bc_matrix.h5 contains gene expression data from Cell Ranger. It has genes as rows, cell barcodes as columns, and UMI counts for each gene in each cell.
Supplementary files format and content: umi_count_matrix.csv is a matrix of read counts with cells as columns and cloneIDs as rows and the count of each clone is each cell.

source_name: Mouse embryo, olfactory and forebrain region

extract_protocol:
Embryos were harvested at E11.5 following maternal euthanasia by CO₂ overdose and cervical dislocation and were subsequently euthanized by decapitation. Mouse embryos were dissected from the uterus, sacrificed, and transferred to ice-cold Hank’s Balanced Salt Solution (HBSS). Fluorescent reporter expression (tdTomato) was assessed using a fluorescence stereomicroscope. Embryos were dissected into different regions containing olfactory and forebrain; eye, trigeminal ganglia  and midbrain and hindbrain; otic and epibranchial ganglia region; and the entire cranial region. Dissected tissues were placed in dissociation buffer containing Collagenase P (2 mg/mL) (Roche, Sigma-Aldrich), TrypLE (1×), and DNase I (1 µL/mL) prepared in HBSS with calcium and magnesium. Samples were then incubated for 20 minutes at 37 C in a preheated shaking incubator set at 150 RPM. After tissue were dissociated to stop the enzymatic were aded ice-cold HBSS supplemented with 2% FBS. Cells were pelleted by centrifugation at 500 × g for 15 minutes at 4 °C, resuspended in HBSS containing 2% FBS, and kept on ice. Prior to downstream applications, single-cell suspensions were filtered through a 40 µm cell strainer.  Flow cytometry sorting was performed using FACSAria Fusion or FACSAria III instruments (BD) equipped with a 100 µm nozzle and a 1.5 neutral density filter, and controlled via FACSDiva software (BD).
Cells (~5,000–10,000 per reaction) were processed using the 10X Genomics Chromium V3.1 kit. cDNA was synthesized and amplified by 12 PCR cycles. Gene expression libraries were prepared and indexed using Single Index Plate T Set A. CloneID sequences were enriched via nested PCR with Q5 polymerase, purified between steps using 0.8× AMPure beads, and all libraries were quantified with BioAnalyzer and/or Qubit.

treatment_protocol: At embryonic days 7.5 and 8.5 (E7.5-E8.5), pregnant CD-1 female mice were anesthetized with isoflurane, maintained on a heated surface, and given preoperative analgesia (buprenorphine, 0.05–0.1 mg/kg, subcutaneous). After preparation and sterilization of the abdominal surgical site, the uterus was gently exteriorized into a Petri dish containing PBS. Embryos were visualized using a Vevo2100 ultrasound system, and 46 nL of lentivirus was injected through the uterine wall into the amniotic cavity. The uterus was then returned to the abdomen, muscle incisions were closed with absorbable sutures, and the skin was sealed with sutures or staples. Animals recovered on a heating pad under supervision and received postoperative analgesia.

tag: developmental stage

tag: injection time

value: CD-1 (wild-type)

value: clonally barcoded lenitvirus injection (pMR671_LV_TOM_bc)


title: cell-free DNA from EPOC patient GR-004

value: Man

value: Active

tag: obesity

value: Sharpening with Bronchoconstriction

tag: exacerbations


title: cell-free DNA from EPOC patient GR-005

value: EPOC


title: nmumg_hpr_dlbd_dn450_3

description:
Library name: nmumg_hpr_dlbd_dn450_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Lung ILC2 ZSgreen_neg_3

description:
Library name: 4_S93
gene_names_counts_ILC2_DN3.csv
gene_names_counts_ILC2.csv

value: Lung

tag: cell type

value: neg

value: No treatment

tag: batch


title: Day7.organoid.Rep2_Cell_59

description: Library name: Cell_59

tag: strain

tag: cell source

value: P2 mouse cochlear greater epithelial ridge cells

tag: timepoint

tag: replicate


title: cell-free DNA from EPOC patient GR-002

tag: tissue

tag: age


title: Clonally traced olfactory and forebrain region and surrounding tissue 2, embryonic day (E) 11.5

description: Library name: exp2_olfac2

value: Mouse embryo, olfactory and forebrain region

tag: genotype

tag: treatment


title: nmumg_hpr_dlbd_dn300_4

description:
Library name: nmumg_hpr_dlbd_dn300_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line


title: nmumg_hpr_dlbd_dn300_3

description:
Library name: nmumg_hpr_dlbd_dn300_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_hpr_dlbd_dn450_4

description:
Library name: nmumg_hpr_dlbd_dn450_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_58

description: Library name: Cell_58

value: organoid


title: Clonally traced otic and epibranchial ganglia region and surrounding tissue 1, embryonic day (E) 11.5

description: Library name: exp2_otic1

source_name: Mouse embryo, otic and epibranchial ganglia region


title: cell-free DNA from EPOC patient GR-001

value: Whole blood cell-free DNA

tag: Sex

tag: group

tag: gold

value: Not sharpening

tag: mmrc


title: nmumg_hpr_dlbd_dn300_2

description:
Library name: nmumg_hpr_dlbd_dn300_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_53

description: Library name: Cell_53


title: Day7.organoid.Rep2_Cell_57

description: Library name: Cell_57


title: Day7.organoid.Rep2_Cell_55

description: Library name: Cell_55


title: Clonally traced eye, trigeminal ganglia, midbrain and hindbrain region and surrounding tissue 3, embryonic day (E) 11.5

description: Library name: exp2_lens3

source_name: Mouse embryo, eye, trigeminal ganglia, midbrain and hindbrain region

tag: developmental stage

tag: injection time


title: cell-free DNA from EPOC patient AL-019

value: d

tag: smoking

tag: obesity

value: Sharpening with emphysema

tag: exacerbations


title: cell-free DNA from EPOC patient AL-020

value: a

value: Former


title: Day7.organoid.Rep2_Cell_56

description: Library name: Cell_56

tag: strain

tag: cell source

tag: cell type


title: Clonally traced eye, trigeminal ganglia, midbrain and hindbrain region and surrounding tissue 2, embryonic day (E) 11.5

description: Library name: exp2_lens2

tag: tissue

value: Mouse embryo, eye, trigeminal ganglia, midbrain and hindbrain region

value: CD-1 (wild-type)

value: clonally barcoded lenitvirus injection (pMR671_LV_TOM_bc)


title: Clonally traced otic and epibranchial ganglia region and surrounding tissue 2, embryonic day (E) 11.5

description: Library name: exp2_otic2

value: Mouse embryo, otic and epibranchial ganglia region


title: cell-free DNA from EPOC patient AL-017

tag: age

value: Man

value: EPOC

value: Active


title: Day7.organoid.Rep2_Cell_54

description: Library name: Cell_54

tag: timepoint

tag: replicate


title: cell-free DNA from EPOC patient AL-018


title: nmumg_hpr_dlbd_dn100_4

description:
Library name: nmumg_hpr_dlbd_dn100_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line

value: NMuMG

tag: treatment

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: nmumg_hpr_dlbd_dn100_5

description:
Library name: nmumg_hpr_dlbd_dn100_5
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_hpr_dlbd_dn100_3

description:
Library name: nmumg_hpr_dlbd_dn100_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient AL-016

tag: Sex

tag: group


title: nmumg_hpr_dlbd_dn300_1

description:
Library name: nmumg_hpr_dlbd_dn300_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: cell-free DNA from EPOC patient AL-010

tag: gold

tag: mmrc


title: cell-free DNA from EPOC patient AL-014


title: nmumg_hpr_dlbd_dn100_1

description:
Library name: nmumg_hpr_dlbd_dn100_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_hpr_del_lbd_2

description:
Library name: nmumg_hpr_del_lbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: RAW 264.7 cells, DV infection rep2

city: Bengaluru

first: Debayani

last: Chakraborty

address: CV Raman road

department: Chemical Engineering

country: India

institute: Indian Institute of Science

description:
Library name: Sample6
Column name in raw_counts.tsv: S2

data_processing:
Raw files were quality checked with FastQC v0.11.9 and trimmed with Trim Galore! v0.6.7. with default parameters
The trimmed sequences were aligned to reference genome GRCm39 with STAR v2.7.11b in one pass mode
featureCounts v2.0.3 was used to count gene level reads with parameters “-t gene -p --countReadPairs -s 2”
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file contains raw counts for each sample
Supplementary files format and content: csv file contains Deseq2 normalised counts for each sample

extract_protocol:
After treatment, cells were washed with PBS and lysed with TRIzol reagent (Invitrogen)
The first step is selectively purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented using divalent cations under elevated temperature. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA where Uracil is added instead of Thymine. The strand specificity is preserved by a USER enzyme based digestion of the second strand thereby leaving one functional strand which maps to the DNA strand which it was transcribed from. The USER digested single strand molecules are enriched and indexed in a limited cycle PCR followed by AMPure bead purification to create final cDNA library for sequencing.

value: macrophage

value: DENV

tag: batch


title: nmumg_hpr_del_lbd_3

description:
Library name: nmumg_hpr_del_lbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep2_Cell_50

description: Library name: Cell_50

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: mm10 (GRCm38)
Supplementary files format and content: text file with raw read counts

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid


title: Day7.organoid.Rep2_Cell_48

description: Library name: Cell_48


title: cell-free DNA from EPOC patient AL-013

value: Whole blood cell-free DNA

tag: smoking

value: Not sharpening


title: Day7.organoid.Rep2_Cell_52

description: Library name: Cell_52


title: RAW 264.7 cells, 25-HC treatment rep1

description:
Library name: Sample4
Column name in raw_counts.tsv: HC_Raw4_4


title: RAW 264.7 cells, control rep2

description:
Library name: Sample5
Column name in raw_counts.tsv: S1

value: control


title: Day7.organoid.Rep2_Cell_51

description: Library name: Cell_51


title: RAW 264.7 cells, 25-HC treatment, DV infection rep1

description:
Library name: Sample3
Column name in raw_counts.tsv: Sample3

value: 25-HC, DV


title: RAW 264.7 cells, 25-HC treatment, DV infection rep2

description:
Library name: Sample7
Column name in raw_counts.tsv: S3


title: nmumg_hpr_del_lbd_1

description:
Library name: nmumg_hpr_del_lbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: SC_EAE_m236_Arg1_negative

city: Vienna

first: Omar

last: Sharif

address: Schwarzspanier Strasse

department: Centre for Physiology and Pharmacology, Vascular Biology and Thrombosis research

country: Austria

institute: Medical University of Vienna

data_processing:
conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard)
Sequencing reads were mapped using STAR aligner (v2.7.10b) / Ensembl annotation e100
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw read counts mapped to genes from the mouse genome

source_name: spinal cord

extract_protocol:
Total RNA was prepared from 200,000 spinal cord FACS sorted Ly6G-CD3-CD45+CX3CR1+YFP+ or 100,000 Ly6G-CD3-CD45+CX3CR1+YFP- cells of EAE suffering Arg1tm1Lky animals at peak-disease using TRIzol Reagent (Ambion, #15596018) and quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity number (RIN) was determined using the 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA).
RNA-Seq library preparation using the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). NGS library concentrations were quantified with Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA). For sequencing, samples were diluted and pooled into multiplex NGS libraries in equimolar amounts.

value: spinal cord

value: male

value: viable CD3-Ly6G-CD45+CX3CR1+Arg1-

tag: genotype

value: EAE

tag: strain background

tag: disease-state

value: peak-disease


title: Day7.organoid.Rep2_Cell_47

city: Galveston

first: Marie

last: Kubota

institute: University of Texas Medical Branch

description: Library name: Cell_47

extract_protocol:
Harvested organoids were rinsed in PBS and incubated in 0.25% Trypsin-EDTA at 37°C and 5% CO2 for 10-20 min. After the addition of soybean trypsin inhibitor, the samples were mechanically dissociated. Single cells were manually collected using a glass micropipette (50-60µm inner diameter) and transferred into 96-well plates.
SmartSeq2 protocol

tag: strain

tag: cell source


title: Day7.organoid.Rep2_Cell_49

description: Library name: Cell_49

tag: cell type


title: Day7.organoid.Rep2_Cell_46

description: Library name: Cell_46


title: SC_EAE_m235_Arg1_negative

tag: tissue


title: nmumg_hpr_dbd_4

description:
Library name: nmumg_hpr_dbd_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: RAW 264.7 cells, DV infection rep1

description:
Library name: Sample2
Column name in raw_counts.tsv: Sample2


title: nmumg_hpr_dbd_3

description:
Library name: nmumg_hpr_dbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: SC_EAE_m6_Arg1_negative


title: nmumg_hpr_dbd_2

description:
Library name: nmumg_hpr_dbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Clonally traced eye, trigeminal ganglia, midbrain and hindbrain region and surrounding tissue 1, embryonic day (E) 11.5

description: Library name: exp2_lens1

value: Mouse embryo, eye, trigeminal ganglia, midbrain and hindbrain region

tag: developmental stage

tag: injection time

value: CD-1 (wild-type)

value: clonally barcoded lenitvirus injection (pMR671_LV_TOM_bc)


title: Day7.organoid.Rep2_Cell_44

description: Library name: Cell_44

tag: timepoint

tag: replicate


title: RAW 264.7 cells, control rep1

description:
Library name: Sample1
Column name in raw_counts.tsv: Sample1

tag: cell line

tag: treatment


title: Day7.organoid.Rep2_Cell_45

description: Library name: Cell_45


title: nmumg_hpr_dbd_1

description:
Library name: nmumg_hpr_dbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: SC_EAE_m2_Arg1_negative

tag: Sex


title: SC_EAE_m236_Arg1_positive

value: viable CD3-Ly6G-CD45+CX3CR1+Arg1+


title: SC_EAE_m234_Arg1_negative


title: nmumg_hgr_wt_lig_3

description:
Library name: nmumg_hgr_wt_lig_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: incubation in 100nM of Dex (dexamethasone ) for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep2_Cell_42

description: Library name: Cell_42

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid


title: Day7.organoid.Rep2_Cell_43

description: Library name: Cell_43


title: nmumg_hpr_dlbd_dn100_2

description:
Library name: nmumg_hpr_dlbd_dn100_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_hgr_wt_lig_4

description:
Library name: nmumg_hgr_wt_lig_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KSS5LACT-B3

city: Urbana

first: Rishabh

last: Singh

state: Iillinois

address: 1604 Melrose VAlley Ct

department: Agronomy

institute: Kansas State University

description:
Library name: Sample 47
150bp-paired end illumina sequencing

data_processing:
Trimmomatic + FastQC + STAR + DESeq2
Quality of the raw RNA-Seq data was assessed and the adaptor sequences were trimmed using Trimmomatic with default parameters (Bolger et al. 2014).
Trimmed reads were aligned to the Palmer amaranth genome (Raiyemo et al. 2025; A. palmeri Hap1; JBEFMX000000000) using STAR (Dobin et al. 2013) with the  --quantModeGeneCounts function, which simultaneously performed alignment and generated per-gene read counts for each sample
Read counts per gene were then subjected to a pairwise differential gene expression (DGE) analysis using DEseq2 (Love et al. 2014).
Assembly: Reads were aligned to Palmer amaranth genome
Supplementary files format and content: csv

organism: Amaranthus palmeri

source_name: leaf

growth_protocol: plants were raised from seeds and grown under growth chamber conditions with at 32/22 C day/night (d/n) temperatures, 60 ± 10% relative humidity, and 16/8 d/n photoperiod, provided by fluorescent bulbs delivering 500 μ mol m-2 s-1 illumination at plant canopy level.

extract_protocol:
Total RNA was extracted using GeneJET Plant RNA Purification Mini Kit® (Thermo Fischer Scientific) following manufacturer’s instructions
stranded polyA
150bp-paired end illumina sequencing

treatment_protocol: all herbicides were applied at 10-12 cm height stage using a bench type sparayer caliberated to deliver 187L/ha.

value: leaf

tag: phenotype

value: Susceptible

value: lactofen


title: KSS7LACT-B3

description:
Library name: Sample 48
150bp-paired end illumina sequencing

tag: batch


title: Day7.organoid.Rep1_Cell_41

description: Library name: Cell_41


title: RAW 264.7 cells, 25-HC treatment rep2

description:
Library name: Sample8
Column name in raw_counts.tsv: S4

value: macrophage


title: KSS3LACT-B3

description:
Library name: Sample 46
150bp-paired end illumina sequencing


title: SC_EAE_m235_Arg1_positive

value: spinal cord

value: male


title: cell-free DNA from EPOC patient AL-015

data_processing:
ChAMP R package was used to read the beta intensities from the .idat files with the default parameters, filters and normalization.
Multivariate batch effect removal was applied using ARSyN R package based on the gold sample labels and back to the beta scale.

value: Whole blood cell-free DNA

tag: age

value: Man

tag: group

value: EPOC

tag: gold

value: d

tag: smoking

value: Former

tag: obesity

value: Sharpening with emphysema

tag: exacerbations

tag: mmrc


title: nmumg_hgr_wt_lig_2

description:
Library name: nmumg_hgr_wt_lig_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG


title: SC_EAE_m6_Arg1_positive

tag: tissue

tag: cell type

value: viable CD3-Ly6G-CD45+CX3CR1+Arg1+

tag: genotype

value: EAE

tag: strain background

tag: disease-state

value: peak-disease


title: Day7.organoid.Rep1_Cell_40

description: Library name: Cell_40

tag: strain

tag: cell source

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid

tag: timepoint

tag: replicate


title: KSS7NT-B3

description:
Library name: Sample 45
150bp-paired end illumina sequencing

value: leaf

tag: phenotype

value: Susceptible

tag: treatment

value: control

tag: batch


title: KSS3NT-B3

description:
Library name: Sample 43
150bp-paired end illumina sequencing


title: SC_EAE_m2_Arg1_positive

value: spinal cord

tag: Sex


title: SC_EAE_m234_Arg1_positive

value: male


title: Day7.organoid.Rep1_Cell_38

description: Library name: Cell_38


title: nmumg_hgr_wt_lig_1

description:
Library name: nmumg_hgr_wt_lig_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

tag: cell line

value: incubation in 100nM of Dex (dexamethasone ) for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep1_Cell_39

description: Library name: Cell_39


title: nmumg_hgr_wt_6

description:
Library name: nmumg_hgr_wt_6
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep1_Cell_37

description: Library name: Cell_37