title: 3D-Plasma-V1-282

description:
282
3D-Plasma-V1-282


title: 3D-Plasma-V1-279

status: Public on Nov 03 2022

type: SRA

city: Chicoutimi

first: Luigi

last: Bouchard

state: Quebec

address: 305 rue Saint-Vallier, Pavillon des Augustines

department: Biochimie et génomique fonctionnelle

country: Canada

institute: Université de Sherbrooke

description:
279
3D-Plasma-V1-279

library_source: transcriptomic

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with FASTX-Toolkit. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using STAR. As rRNA contamination was almost inexistant in our samples (average of 1.04±0.90% of total mapped reads based on metrics from STAR), the mapping step to the rRNA was removed to speed tup the process.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple sample (PMID : 30956140).
Samples with < 1M miRNAs reads were considered outliers and removed from the downstream analysis (differential analysis using DESeq2 package).
DESeq2 function collapseReplicates was used to combined technical replicates in the analysis for data that were extracted and sequenced twice. Technical replicate have the same ID and fastq files contains either "pilote" or "projet". Technical replicate are identified in the technical replicates column (N = 12 originally, 9 gave consent for genetic data sharing)
Assembly: GRCh37
Supplementary files format and content: tab-seperated value files include raw read counts (non-normalized) for each Sample
Supplementary files format and content: 3D_Plasma_miRNA_v1_geo_rawcounts.txt

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from either 500μl of plasma kept at −80 °C until extraction. Seventy-five μl of nuclease-free water was used to eluate total RNA which was then precipitated following the method described by Burgos et al. (PMID: 23525801). Briefly, 35 μl of cold (4°C) 7 M ammonium acetate solution (ThermoFisher Scientific, catalogue # 02002268) were added to 70μl of total RNA. This was followed by the addition of 420μl of chilled (−20°C) absolute ethanol (Commercial Alcohols, ON, Canada; catalogue # P006EAAN) and overnight precipitation at −20°C. The mix was then centrifuged at 16 000g at 4°C for 30 min. RNA pellets were then washed twice with 200 μl of cold 80% ethanol followed by centrifugation at 16 000g at 4°C for 5min. It was then dried for 30min at room temperature and 5μl of nuclease-free water was added. The total volume was used for library preparation.
Samples were randomized before library preparation. An adapted version of the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) protocol from Burgos et al. (PMID: 23525801) was used to manage low concentrated miRNA samples. In this protocol, half of the standard volumes were used for ligation (3′ and 5′ ends) of RNA sample (5μl), reverse transcription, barcoding (index 1-20: one index per sample) and PCR amplification (15 cycles) to preserve the ratio between RNA amount (which is lower in plasma samples) and the reagents. Purification and size-selection (145-160bp) of the libraries were done by migration on a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, catalogue # EC6265BOX) followed by elution in 300 μl of nuclease-free water and overnight incubation at 500 RPM at room temperature on an incubating microplate shaker (VWR, ON, Canada, catalogue #12620-930). The libraries were then precipitated according to the manufacturer's instructions (including incubation of the precipitation mix at −80°C for 30min) and were resuspended in 25 μl of 10 mM Tris-HCI pH 8.5 buffer. Library sequencing, including quality control and sample pooling, was performed at the McGill University and Génome Québec Innovation Centre (Québec, Canada). Libraries were first quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and the average size fragment was determined using a LabChip GX II (PerkinElmer) instrument. The libraries were normalized and pooled before being denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq S1 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 1x100 cycles (single-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads. Ten samples were extracted and sequenced twice to account for batch preparation and to confirm standardization.

tag: tissue

value: Plasma

tag: Sex

value: female

tag: pregnancy status_1

value: Normal


title: 3D-Plasma-V1-275

description:
275
3D-Plasma-V1-275

value: Gestational diabetes mellitus


title: 3D-Plasma-V1-274

description:
274
3D-Plasma-V1-274


title: 3D-Plasma-V1-272

description:
272
3D-Plasma-V1-272


title: TNP2 KO DAY12 LGLUT biological replicate 3, technical replicate 2

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: RNA-Seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.2.31) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters used were “--star-output-genome-bam --forward-prob 1”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

molecule: polyA RNA

source_name: Melanoma cells MEXF 2090

growth_protocol: Cells were grown in RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
3’ mRNA-Seq libraries were prepared with the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit.  Total RNA was quantified using via the RNA QuantiFluor RNA system E3310 on the GloMax (Promega) Multi Detection system following the maufacturer's guidelines.  RNA quality was checked via the High Sensitivity RNA ScreenTape using the TapeStation 4200 (Agilent).  RNA was normalised to 30 ng and used for cDNA synthesis and library preparation using the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit according to the manufacturer’s instructions.  Libraries were sequenced on the Illumina HiSeq 4000 with single ended reads

treatment_protocol: Cells were grown in the absence of glutamine (RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2) for 12d

tag: cell line

value: Melanoma cells MEXF 2090

tag: genotype

value: TNP2 KO

tag: timepoint

value: DAY 12

tag: treatment

value: L-GLUT


title: 3D-Plasma-V1-281

description:
281
3D-Plasma-V1-281


title: KrasC57_replicate3

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

country: USA

institute: National Institutes of Health

data_processing:
Eight mRNA-seq libraries were sequenced with Illumina chemistry.
Samples were trimmed for adapters and low quality bases using Cutadapt 1.18 software and aligned with reference mouse mm10 genome using STAR 2.7.6a software.
Quantification was carried out with RSEM 1.3.0 using the transcriptome bam file created by STAR.
Basecalling was performed by RTA.
Demultiplexing and FASTQ generation was performed using bcl2fastq.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.36).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.1) with parameters: STAR --genomeDir $star_genome --readFilesIn R1_trimmed.fastq R2_trimmed.fastq --outTmpDir /logs/star --outSAMunmapped Within -- outFilterType BySJout --outFilterMultimapNmax 20 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 -- alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- sjdbScore 1 --runThreadN 8 --genomeLoad NoSharedMemory -- outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.2.22).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Assembly: mm10
Supplementary files format and content: Comma-Separated Values (.csv) file containing filtered raw counts produced by RSEM

organism: Mus musculus

source_name: mouse primary keratinocytes

growth_protocol: Primary mouse keratinocytes and hair follicle buds were isolated from newborn pups and cultured in modified Eagle's medium (EMEM, Lonza 06-174G), 8% Chelex-treated FBS (Gemini Bio Products 100-106), and 0.05 mmol/L calcium unless otherwise indicated.

extract_protocol:
mRNA was extracted by Psomogen using standard protocols.
TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: The Cre recombinase (Cre) was introduced into primary keratinocytes using an adenoviral construct driven by a cytomegalovirus promoter.

tag: background strain

tag: genotype/variation

value: LSL-KrasG12D mice


title: TNP2 KO DAY12 LGLUT biological replicate 3, technical replicate 1

description: RNA-Seq


title: 3D-Plasma-V1-267

description:
267
3D-Plasma-V1-267


title: 3D-Plasma-V1-264

description:
264
3D-Plasma-V1-264


title: 3D-Plasma-V1-263

description:
263
3D-Plasma-V1-263


title: 3D-Plasma-V1-266

description:
266
3D-Plasma-V1-266


title: 3D-Plasma-V1-265

description:
265
3D-Plasma-V1-265


title: 3D-Plasma-V1-268

description:
268
3D-Plasma-V1-268


title: TNP2 KO DAY12 LGLUT biological replicate 2, technical replicate 3

description: RNA-Seq


title: 3D-Plasma-V1-262

description:
262
3D-Plasma-V1-262


title: 3D-Plasma-V1-261

description:
261
3D-Plasma-V1-261


title: 3D-Plasma-V1-260

description:
260
3D-Plasma-V1-260


title: 3D-Plasma-V1-259

description:
259
3D-Plasma-V1-259


title: TNP2 KO DAY12 LGLUT biological replicate 2, technical replicate 1

description: RNA-Seq


title: TNP2 KO DAY12 LGLUT biological replicate 2, technical replicate 2

description: RNA-Seq


title: Day28,Dysf,Replicate2

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
PolyA selected RNA was sequenced by Genewiz (Azenta) using Illumina HiSeq 2x150 bp sequencing, single index package.
Partek Flow was used for RNA-seq analysis. In brief, pre-alignment QC/QA analysis was performed on the FASTQ files, followed by read alignment on human whole genome hg38 using STAR.
The aligned reads were quantified to the hg38 RefSeq Transcripts 98 using the Quantify to annotation model on Partek and gene counts were filtered (exclude features where maximum < 50.0).
Filtered gene counts were normalized using median ratio for DESeq2 analysis to measure differential gene expression among different populations of CD8+ T cells.
Differentially expressed genes (DEGs) were identified for genes showing fold change ≥ 2 and p-value <0.05.
Assembly: hg38
Supplementary files format and content: normalized using median ratio for DESeq2 analysis

source_name: Cord blood

growth_protocol: Human cord blood mononuclear cells (CBMCs) were isolated and CD8+ T cells were expanded in vitro by TCR stimulation (soluble anti-CD3) from day 0-7 (acute) or day 0-28 (chronic).

extract_protocol:
RNA was isolated using PicoPure RNA Isolation Kit (Applied Biosystems) from frozen cell pellets of human CD8+ T cells that were FACS-purified from days 0 (naïve), 7, and 28. following the kit protocol.
Libraries were prepared for Illumina HiSeq by Genewiz (Azenta), with PolyA selection.

treatment_protocol: CD8+ T cells under chronic stimulation were treated with TGFB1 (5 ng/ml) starting from day 7. Reprogrammed treatments were added to TGFB1 treated cells starting from day 14 as follows: TGFR1i (Reprog.I), TGFBR1i+BMPa (Reprog.II), TGFBR1i+BMPa+Vitamin C (starting from day 21) (Reprog.III).

value: Cord blood

tag: cell type


title: TNP2 KO DAY12 LGLUT biological replicate 1, technical replicate 1

description: RNA-Seq


title: 3D-Plasma-V1-258

description:
258
3D-Plasma-V1-258


title: Day0,Naïve,Replicate1

value: No treatment


title: 3D-Plasma-V1-252

description:
252
3D-Plasma-V1-252


title: 3D-Plasma-V1-251

description:
251
3D-Plasma-V1-251


title: 3D-Plasma-V1-254

description:
254
3D-Plasma-V1-254


title: 3D-Plasma-V1-256

description:
256
3D-Plasma-V1-256


title: 3D-Plasma-V1-257

description:
257
3D-Plasma-V1-257


title: Day28,ReprogI,Replicate2


title: SUZ12 KO DAY12 LGLUT biological replicate 3, technical replicate 3

description: RNA-Seq

value: SUZ12 KO


title: Day28,Dysf,Replicate1


title: 3D-Plasma-V1-249

description:
249
3D-Plasma-V1-249


title: KrasC57_replicate2


title: KrasC57_replicate1


title: 3D-Plasma-V1-255

description:
255
3D-Plasma-V1-255


title: 3D-Plasma-V1-248

description:
248
3D-Plasma-V1-248


title: 3D-Plasma-V1-250

description:
250
3D-Plasma-V1-250


title: Day28,ReprogI,Replicate1


title: Day0,Naïve,Replicate2


title: 3D-Plasma-V1-253

description:
253
3D-Plasma-V1-253

tag: pregnancy status_2

value: Other pregnancy complications


title: TNP2 KO DAY12 LGLUT biological replicate 1, technical replicate 2

description: RNA-Seq


title: TNP2 KO DAY12 LGLUT biological replicate 1, technical replicate 3

description: RNA-Seq


title: Day28,ReprogII,Replicate2


title: 3D-Plasma-V1-246

description:
246
3D-Plasma-V1-246


title: SUZ12 KO DAY12 LGLUT biological replicate 3, technical replicate 1

description: RNA-Seq


title: 3D-Plasma-V1-244

description:
244
3D-Plasma-V1-244


title: SUZ12 KO DAY12 LGLUT biological replicate 2, technical replicate 3

description: RNA-Seq


title: SUZ12 KO DAY12 LGLUT biological replicate 3, technical replicate 2

description: RNA-Seq


title: 3D-Plasma-V1-245

description:
245
3D-Plasma-V1-245


title: SUZ12 KO DAY12 LGLUT biological replicate 2, technical replicate 2

description: RNA-Seq


title: 3D-Plasma-V1-243

description:
243
3D-Plasma-V1-243


title: Day28,ReprogIII,Replicate2


title: SUZ12 KO DAY12 LGLUT biological replicate 2, technical replicate 1

description: RNA-Seq


title: 3D-Plasma-V1-237

description:
237
3D-Plasma-V1-237


title: 3D-Plasma-V1-238

description:
238
3D-Plasma-V1-238


title: SUZ12 KO DAY12 LGLUT biological replicate 1, technical replicate 3

description: RNA-Seq


title: Day28,ReprogII,Replicate1


title: SUZ12 KO DAY12 LGLUT biological replicate 1, technical replicate 2

description: RNA-Seq


title: 3D-Plasma-V1-241

description:
241
3D-Plasma-V1-241


title: Day28,ChronicTCR,Replicate2

value: Chronic TCR


title: Day28,ChronicTCR,Replicate1


title: 3D-Plasma-V1-236

description:
236
3D-Plasma-V1-236


title: Day28,ReprogIII,Replicate1


title: 3D-Plasma-V1-130_2

description:
130_2
3D-Plasma-V1-130_2
technical replicate


title: Day28,AcuteTCR,Replicate2

value: Acute TCR


title: 3D-Plasma-V1-247

description:
247
3D-Plasma-V1-247


title: 3D-Plasma-V1-242

description:
242
3D-Plasma-V1-242


title: 3D-Plasma-V1-239

description:
239
3D-Plasma-V1-239


title: 3D-Plasma-V1-128_2

description:
128_2
3D-Plasma-V1-128_2
technical replicate


title: SUZ12 KO DAY12 LGLUT biological replicate 1, technical replicate 1

description: RNA-Seq


title: 3D-Plasma-V1-127_2

description:
127_2
3D-Plasma-V1-127_2
technical replicate


title: 3D-Plasma-V1-126_2

description:
126_2
3D-Plasma-V1-126_2
technical replicate


title: SMARCD1 KO DAY12 LGLUT biological replicate 3, technical replicate 3

description: RNA-Seq

value: SMARCD1 KO


title: 3D-Plasma-V1-240

description:
240
3D-Plasma-V1-240


title: 3D-Plasma-V1-122_2

description:
122_2
3D-Plasma-V1-122_2
technical replicate


title: 3D-Plasma-V1-121_2

description:
121_2
3D-Plasma-V1-121_2
technical replicate


title: 3D-Plasma-V1-120_2

description:
120_2
3D-Plasma-V1-120_2
technical replicate


title: SMARCD1 KO DAY12 LGLUT biological replicate 3, technical replicate 2

description: RNA-Seq


title: 3D-Plasma-V1-118_2

description:
118_2
3D-Plasma-V1-118_2
technical replicate


title: 3D-Plasma-V1-117_2

description:
117_2
3D-Plasma-V1-117_2
technical replicate


title: Hippocampus, temporal lobe epielpsy, H16.06.009

city: Seattle

first: Anatoly

last: Buchin

state: Washington

address: 1616 Eastlake Ave E

institute: Cajal Neuroscience Inc

description:
DG_RNAseq_data_processed.csv.gz
DG_RNAseq_data_processed_annotations.csv.gz
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
NW_TX0011-5

data_processing:
Alignment of reads was performed by 10x Cell Ranger v3
Gene expression was quantified using the default 10x Cell Ranger v3 pipeline
Introns were annotated as “mRNA,” and intronic reads were included in expression quantification.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include UMI counts for each sample

source_name: Brain tissue, Hippocampus

extract_protocol:
Single nucleus suspensions were frozen in a solution of 1X PBS, 1% BSA, 10% DMSO, and 0.5% RNAsin Plus RNase inhibitor (Promega, N2611) and stored at -80°C. At the time of use, frozen nuclei were thawed at 37°C and processed for loading on the 10x Chromium instrument as described (dx.doi.org/10.17504/protocols.io.nx3dfqn)
Samples were processed using the 10x Chromium Single Cell 3’ Reagent Kit v3.

value: F

tag: age

value: Brain tissue, Hippocampus

value: Neuronal and glial cells

value: WT

value: no treatment

tag: subject status

value: epilepsy patient


title: Hippocampus, temporal lobe epilepsy, H16.06.010

description:
DG_RNAseq_data_processed.csv.gz
DG_RNAseq_data_processed_annotations.csv.gz
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
NW_TX0014-1

value: M


title: Hippocampus, temporal lobe epilepsy, H16.06.008

description:
DG_RNAseq_data_processed.csv.gz
DG_RNAseq_data_processed_annotations.csv.gz
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
NW_TX0012-1


title: SMARCD1 KO DAY12 LGLUT biological replicate 2, technical replicate 2

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: DAY 12


title: SMARCD1 KO DAY12 LGLUT biological replicate 3, technical replicate 1

description: RNA-Seq

value: L-GLUT


title: Hippocampus, temporal lobe epilepsy, H17.06.015

description:
DG_RNAseq_data_processed.csv.gz
DG_RNAseq_data_processed_annotations.csv.gz
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
NW_TX0014-3


title: SMARCD1 KO DAY12 LGLUT biological replicate 2, technical replicate 3

description: RNA-Seq


title: SMARCD1 KO DAY12 LGLUT biological replicate 2, technical replicate 1

description: RNA-Seq


title: Proband

city: Barcelona

first: Agustín

middle: Sánchez

last: Belmonte

state: Barcelona

address: Nazaret 115 -117

department: Systems Oncology Program

country: Spain

institute: Vall d ́Hebron Institute of Oncology (VHIO)

data_processing:
"cellranger count" did the alignment to the GRCh38/hg38 transcriptome, generating metrics, files and matrices required for secondary analysis.
Data were processed with cellranger-arc-2.0.0, Loupe Browser 6, and scanpy 1.7.2
Genome_build: hg19
Supplementary_files_format_and_content: raw, feature and matrix files

source_name: Blood sample

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples by centrifugation on a Ficoll cushion 30 min at 1800rpm at RT, and washed several times in PBS.

extract_protocol:
PBMCs were filtered with 40 μm Flowmi Cell Strainer and counted. Viability was assessed (>90%) and cells were subjected to single cell isolation.
Cell samples were loaded onto a 10x Chromium Single Cell Controller chip B (10x Genomics) for a targeted recovery of ~10,000 cells per condition, as described in the manufacturer's protocol (Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, PN-1000075). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended by the manufacturer.

treatment_protocol: Prior extraction, Fc receptors were blocked with Fcr Blocking Reagent (Miltenyi Biotec, 130-059-901) and dead cells were removed with Dead Cell Removal kit (Miltenyi Biotec, 130-090-101).

value: Peripheral blood mononuclear cells

value: PBMCs with MAD1L1 gene mutations in homocigosis ( c.196C>T; p.Q66*) (c.1882G>T; p.E628*)

tag: clone/replicate

value: female patient


title: SMARCD1 KO DAY12 LGLUT biological replicate 1, technical replicate 3

description: RNA-Seq


title: Day28,AcuteTCR,Replicate1

value: Cord blood


title: Patient 6 (P6_INF)

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

data_processing:
Raw fastqs were processed using the standard CellRanger "count" pipelile
Processed files from CellRanger were co-processed using Seuratand Monocle in R
Assembly: GrCH38
Supplementary files format and content: TSV and MTX files from CellRanger

source_name: with cryptococcus

extract_protocol:
Human BAL cells were enriched for phagocytic populations (lineage removal using negative selection of CD3, CD19, CD20, and CD56).
Libraries were made of pairs of controls and co-incubated sets using the 10X Chromium Controller and the Chromium Next Gem Single Cell 3’ GEM, Library, and Gel Bead Kit v3.1 (10X Genomics Inc., Pleasanton, CA)

treatment_protocol: Enriched BAL cells were incubated with C. neoformans strain H99 at a 1:1 ratio (1 × 10^6 cells each) with 1 μg/ml anti-GXM mAb F12D2 at 37°C, 5% CO2 for 2h in 100 μl of R10 media. Controls were phagocytic populations from the same human samples in media alone incubated under the same conditions. Samples were then washed once and then resuspended with PBS + 2% BSA.

value: Human BAL cells

value: 2h incubation with C. neoformans


title: Patient 3 (P3_INF)


title: Patient 4 (P4)

source_name: Naïve

value: 2h incubation


title: Patient 3 (P3)


title: Patient 6 (P6)


title: Patient 1 (P1_INF)


title: Patient 4 (P4_INF)


title: Father

value: PBMCs with MAD1L1 gene mutation in heterocygosis (c.1882G>T; p.E628*)

value: male progenitor


title: Patient 1 (P1)


title: SMARCD1 KO DAY12 LGLUT biological replicate 1, technical replicate 2

description: RNA-Seq

value: SMARCD1 KO


title: RICU220106-1_002A (PBMC)

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

data_processing:
sequence reads were mapped to the human reference genome GRCh38 by HISAT2 (version 2.2.0)
Read counts were calculated by featureCounts (Version 2.0.0)
Supplementary files format and content: GRCh38
Supplementary files format and content: tab delimited text file include raw read counts for each sample

source_name: PBMC

extract_protocol:
PAXgene Blood miRNA Kit
Universal Plus mRNA-Seq library preparation kit with NuQuant

value: PBMC

tag: time

tag: condition

value: Non-Responder

tag: patient


title: 3D-Plasma-V1-119_2

description:
119_2
3D-Plasma-V1-119_2
technical replicate

tag: tissue

value: Plasma

value: female

value: Normal


title: Control 2

value: wild-ype PBMCs isolated from blood sample

value: female control


title: RICU211202-1_002A (PBMC)


title: Control 1

value: Peripheral blood mononuclear cells

value: male control


title: RICU210527-1_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 3, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: HIST1H1B KO

value: DAY 12

value: L-GLUT


title: RICU210517-1_002A (PBMC)


title: SMARCD1 KO DAY12 LGLUT biological replicate 1, technical replicate 1

description: RNA-Seq


title: RICU210504-1_002A (PBMC)


title: RICU211216-1_002A (PBMC)


title: Mother

value: PBMCs with MAD1L1 gene mutation in heterocygosis ( c.196C>T; p.Q66*)

value: female progenitor


title: RICU210506-2_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 3, technical replicate 2

description: RNA-Seq


title: RICU201215-1_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 3, technical replicate 1

description: RNA-Seq


title: RICU201123-2_002A (PBMC)


title: RICU201013-1_002A (PBMC)


title: RICU200917-1_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 2, technical replicate 2

description: RNA-Seq


title: HIST1H1B KO DAY12 LGLUT biological replicate 2, technical replicate 3

description: RNA-Seq


title: HIST1H1B KO DAY12 LGLUT biological replicate 2, technical replicate 1

description: RNA-Seq


title: RICU200130-2_002A (PBMC)


title: RICU200122-1_002A (PBMC)


title: RICU200120-1_002A (PBMC)


title: RICU220119-2_002A (PBMC)

value: Responder


title: RICU211201-2_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 1, technical replicate 3

description: RNA-Seq


title: RICU211104-1_002A (PBMC)


title: RICU211125-2_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 1, technical replicate 2

description: RNA-Seq


title: RICU211019-1_002A (PBMC)


title: HIST1H1B KO DAY12 LGLUT biological replicate 1, technical replicate 1

description: RNA-Seq


title: RICU210930-1_002A (PBMC)


title: RICU210615-2_002A (PBMC)


title: RICU210610-2_002A (PBMC)


title: EZH2 KO DAY12 LGLUT biological replicate 3, technical replicate 3

description: RNA-Seq

value: EZH2 KO


title: RICU210519-1_002A (PBMC)

value: PBMC


title: EZH2 KO DAY12 LGLUT biological replicate 3, technical replicate 2

description: RNA-Seq


title: RICU210406-1_002A (PBMC)


title: RICU210203-1_002A (PBMC)


title: EZH2 KO DAY12 LGLUT biological replicate 3, technical replicate 1

description: RNA-Seq


title: RICU210325-1_002A (PBMC)


title: RICU210512-2_002A (PBMC)


title: Sample 106 (Ion-N-2H-1)

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: ON

address: 251 Sir Frederick Banting Driveway

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to 8x60K Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (Agilent Technologies, Inc., Santa Clara, USA) slides in a hybridization chamber for 17 h at 65°C rotating at 10 rpm.

scan_protocol: Microarray slides were washed according to manufacturer’s protocol and scanned on an Agilent G2505B scanner. Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Immortalized Lung Epithelial cells (FE1)

label_protocol: In brief, 200 ng of total RNA per cell pellet sample or Universal Mouse Reference RNA (UMRR; Agilent Technologies) were used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: FE1 immortalized alveolar lung epithelial cells were cultured as described in Decan et al 2015, in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture F-12HAM (DMEM F12HAM) supplemented with 2 % fetal bovine serum (FBS), 1 ng/mL epidermal growth factor (EGF), 100 U/mL penicillin G, and 100 µg/mL streptomycin and maintained at 37°C, with 5 % CO2.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Decan et al., 2015. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol (with a 2 min incubation in water prior to elution). Total RNA concentration and purity was determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥5 were used for subsequent microarray experiments.

treatment_protocol: Cells were plated at a cell density of 130 000 cells/well in 6-well plates. Following overnight incubation, cells were exposed to 1.8 mL of 1, 5, 10, and 25 µg/mL CuO NPs, CuO MPs or 7 µg/mL CuCl2. For all exposures, blank media exposed cells served as negative controls. For CuCl2 experiments, cells treated with 5 µg/mL NaCl were also used as additional control to rule out the possible contribution of Cl ions to the observed cellular toxicity in CuCl2 exposures. Following 2, 24, and 48 h of exposure, cell supernatant was harvested, cells were washed with PBS, trypsinized and suspended in fresh cell culture media. An aliquot of cell suspension was used for Trypan Blue dye exclusion staining and the rest of the cells were pelleted by centrifugation (8000 rpm, 10 minutes, 4°C) and frozen at -80°C for microarray analysis. Three biological replicates were used for each condition.

tag: strain

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: Sodium Chloride

tag: time point

value: 2 Hour

tag: dose

value: 5 ug/mL

tag: biological replicate

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: RICU210126-1_002A (PBMC)


title: EZH2 KO DAY12 LGLUT biological replicate 2, technical replicate 3

description: RNA-Seq

tag: cell line

tag: genotype

tag: timepoint


title: RICU210106-2_002A (PBMC)


title: Sample 104 (Ion-L-24H-1)

tag: treatment

value: Copper Chloride Dihydrate

value: 24 Hour

value: 7 ug/mL


title: RICU201208-2_002A (PBMC)


title: Sample 107 (Ion-L-2H-2)


title: EZH2 KO DAY12 LGLUT biological replicate 2, technical replicate 2

description: RNA-Seq

value: Melanoma cells MEXF 2090


title: RICU201201-1_002A (PBMC)


title: EZH2 KO DAY12 LGLUT biological replicate 2, technical replicate 1

description: RNA-Seq

value: DAY 12


title: Sample 101 (Ion-L-48H-1)

value: 48 Hour


title: Sample 99 (Ion-N-48H-1)


title: RICU201102-1_002A (PBMC)


title: Sample 102 (M-2H-1)

value: Blank Media

value: 0 ug/mL


title: Sample 103 (M-24H-1)


title: Sample 100 (Ion-N-24H-1)


title: Sample 97 (M-48H-2)


title: EZH2 KO DAY12 LGLUT biological replicate 1, technical replicate 3

description: RNA-Seq

value: L-GLUT


title: RICU200909-1_002A (PBMC)

value: Responder


title: RICU191230-1_002A (PBMC)

value: PBMC


title: EZH2 KO DAY12 LGLUT biological replicate 1, technical replicate 2

description: RNA-Seq

value: EZH2 KO


title: Sample 95 (Ion-L-24H-2)

value: MutaMouse

value: Immortalized Lung Epithelial cells


title: RICU200908-3_002A (PBMC)


title: RICU190903-1_002A (PBMC)


title: RICU201125-1_002A (PBMC)


title: RICU211230-1_001A (PBMC)

value: Non-Responder


title: RICU211125-1_001A (PBMC)


title: RICU211208-1_001A (PBMC)


title: EED KO DAY12 LGLUT biological replicate 3, technical replicate 3

description: RNA-Seq

value: EED KO


title: Sample 98 (Ion-L-2H-1)

value: 2 Hour

value: 11 mouse cell lines


title: Sample 105 (M-48H-1)


title: RICU210520-1_001A (PBMC)


title: Sample 94 (Ion-N-24H-2)

value: Sodium Chloride

value: 24 Hour

value: 5 ug/mL


title: Sample 96 (Ion-N-48H-2)


title: RICU210510-1_001A (PBMC)


title: EED KO DAY12 LGLUT biological replicate 3, technical replicate 2

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: DAY 12


title: Sample 93 (Ion-L-48H-2)

value: Copper Chloride Dihydrate

value: 48 Hour

value: 7 ug/mL


title: Sample 91 (M-2H-2)

value: Blank Media

value: 0 ug/mL


title: Sample 92 (M-24H-2)


title: RICU210429-2_001A (PBMC)

value: PBMC


title: RICU210429-1_001A (PBMC)


title: RICU201116-1_001A (PBMC)


title: RICU200910-1_001A (PBMC)


title: RICU201006-1_001A (PBMC)


title: RICU200116-1_001A (PBMC)


title: EED KO DAY12 LGLUT biological replicate 2, technical replicate 3

description: RNA-Seq

value: L-GLUT


title: EED KO DAY12 LGLUT biological replicate 3, technical replicate 1

description: RNA-Seq


title: EED KO DAY12 LGLUT biological replicate 2, technical replicate 1

description: RNA-Seq


title: EZH2 KO DAY12 LGLUT biological replicate 1, technical replicate 1

description: RNA-Seq

value: EZH2 KO


title: Cox10_deficient lung_rep 2

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

data_processing:
remove adaptor with 'trim_galore'
align the reading to genome with 'Hisat2'
sort the SAM file and convert it to BAM file
create table counts with 'featurecounts'
generate DEG table with DeSeq2 in R
Assembly: mm10
Supplementary files format and content: csv file include log2 fold change and p value

source_name: lung

extract_protocol:
Embronic lungs were collected, snap freezed in liquid nitrogen, and RNAs were extracted with the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: Embryonic lung

tag: developmental stage

value: Cox10f/f; ShhCre/+

tag: state

value: mutant sample


title: RICU201208-1_001A (PBMC)

value: Non-Responder


title: RICU200121-1_001A (PBMC)


title: Cox10_deficient lung_rep 3


title: EED KO DAY12 LGLUT biological replicate 1, technical replicate 3

description: RNA-Seq

value: EED KO


title: EED KO DAY12 LGLUT biological replicate 2, technical replicate 2

description: RNA-Seq


title: RICU200113-1_001A (PBMC)


title: EED KO DAY12 LGLUT biological replicate 1, technical replicate 2

description: RNA-Seq


title: RICU220114-1_001A (PBMC)

value: Responder


title: Cox10_deficient lung_rep 1


title: Cox10_control lung_rep 3

value: Cox10f/+; ShhCre/+

value: control sample


title: Sample 87 (Ion-N-2H-2)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: Sodium Chloride

value: 2 Hour

value: 5 ug/mL

value: 11 mouse cell lines


title: Sample 88 (Ion-L-48H-3)

value: Copper Chloride Dihydrate

value: 48 Hour

value: 7 ug/mL


title: Sample 86 (Ion-N-24H-3)

value: 24 Hour


title: Sample 85 (Ion-L-24H-3)


title: Sample 89 (Ion-N-48H-3)


title: Cox10_control lung_rep 2

value: lung

value: Embryonic lung


title: RICU211126-1_001A (PBMC)

value: PBMC


title: TNP2 KO DAY0 NT biological replicate 3, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: TNP2 KO

value: DAY 0

value: NT


title: Cox10_control lung_rep 1

value: Cox10f/+; ShhCre/+

value: control sample


title: RICU211117-1_001A (PBMC)

value: Responder


title: RICU211028-1_001A (PBMC)


title: Tfam_deficient lung_rep 3

value: Tfamf/f; ShhCre/+

value: mutant sample


title: Sample 84 (Ion-L-2H-3)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: 2 Hour

value: 11 mouse cell lines


title: TNP2 KO DAY0 NT biological replicate 3, technical replicate 1

description: RNA-Seq


title: RICU211012-1_001A (PBMC)


title: Tfam_deficient lung_rep 2


title: TNP2 KO DAY0 NT biological replicate 2, technical replicate 3

description: RNA-Seq


title: Sample 83 (Ion-N-2H-3)

value: Sodium Chloride

value: 5 ug/mL


title: RICU210924-1_001A (PBMC)


title: Tfam_deficient lung_rep 1

value: lung

value: Embryonic lung


title: TNP2 KO DAY0 NT biological replicate 2, technical replicate 2

description: RNA-Seq

value: Melanoma cells MEXF 2090


title: Sample 81 (M-24H-3)

value: Blank Media

value: 24 Hour

value: 0 ug/mL


title: EED KO DAY12 LGLUT biological replicate 1, technical replicate 1

description: RNA-Seq

value: EED KO

value: DAY 12

value: L-GLUT


title: TNP2 KO DAY0 NT biological replicate 3, technical replicate 2

description: RNA-Seq

value: TNP2 KO

value: DAY 0

value: NT


title: RICU210608-1_001A (PBMC)

value: PBMC

value: Responder


title: Tfam_control lung_rep 3

value: Tfamf/+; ShhCre/+

value: control sample


title: TNP2 KO DAY0 NT biological replicate 2, technical replicate 1

description: RNA-Seq


title: Tfam_control lung_rep 2


title: Tfam_control lung_rep 1


title: RICU210512-1_001A (PBMC)


title: TNP2 KO DAY0 NT biological replicate 1, technical replicate 2

description: RNA-Seq


title: RICU210604-2_001A (PBMC)


title: Rptor_deficient lung_rep 3

value: Rptorf/f; ShhCre/+

value: mutant sample


title: TNP2 KO DAY0 NT biological replicate 1, technical replicate 1

description: RNA-Seq


title: SUZ12 KO DAY0 NT biological replicate 3, technical replicate 3

description: RNA-Seq

value: SUZ12 KO


title: RICU210319-1_001A (PBMC)


title: Sample 82 (M-2H-3)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: 2 Hour

value: 11 mouse cell lines


title: Rptor_deficient lung_rep 1

value: lung

value: Embryonic lung


title: RICU210128-1_001A (PBMC)


title: TNP2 KO DAY0 NT biological replicate 1, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090


title: SUZ12 KO DAY0 NT biological replicate 3, technical replicate 2

description: RNA-Seq


title: RICU210505-1_001A (PBMC)


title: SUZ12 KO DAY0 NT biological replicate 3, technical replicate 1

description: RNA-Seq


title: SUZ12 KO DAY0 NT biological replicate 2, technical replicate 3

description: RNA-Seq


title: Rptor_control lung_rep 2

value: Rptorf/+; ShhCre/+


title: RICU201230-2_001A (PBMC)


title: Rptor_deficient lung_rep 2


title: Sample 80 (MP-10-48H-3)

value: CuO Microparticle

value: 48 Hour

value: 10 ug/mL


title: RICU210330-4_001A (PBMC)

value: PBMC

value: Responder


title: Sample 78 (MP-25-48H-3)

value: 25 ug/mL


title: RICU210121-1_001A (PBMC)


title: Sample 77 (M-48H-4)

value: Blank Media

value: 0 ug/mL


title: Sample 76 (NP-10-48H-2)

value: CuO Nanoparticle


title: Sample 73 (MP-1-48H-3)

value: MutaMouse

value: 1 ug/mL


title: Sample 74 (NP-1-24H-4)

value: Immortalized Lung Epithelial cells

value: 24 Hour


title: Sample 79 (NP-1-48H-3)

value: 11 mouse cell lines


title: SUZ12 KO DAY0 NT biological replicate 2, technical replicate 2

description: RNA-Seq

value: SUZ12 KO

value: DAY 0

value: NT


title: Sample 72 (MP-5-48H-2)

value: CuO Microparticle

value: 5 ug/mL


title: Sample 70 (M-48H-3)

value: 48 Hour


title: Rptor_control lung_rep 3

value: lung

value: Embryonic lung

value: Rptorf/+; ShhCre/+

value: control sample


title: SUZ12 KO DAY0 NT biological replicate 2, technical replicate 1

description: RNA-Seq

value: Melanoma cells MEXF 2090


title: RICU201201-2_001A (PBMC)

value: PBMC

value: Responder


title: Raptor-ShhCre Mutant rep3

description: Mutant lung

data_processing:
remove adaptor with 'trim_galore'
align the reading to genome with 'Hisat2'
sort the SAM file and convert it to BAM file
create table counts with 'featurecounts'
generate DEG table with DeSeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: csv file

source_name: Embryonic lung

value: Raptorf/f; ShhCre/+

value: Mouse embryonic lung

tag: Stage


title: RICU201124-1_001A (PBMC)


title: Raptor-ShhCre Mutant rep2

description: Mutant lung


title: SUZ12 KO DAY0 NT biological replicate 1, technical replicate 3

description: RNA-Seq


title: RICU201118-1_001A (PBMC)


title: Sample 71 (MP-25-48H-2)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: 25 ug/mL


title: RICU201026-1_001A (PBMC)


title: Rptor_control lung_rep 1


title: Raptor-ShhCre Mutant rep1

description: Mutant lung


title: Raptor-ShhCre Control rep3

description: Control lung

value: Raptorf/+; ShhCre/+


title: RICU200902-1_001A (PBMC)


title: SUZ12 KO DAY0 NT biological replicate 1, technical replicate 1

description: RNA-Seq

value: SUZ12 KO

value: DAY 0

value: NT


title: Sample 68 (NP-10-24H-3)

value: CuO Nanoparticle

value: 24 Hour

value: 10 ug/mL

value: 11 mouse cell lines


title: Raptor-ShhCre Control rep2

description: Control lung


title: SMARCD1 KO DAY0 NT biological replicate 3, technical replicate 3

description: RNA-Seq

value: SMARCD1 KO


title: SMARCD1 KO DAY0 NT biological replicate 3, technical replicate 2

description: RNA-Seq

value: Melanoma cells MEXF 2090


title: SUZ12 KO DAY0 NT biological replicate 1, technical replicate 2

description: RNA-Seq


title: Raptor-ShhCre Control rep1

description: Control lung


title: RICU190827-1_001A (PBMC)

value: PBMC


title: RICU191223-1_001A (PBMC)

value: Responder


title: Sample 75 (NP-5-48H-2)

value: 48 Hour

value: 5 ug/mL


title: Sample 66 (MP-5-24H-2)

value: MutaMouse

value: CuO Microparticle


title: ISS2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

data_processing:
The instrument model is BGISEQ-500
The original sequencing data contained reads with low quality, joint contamination and high unknown base N content. These reads needed to be removed before data analysis to ensure the reliability of the results
After clean reads were obtained, clean reads were aligned to the reference genome sequence using HISAT
Clean reads were aligned to the reference gene sequence using Bowtie2 to obtain alignment results.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol:
Total RNA from spleen
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: Oral dosing

value: spleen

tag: agent

value: Busulfan


title: ISS3


title: SMARCD1 KO DAY0 NT biological replicate 3, technical replicate 1

description: RNA-Seq


title: SMARCD1 KO DAY0 NT biological replicate 2, technical replicate 2

description: RNA-Seq


title: ISS1


title: SMARCD1 KO DAY0 NT biological replicate 2, technical replicate 3

description: RNA-Seq


title: SMARCD1 KO DAY0 NT biological replicate 2, technical replicate 1

description: RNA-Seq


title: ISFC3

value: Busulfan+Con-FMT


title: Sample 64 (NP-5-24H-3)

value: Immortalized Lung Epithelial cells


title: RICU200901-1_001A (PBMC)


title: ISFC2


title: Sample 69 (MP-10-48H-2)


title: SMARCD1 KO DAY0 NT biological replicate 1, technical replicate 3

description: RNA-Seq

value: DAY 0

value: NT


title: ISFC1


title: SMARCD1 KO DAY0 NT biological replicate 1, technical replicate 2

description: RNA-Seq


title: Sample 67 (NP-25-24H-3)

value: CuO Nanoparticle

value: 24 Hour

value: 25 ug/mL


title: Sample 65 (M-24H-4)

value: Blank Media

value: 0 ug/mL

value: 11 mouse cell lines


title: anti-IgG antibody pulldown from PNT2 cells experiment A1

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.5
narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: narrowPeak were normalized with control IgG pulldown

molecule: genomic DNA

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell type

value: Prostate epithelium

tag: chip antibody


title: BAL sample patient 18, covid pos

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: filtered_feature_bc_matrix_sampleName.h5 = count matrix of genes and antibodies; metaData_allBAL-umap.csv = metadata of umap in fig 2A; metaData_zoomMF-umap.csv = metadata of umap in fig 1B; metaData_zoomMF-diffMap.csv = metadata of diffusion map in fig1F; usedABs.csv = list of ABs used for TotalVI analysis

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline (v4.0) and aligning to the GRCh38 genome build. For more detail, see Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files:h5 files

source_name: Lung

extract_protocol:
Extraction method explained in Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
Library construction explained in Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
All samples are CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Lung

value: Bronchoalveolar lavage

tag: covid status

value: positive

tag: sample type

value: citeSeq


title: anti-CIC antibody pulldown from PNT2 cells experiment A1

value: CIC (Thermo #PA146018)


title: BAL sample patient 19, covid pos

tag: tissue


title: Sample 62 (MP-1-24H-3)

tag: strain

value: MutaMouse

value: CuO Microparticle

value: 1 ug/mL


title: Sample 60 (NP-5-24H-2)

value: Immortalized Lung Epithelial cells

tag: time point

value: 5 ug/mL


title: Sample 58 (NP-10-24H-2)

value: CuO Nanoparticle

tag: dose

value: 10 ug/mL


title: Sample 59 (MP-5-48H-3)

value: 48 Hour

tag: biological replicate


title: ISFA3

value: spleen


title: Sample 63 (MP-10-24H-2)

tag: cell line

value: 24 Hour


title: BAL sample patient 17, covid neg

value: negative


title: ISFA2


title: SMARCD1 KO DAY0 NT biological replicate 1, technical replicate 1

description: RNA-Seq

value: Melanoma cells MEXF 2090

tag: genotype

value: SMARCD1 KO

value: DAY 0

value: NT


title: HIST1H1B KO DAY0 NT biological replicate 3, technical replicate 3

description: RNA-Seq

value: HIST1H1B KO

tag: timepoint


title: BAL sample patient 16, covid pos

value: Lung

value: Bronchoalveolar lavage

value: positive

value: citeSeq


title: Sample 90 (M-48H-3)

value: MutaMouse

value: Immortalized Lung Epithelial cells

tag: treatment

value: Blank Media

value: 0 ug/mL

value: 11 mouse cell lines


title: Sample 61 (NP-1-24H-3)

value: CuO Nanoparticle

value: 1 ug/mL


title: HIST1H1B KO DAY0 NT biological replicate 3, technical replicate 2

description: RNA-Seq


title: Sample 57 (MP-1-48H-4)

value: CuO Microparticle

value: 48 Hour


title: BAL sample patient 15, covid neg

value: negative


title: ISC3

value: spleen

value: Blank


title: ISFA1


title: HIST1H1B KO DAY0 NT biological replicate 2, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: HIST1H1B KO

value: DAY 0

value: NT


title: BAL sample patient 13, covid neg

value: Lung

value: Bronchoalveolar lavage

value: citeSeq


title: ISC2


title: HIST1H1B KO DAY0 NT biological replicate 2, technical replicate 2

description: RNA-Seq


title: Sample 56 (NP-25-24H-2)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: 24 Hour

value: 25 ug/mL


title: HIST1H1B KO DAY0 NT biological replicate 2, technical replicate 1

description: RNA-Seq


title: Sample 54 (NP-10-24H-1)

value: CuO Nanoparticle

value: 10 ug/mL

value: 11 mouse cell lines


title: BAL sample patient 11, covid neg, but bacterial infection

value: negative, bacterial infection


title: Sample 55 (M-24H-3)

value: Blank Media

value: 0 ug/mL


title: PF70_2

city: Armilla

first: Antonio

middle: M

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

institute: CSIC

description:
NGS041-20-8_S8
processed data file: pfRBP33.tsv

data_processing:
TruSeq RNA Single Indexes (set A&B)
The resulting 75-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using the ‘align’ program of the Subread package with option unique=TRUE
Reads assignment to mRNAs and counting were carried out using the ‘featureCounts’ program of the Subread package (options -t gene -B -C)
Replicates were compared using the edgeR package
Genome_build: 427 2018 version 4.9
Supplementary_files_format_and_content: edgeR output, tab-delimited text file

organism: Trypanosoma brucei brucei

source_name: Cultured trypanosomes

growth_protocol: Grown in HMI-9 medium at 37ºC (bloodstream) or SDM-79 medium at 27ºC (procyclic)

extract_protocol:
Cells were centrifuged and RNA was extracted using the RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA® Illumina

treatment_protocol: ± 1 µg/ml tetracycline for RNAi induction

value: Procyclic forms, 449 strain

value: trasfected with pGR70 (RNAi plasmid)

tag: sample group

value: RNAi induced


title: BAL sample patient 14, covid pos

value: positive


title: HIST1H1B KO DAY0 NT biological replicate 1, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: HIST1H1B KO

value: DAY 0

value: NT


title: PF70_1

description:
NGS041-20-7
processed data file: pfRBP33.tsv


title: BAL sample patient 9, healthy control

value: Lung

value: Bronchoalveolar lavage

value: negative, healthy

value: citeSeq


title: Sample 53 (MP-25-24H-3)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: CuO Microparticle

value: 24 Hour

value: 25 ug/mL


title: HIST1H1B KO DAY0 NT biological replicate 1, technical replicate 2

description: RNA-Seq


title: Sample 50 (MP-5-2H-2)

value: 2 Hour

value: 5 ug/mL

value: 11 mouse cell lines


title: 449_3

description:
NGS041-20-3_S3
processed data file: pfRBP33.tsv

value: Procyclic forms, 449 strain

value: untransfected

value: control


title: HIST1H1B KO DAY0 NT biological replicate 1, technical replicate 1

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: HIST1H1B KO

value: DAY 0


title: Sample 52 (MP-1-2H-3)

value: 1 ug/mL


title: BAL sample patient 8, covid pos

value: Lung

value: Bronchoalveolar lavage

value: positive


title: PF70_3

description:
NGS041-20-9_S9
processed data file: pfRBP33.tsv

value: trasfected with pGR70 (RNAi plasmid)

value: RNAi induced


title: EZH2 KO DAY0 NT biological replicate 3, technical replicate 3

description: RNA-Seq

value: EZH2 KO

value: NT


title: BAL sample patient 10, healthy control

value: negative, healthy

value: citeSeq


title: 449_2

description:
NGS041-20-2_S2
processed data file: pfRBP33.tsv


title: EZH2 KO DAY0 NT biological replicate 3, technical replicate 2

description: RNA-Seq


title: 449_1

description:
NGS041-20-1_S1
processed data file: pfRBP33.tsv


title: EZH2 KO DAY0 NT biological replicate 3, technical replicate 1

description: RNA-Seq


title: BAL sample patient 6, covid pos


title: Sample 47 (MP-10-2H-2)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: CuO Microparticle

value: 2 Hour

value: 10 ug/mL

value: 11 mouse cell lines


title: Sample 46 (MP-25-2H-2)

value: 25 ug/mL


title: BAL sample patient 5, covid pos

value: scRnaSeq


title: EZH2 KO DAY0 NT biological replicate 2, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: DAY 0


title: BAL sample patient 7, covid neg

value: Lung

value: Bronchoalveolar lavage

value: negative


title: BAL sample patient 4, covid neg


title: EZH2 KO DAY0 NT biological replicate 2, technical replicate 2

description: RNA-Seq

value: EZH2 KO


title: BF70_1

description:
NGS041-20-4_S4
processed data file: bfRBP33.tsv

value: Bloodstream forms, S16 strain

value: trasfected with pGR70 (RNAi plasmid)

value: RNAi induced


title: BAL sample patient 3, covid neg


title: Sample 48 (NP-25-24H-1)

value: MutaMouse

value: CuO Nanoparticle

value: 24 Hour


title: S16_3

description:
NGS041-20-12_S12
processed data file: bfRBP33.tsv

value: untransfected

value: control


title: Sample 49 (MP-5-24H-3)

value: Immortalized Lung Epithelial cells

value: CuO Microparticle

value: 5 ug/mL

value: 11 mouse cell lines


title: Sample 44 (M-2H-4)

value: Blank Media

value: 2 Hour

value: 0 ug/mL


title: Sample 43 (NP-25-2H-2)

value: 25 ug/mL


title: BAL sample patient 2, covid neg

value: Lung

value: Bronchoalveolar lavage

value: negative

value: citeSeq


title: S16_2

description:
NGS041-20-11_S11
processed data file: bfRBP33.tsv

value: Bloodstream forms, S16 strain


title: Sample 45 (NP-5-2H-2)

value: MutaMouse

value: CuO Nanoparticle


title: Sample 41 (NP-1-48H-4)

value: 48 Hour

value: 1 ug/mL


title: BAL sample patient 1, covid pos

value: positive


title: S16_1

description:
NGS041-20-10_S10
processed data file: bfRBP33.tsv

value: untransfected

value: control


title: EZH2 KO DAY0 NT biological replicate 1, technical replicate 2

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: EZH2 KO

value: DAY 0

value: NT


title: Sample 42 (NP-10-48H-3)

value: Immortalized Lung Epithelial cells

value: 10 ug/mL

value: 11 mouse cell lines


title: EZH2 KO DAY0 NT biological replicate 1, technical replicate 1

description: RNA-Seq


title: RNAi3 [ATAC-seq]

data_processing:
75-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using bowtie2 with options --no-unal --no-mixed -5 5 -3 5
Fragments corresponding to nucleosome-free regions were extracted from BAM files using alignmentSieve (deeptools) with options --minMappingQuality 30 --maxFragmentLength 100 --ATACshift --ignoreDuplicates -bl mito.bed
Peaks were called using MACS2 callpeak with options -g 3.5e7 --nomodel -f BAMPE -B --keep-dup all -c genomic_control
bedGraph files were generated using MACS2 bdgcmp with option -m ppois
Genome_build: 427 2018 version 4.9
Supplementary_files_format_and_content: bigWig files generated from bedGraph files using bedGraphToBigWig

growth_protocol: Grown in HMI-9 medium at 37ºC

extract_protocol:
Cells were washed, permeabilized with 40 uM digitonin for 5 min at RT, and incubated with Tn5 transposase for 30 min at 37ºC. DNA was purified using Qiagen MinElute Kit
Amplification was carried out with 2× KAPA HiFi mix and 1.25 uM of Nextera primers

value: trasfected with pGR70 (RNAi plasmid)

value: RNAi induced


title: AG

city: jinan

first: huasu

last: zhu

address: No.107 wenhua west load

institute: Qilu hospital of shandong university

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: FPKM(txt)

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: pre-B acute lymphoblastic leukemia


title: Control


title: RNAi2 [ATAC-seq]

value: Bloodstream forms, S16 strain


title: Unperturbed TNP2 biological replicate 2

data_processing:
bcl2fastq2 v2.2.0
alignment, peak calling and differential accessibility analysis was carried pout using nfcore/atacseq v1.2.2 pipeline
Assembly: hg19
Supplementary files format and content: Quantified consensus peak set count matrix across all samples in tab-delimited format
Supplementary files format and content: Normalized bigWig files

source_name: PDX MEFX 2090

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, 50.000 MEXF 2090 cells were pelleted by centrifugation and re-suspended in 50 μl of cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin). After incubation on ice for 3 min, 1 ml of lysis buffer without NP40 and digitonin was added. Nuclei were pelleted by centrifugation for 10 min at 500 g, 4°C. The supernatant was discarded, and nuclei were re-suspended in 50 μl of reaction buffer containing 2.5 μl of Tn5 transposase (made in-house), 25 μl of 2× TDE buffer (20 mM Tris–HCl, pH 7.6, and 10 mM MgCl2, 20% Dimethyl Formamide), 16.5 μl of PBS, 0.5 μl of 1% digitonin, and 0.5 μl of 10% Tween-20. The reaction was incubated at 37°C for 30 min with mixing (600 RPM).
Library preparation was done as per (Corces et al., 2017).

value: PDX MEFX 2090

value: TNP2 KO

tag: stress

value: Unperturbed


title: Sample 39 (NP-5-48H-3)

value: MutaMouse

value: CuO Nanoparticle

value: 48 Hour

value: 5 ug/mL


title: RNAi1 [ATAC-seq]


title: EED KO DAY0 NT biological replicate 3, technical replicate 3

description: RNA-Seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.2.31) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters used were “--star-output-genome-bam --forward-prob 1”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

value: Melanoma cells MEXF 2090

value: EED KO


title: EED KO DAY0 NT biological replicate 3, technical replicate 2

description: RNA-Seq

value: DAY 0

value: NT


title: Unperturbed TNP2 biological replicate 1


title: control3 [ATAC-seq]

value: untransfected

value: control


title: EED KO DAY0 NT biological replicate 3, technical replicate 1

description: RNA-Seq


title: control2 [ATAC-seq]


title: Unperturbed SUZ12 biological replicate 2

value: SUZ12 KO


title: EED KO DAY0 NT biological replicate 2, technical replicate 3

description: RNA-Seq


title: EED KO DAY0 NT biological replicate 2, technical replicate 2

description: RNA-Seq


title: Unperturbed SUZ12 biological replicate 1


title: control1 [ATAC-seq]


title: Unperturbed SMARCD1 biological replicate 2

value: SMARCD1 KO


title: EED KO DAY0 NT biological replicate 2, technical replicate 1

description: RNA-Seq


title: Purified genomic DNA [ATAC-seq]

source_name: Purified genomic DNA from bloodstream T. brucei

value: genomic


title: Sample 35 (M-48H-2)

value: Immortalized Lung Epithelial cells

value: Blank Media

value: 0 ug/mL

value: 11 mouse cell lines


title: Sample 37 (NP-10-48H-1)

value: MutaMouse

value: 10 ug/mL


title: Sample 38 (NP-1-2H-3)

value: CuO Nanoparticle

value: 2 Hour

value: 1 ug/mL


title: Unperturbed SMARCD1 biological replicate 1

value: PDX MEFX 2090

value: Unperturbed


title: EED KO DAY0 NT biological replicate 1, technical replicate 3

description: RNA-Seq

source_name: Melanoma cells MEXF 2090

value: Melanoma cells MEXF 2090

value: EED KO

value: DAY 0

value: NT


title: Sample 36 (NP-5-48H-1)

value: 48 Hour

value: 5 ug/mL


title: Unperturbed HIST1H1B biological replicate 1

value: HIST1H1B KO


title: EED KO DAY0 NT biological replicate 1, technical replicate 2

description: RNA-Seq


title: Sample 34 (NP-1-48H-1)

value: Immortalized Lung Epithelial cells


title: RIP-seq E. faecalis KhpB Ab1

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

country: Germany

institute: Würzburg University

organism: Enterococcus faecalis V583

source_name: bacterial culture, IP

growth_protocol: E. faecalis V583 and E. faecium AUS004 were grown at 37°C in M17 medium supplemented with 0.5% glucose with one third of media and two thirds oxygen until logarithmic/early stationary phase at an OD600 of 2.0.

extract_protocol:
Gradient samples were denatured with 1% SDS and RNA was PCI extracted, and ethanol precipitated. 5 µl of the resulting samples were diluted in 45 µl DEPC-treated water. 10 µl were mixedwith 10 µl of a 1:100 diluted ERCC spike-in mix 2 (Thermo Fisher) and subjected to library preparation. In RIP-seq, RNA-protein interaction was denatured by 1% SDS and PCI extraction. RNA was precipitated with ethanol and submitted to library preparation.
The RNA samples were fragmented using ultrasound (4 pulses of 30 s at 4°C) followed by 3′-adapter ligation. First strand cDNA synthesis was performed using M-MLV reverse transcriptase. After purification, the 5′-Illumina TruSeq sequencing adapters were ligated to the 3′end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10–20 ng/µl by high-fidelity DNA polymerase and purified with Agencourt AMPure XP kit (Beckman Coulter). cDNA samples were pooled with according to input concentration, a size range of 200–550 bp was eluted from a preparative agarose gel. This size-selected cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 ntsingle-end read length.

treatment_protocol: DNase I treatment, ERCC spike-in supplementation for Grad-seq. Two polyclonal rabbit antibodies against full-length KhpB were produced by Eurogentec and used for the RIP-seq experiment.

value: wt

tag: growth state

value: OD 2


title: Sample 33 (MP-1-2H-4)

value: MutaMouse

value: CuO Microparticle

value: 11 mouse cell lines


title: Sample 31 (MP-10-48H-1)

value: 10 ug/mL


title: Sample 32 (MP-10-2H-3)

value: 2 Hour


title: RIP-seq E. faecalis KhpB Ab2


title: Sample 30 (MP-25-48H-1)

value: 25 ug/mL


title: EED KO DAY0 NT biological replicate 1, technical replicate 1

description: RNA-Seq

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
3’ mRNA-Seq libraries were prepared with the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit.  Total RNA was quantified using via the RNA QuantiFluor RNA system E3310 on the GloMax (Promega) Multi Detection system following the maufacturer's guidelines.  RNA quality was checked via the High Sensitivity RNA ScreenTape using the TapeStation 4200 (Agilent).  RNA was normalised to 30 ng and used for cDNA synthesis and library preparation using the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit according to the manufacturer’s instructions.  Libraries were sequenced on the Illumina HiSeq 4000 with single ended reads


title: Unperturbed EZH2 biological replicate 2

value: PDX MEFX 2090

value: EZH2 KO

value: Unperturbed


title: RIP-seq E. faecalis KhpB ctrl1


title: Rat5_Proximal_Achilles

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
hisat2 --no-mixed --no-discordant –no-unal -1 target_R1.fastq -2 target_R2.fastq | samtools view -bS -o HISAT2.Aligned.bam(hisat2 v2.2.1)
samtools sort -n HISAT2.Aligned.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – HISAT2.Aligned.sortedByCoord.bam (samtools v1.9)
featureCounts -p -a ensembl_rn6.gtf -s 2 -o reverse_stranded.txt HISAT2.Aligned.sortedByCoord.bam (featureCounts v2.0.1)
Genome_build: rn6
Supplementary_files_format_and_content: Tab Separated File (TSV)
Supplementary_files_format_and_content: count matrix

organism: Rattus norvegicus

source_name: Proximal region of Achilles tendon

growth_protocol: None; 8-week-old healthy rats used

extract_protocol:
Achilles tendons were harvested by making a transverse incision just distal to the myotendinous junction and proximal to the enthesis. Tendons were measured manually using a tape measure and then divided into three equal segments – proximal, middle, and distal. Segments from each limb were combined into a single sample. Samples were minced and then pulse homogenized in Qiazol containing 1 ug of glycogen using a TissueRuptur (Qiagen, Germantown, MD, USA). To isolate RNA, a miRNA Micro Kit with added DNase I was used (Qiagen). Following RNA isolation, total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA concentrations were measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA).
Preparation of RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine. Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina NovaSeq6000 sequencer with pair-end 50 cycles. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.

treatment_protocol: None; 8-week-old healthy rats used

tag: region

value: tendon

tag: age


title: Sample 28 (MP-5-2H-3)


title: Sample 29 (MP-1-48H-1)

value: 1 ug/mL


title: Sample 27 (MP-25-2H-3)


title: Unperturbed HIST1H1B biological replicate 2


title: Grad-seq E. faecalis fraction P

data_processing:
Library strategy: Grad-seq
READemption 0.4.5
Genome_build: NC_004668.1  NC_004669.1  NC_004670.1  NC_004671.1  NC_017022.1  NC_017023.1  NC_017024.1  NC_017032.1
Supplementary_files_format_and_content: wig

source_name: bacterial culture, gradient fractionation


title: Rat5_Middle_Achilles

source_name: Middle region of Achilles tendon


title: Unperturbed EED biological replicate 1

value: EED KO


title: Unperturbed EED biological replicate 2


title: Rat4_Proximal_Achilles


title: Grad-seq E. faecalis fraction 19


title: RIP-seq E. faecalis KhpB ctrl2


title: Rat5_Distal_Achilles

source_name: Distal region of Achilles tendon


title: Grad-seq E. faecalis fraction 20


title: Unperturbed EZH2 biological replicate 1


title: Grad-seq E. faecalis fraction 18


title: Rat4_Middle_Achilles


title: Stress TNP2 biological replicate 1

value: TNP2 KO

value: glutamine deprivation


title: Stress SUZ12 biological replicate 2

value: SUZ12 KO


title: Grad-seq E. faecalis fraction 17

value: wt


title: Grad-seq E. faecalis fraction 16

value: OD 2


title: Stress TNP2 biological replicate 2


title: Sample 25 (MP-5-48H-1)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: 48 Hour

value: 5 ug/mL


title: Rat4_Distal_Achilles


title: Sample 23 (NP-1-24H-1)

value: CuO Nanoparticle

value: 24 Hour

value: 11 mouse cell lines


title: Sample 24 (NP-10-2H-3)

value: 2 Hour

value: 10 ug/mL


title: Sample 26 (M-48H-1)

value: Blank Media

value: 0 ug/mL


title: Sample 22 (M-24H-2)


title: Rat3_Proximal_Achilles

value: tendon


title: Stress SMARCD1 biological replicate 2

value: PDX MEFX 2090

value: SMARCD1 KO


title: Stress SUZ12 biological replicate 1

value: SUZ12 KO

value: glutamine deprivation


title: Grad-seq E. faecalis fraction 15

value: wt

value: OD 2


title: Rat3_Middle_Achilles


title: Rat3_Distal_Achilles


title: Grad-seq E. faecalis fraction 14


title: Stress SMARCD1 biological replicate 1


title: Grad-seq E. faecalis fraction 13


title: Stress HIST1H1B biological replicate 2

value: HIST1H1B KO


title: Rat2_Proximal_Achilles


title: Stress HIST1H1B biological replicate 1


title: Grad-seq E. faecalis fraction 11


title: Sample 21 (NP-1-2H-4)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: 1 ug/mL


title: Stress EZH2 biological replicate 2

value: EZH2 KO


title: EZH2 KO DAY0 NT biological replicate 1, technical replicate 3

description: RNA-Seq

value: Melanoma cells MEXF 2090

value: DAY 0

value: NT


title: Rat2_Distal_Achilles


title: Stress EZH2 biological replicate 1


title: Sample 20 (NP-5-24H-1)

value: CuO Nanoparticle

value: 24 Hour

value: 5 ug/mL

value: 11 mouse cell lines


title: Grad-seq E. faecalis fraction 9


title: Grad-seq E. faecalis fraction 10


title: Sample 17 (MP-1-24H-1)

value: CuO Microparticle


title: Sample 15 (MP-10-24H-1)

value: 10 ug/mL


title: Stress EED biological replicate 2

value: PDX MEFX 2090

value: EED KO

value: glutamine deprivation


title: EZH2 KO DAY0 NT biological replicate 2, technical replicate 1

description: RNA-Seq


title: Stress EED biological replicate 1


title: Rat1_Distal_Achilles

value: tendon


title: Sample 14 (MP-25-24H-1)

value: MutaMouse

value: 25 ug/mL


title: Rat2_Middle_Achilles


title: Sample 18 (M-24H-1)

value: Immortalized Lung Epithelial cells

value: Blank Media

value: 0 ug/mL


title: Grad-seq E. faecalis fraction 8

value: wt

value: OD 2


title: Grad-seq E. faecalis fraction 7


title: Rat1_Middle_Achilles


title: E5-PfAP2-G-HA input

first: Lucas

last: Michel-Todó

address: Roselló, 149

department: Malaria Epigenetics

institute: ISGlobal

data_processing:
Quality check was perfomed using FastQC (v.0.11.9) and reads were trimmed and repetitive k-mers removed using BBDUK (v.36.99), with parameters ktrim = r, k = 22, and mink = 6
Reads were aligned to the reference genome (P. falciparum 3D7, plasmoDB release 28) using Bowtie2 (v.2.3.0)
Duplicated reads were excluded using PICARD suite (v.4.1.9.0) with the RemoveDuplicates command
Peak calling was performed using MACS2 (v.2.2.7.1) with parameters “-f BAMPE -B -g 2.41e7 --keep-dup all --fe-cutoff 1.5 -nomodel --extsize 150”.
Coverage as RPKMs was generated for each sample at 10 bp resolution, using DeepTools (v. 3.5.0) BamCoverage command with parameters “--normalizeUsing RPKM -bs 10 --smoothLength 200”
Normalized coverage of enrichment over input (log2-transformed) at 10 bp resolution, we used the DeepTools (v. 3.5.0) BamCompare command with parameters “--normalizeUsing RPKM -bs 10 --smoothLength 200 –pseudocount 10”
Assembly: P. falciparum 3D7, plasmoDB release 28
Supplementary files format and content: Bedgraph: Coverage as RPKMs
Supplementary files format and content: Bedgraph: Coverage as input normalized RPKMs (except input samples)
Supplementary files format and content: narrowPeak: Peaks called using MACS2 (except input samples)

organism: Plasmodium falciparum

source_name: Cell Culture

growth_protocol: Plasmodium falciparum parasites (3D7 line) were maintained at a 3% hematocrit with B+ erythrocytes in standard parasite culture medium with Albumax II and no human serum, in a 5% CO2, 3% 02, balance N2 atmosphere.

extract_protocol:
Sorbitol-synchronized cultures at the late trophozoite-early schizont stage were saponin lysated and formaldehyde cross-linked. Chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies) and sonicated using a Covaris M220 sonicator.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 4 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 8-10 cycles on the thermocycler.

value: Cell Culture

tag: parental line

tag: subclone

value: Yes

tag: Stage

value: late trophozoite-early schizont stage

tag: chip antibody


title: Grad-seq E. faecalis fraction 6


title: E5-PfAP2-G-HA H3K9ac

tag: tissue

value: Diagenode, C15410004


title: E5-PfAP2-G-HA H3K9me3

value: Diagenode, C15410193


title: Grad-seq E. faecalis fraction 12


title: Unperturbed H3K4me3 biological replicate 2

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
bcl2fastq2 v2.20.0
We aligned and called peaks using nfcore/chipseq v 1.2.2 (bwa,Macs2)
Assembly: human genome hg19
Supplementary files format and content: Macs2 peak output file
Supplementary files format and content: read coverage files in bigWig format

extract_protocol:
MEXF 2090 cells grown in either unperturbed conditions or under glutamine deprivation for 2 days were cross-linked using 1% formaldehyde for 10 minutes. The reaction was stopped by incubation for five minutes with 0.125M glycine. Cell pellets were washed twice with cold PBS containing protease inhibitor. Nuclear lysates were sonicated using a Bioruptor Pico for 6 cycles, 30s ON, 30s OFF settings.
Libraries were made using NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) kit (NEB, E6440S) following manufacturer’s instructions and were sequenced on an Illumina NovaSeq platform.

value: Unperturbed

value: H3K4me3 (abcam, #ab8580)


title: Unperturbed H3K4me3 biological replicate 1

value: PDX MEFX 2090


title: Grad-seq E. faecalis fraction 5


title: Grad-seq E. faecalis fraction 4


title: Unperturbed H3K4me1 biological replicate 2

value: H3K4me1 (abcam, ab8895)


title: Unperturbed H3K4me1 biological replicate 1


title: Grad-seq E. faecalis fraction 3


title: Sample 12 (M-2H-2)

tag: strain

tag: time point

value: 2 Hour

value: 11 mouse cell lines


title: Sample 13 (NP-25-2H-3)

value: MutaMouse

value: CuO Nanoparticle

tag: dose

value: 25 ug/mL

tag: biological replicate


title: Sample 11 (NP-10-2H-1)

value: Immortalized Lung Epithelial cells

tag: cell line

value: 10 ug/mL


title: Sample 9 (NP-5-2H-1)

value: 5 ug/mL


title: Unperturbed H3K27me3 biological replicate 2


title: Sample 10 (NP-25-2H-1)


title: Unperturbed H3K27me3 biological replicate 1


title: Grad-seq E. faecalis fraction 1

tag: genotype

value: wt

value: OD 2


title: Grad-seq E. faecalis fraction 2


title: NF54-V63 input

value: Cell Culture

value: No

value: late trophozoite-early schizont stage


title: Unperturbed H3K27Ac biological replicate 2

value: Unperturbed


title: 3D7-Imp H3K9me3

value: Diagenode, C15410193


title: Grad-seq E. faecium fraction 20

organism: Enterococcus faecium Aus0004


title: Sample 8 (MP-1-24H-4)

tag: treatment

value: CuO Microparticle

value: 24 Hour

value: 1 ug/mL


title: NF54-V63 H3K9me3


title: Sample 6 (NP-1-2H-1)

value: 2 Hour

value: 11 mouse cell lines


title: Stress H3K4me3 biological replicate 2

value: PDX MEFX 2090

value: glutamine deprivation

value: H3K4me3 (abcam, #ab8580)


title: Grad-seq E. faecium fraction 19


title: Grad-seq E. faecium fraction P


title: NF54 input


title: Grad-seq E. faecium fraction 18


title: Sample 5 (MP-5-2H-1)

value: MutaMouse

value: Immortalized Lung Epithelial cells


title: NF54-V63 H3K9me3_short R1

description: This sample is associated with a short version of R1 which was merged with the full length R1 associated with GSM6351387.


title: Sample 7 (MP-10-24H-3)

value: 10 ug/mL


title: Unperturbed H3K27Ac biological replicate 1


title: Sample 4 (MP-1-2H-1)


title: NF54 H3K9ac

value: Diagenode, C15410004


title: Stress H3K4me3 biological replicate 1


title: Sample 2 (MP-25-2H-1)

value: 25 ug/mL


title: Stress H3K4me1 biological replicate 2

value: H3K4me1 (abcam, ab8895)


title: Stress H3K4me1 biological replicate 1


title: NF54 H3K9me3

value: Cell Culture

value: No

value: late trophozoite-early schizont stage


title: Grad-seq E. faecium fraction 16

value: wt

value: OD 2


title: Stress H3K27me3 biological replicate 2


title: Stress H3K27me3 biological replicate 1


title: Grad-seq E. faecium fraction 15


title: Sample 3 (M-2H-1)

value: Blank Media

value: 0 ug/mL


title: B11 H3K9ac

value: Yes


title: BAFexp_H1_PU1_BC04_Rep2

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Array construction: the 162 bp Cx3cr1 mononucleosome sequence that corresponds to the genomic location: mm9 chr9:119946611-119946762 13 was extended on either side by 35 bp to incorporate linker DNA and BfuAI and XbaI flanking sequences: ACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTTAGCAATGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTG553 GCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCT TCTGTCTGCTTCCTTCGTTTAGTATGTCTA
The DNA sequence was generated by PCR of genomic mouse DNA with BfuAI and XbaI restriction sites cloned into the p208-10.N1N2 16 to generate p208-10-Cx3cr1. Mutant Cx3cr1 arrays were generated by infusion cloning using linearized BfuAI XbaI digested p208-10-Cx3cr1 plasmids. Geneblocks for cloning were obtained from IDT:
TF mutant motif Cx3cr1:
AAAATAACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCCCGTATAGAGATCGTATAGCGTATAGAGCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCTTCTGTCTGCTTCCTTCGTTTAGTATGTCTAGACTACAGTTATTGGTT
Swap1 Cx3cr1:
AAAATAACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTACTTCCCGAATTAGCAATGGTTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCTTCTGTCTGCTTCCTTCGTTTAGTATGTCTAGACTACAGTTATTGGTT
Swap2 Cx3cr1:
AAAATAACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTACTTCCCGAATTAGCAATGGTTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCTTCTGTCTGCTTCCTTCGTTTAGTATGTCTAGACTACAGTTATTGGTT
Transformation to FASTQ: the fast5 raw data files from the Nanopore sequencer were basecalled and converted to fastq format with Guppy Software (Oxford Nanopore Technologies).
Alignment: reads were mapped to the Cx3cr1 Array reference with minimap2, a mapping algorithm specifically designed to analyze nanopore sequencing reads.
Quality Control: BAM files produced by minimap2 were imported into R 44 then filtered and normalized using tidyverse packages 45 .Specifically, reads were excluded if they were identified as multimappers by minimap2 or were located entirely within the non- unique regions of the nucleosome array DNA sequence.
Track Creation: the ends of each read from an array digestion identify the precise nucleotide at which a nuclease was able to access and cleave the DNA in the array. We quantified the endpoints of each read using the hash package and then normalized each dataset to the total number of mapped reads, resulting in provided bigWigs.
Assembly: mm9
Supplementary files format and content: BigWig files represent pile-ups of fragment endpoints, indicating nuclease cleavage sites

source_name: Plasmid-amplified sequence

growth_protocol: Plasmids were amplified in E.coli, purified, and digested with MluI, SmaI and HhaI to release array fragments. Fragments were purified by ethanol precipitation then labeled with579 dCTP-Cy5 (Cytiva PA55021) by end-repair with Klenow fragment DNA polymeraase (3’-5’ exo-) (NEB). Cy5-DNA labeling reactions were carried out at final concentrations of 1 μM DNA, 4 mM Cy5-dCTP and 0.5 U/μL Klenow fragment in the presence of excess 4mM dATP, 4 mM dTTP, and 4 mM dGTP in NEB buffer 2 (50mMNaCl, 10mM Tris-HCl, 10 mM MgCl 2 , 1 mM DTT). The reaction was incubated at 37C for 1 hr. Labeling reactions were purified by phenol:chloroform extraction followed by FPLC purification of the 2.7 kb MluI-SmaI fragment using a Capto HiRes Q anion exchange column (Cytiva 29275878).

extract_protocol: Partially MNase-digested chromatin retaining contiguous oligonucleosomes was used for generation of libraries for nanopore sequencing. Purified DNA was end-repaired and A-tailed with the NEBnext Ultra II end repair module (New England Biolabs), purified with Ampure XP beads (Beckman Coulter) and ligated to AMX adapter from the Oxford Nanopore 1D sequencing Kit (SQK-LSK108, Oxford Nanopore Technologies) using NEB Blunt/TA ligase master mix. Excess adapters were removed by adding 0.5 volumes of Ampure XP beads and washing with ABB buffer from the 1D sequencing kit. Purified library was eluted and loaded to a MinION R9.4 flowcell according to the manufacturer’s instructions and run for 24 h.

treatment_protocol:
Nucleosome Arrays: nucleosome arrays were assembled as previously described 16 . Assembly reactions containing 2 μg of end-labeled DNA fragments and core histones at a 1:1.0 molar ratio of octamers to nucleosomal sites, and 2 M NaCl in a total of 10 μl were incubated at 37°C for 15 min, serially diluted by adding 3.3, 6.7, 5, 3.6, 4.7, 6.7, 10, 30, and 20 μl of 50 mM HEPES (pH 7.5), 1 mM EDTA, 5 mM DTT, and 0.5 mM PMSF in 15 min incubation steps at 30°C, and brought to 0.1 M NaCl by adding 100 μl of 10 mM Tris·HCl (pH 7.5), 1 mM EDTA, IGEPAL, 5 mM DTT, 0.5 mM PMSF, and 20% glycerol, followed by incubation at 30°C for 15 min. Array saturation was determined by EcoRI digestion, performed with a concentration of 2 nM nucleosome array or free DNA in 20 mM HEPES (pH 7.5), 50 mM KCl, 1% glycerol, 5 mM DTT, 100 μg/ml BSA, and 2 U/μl EcoRI. Following a 2 hr incubation at 37°C, digestion products were resolved on 4% polyacrylamide 0.5X TBE gels and analyzed as described 16 . Cx3cr1 mononucleosomes were reconstituted by dialysis with the Cy5 end-labeled 162bp Cx3cr1 DNA fragment and recombinant human histones as described previously 13.
TF Binding: binding reactions for the DNase I digestion, MNase, and Restriction enzyme assays were carried out with 1 nM (1.5 ng/μl) of nucleosome array (13 nM of nucleosomes) in 6 mM HEPES (pH 7.5), 35 mM KCl, 1.5% glycerol, 2 mM DTT, 250 μg/ml BSA. In experiments with compacted nucleosome arrays, 13 nM purified histone H1 (Calbiochem) was incubated with the nucleosome arrays at room temperature for 1 hr. Purified transcription factors were then incubated with the nucleosome arrays at room temperature for 1 hr. For cBAF remodeling assays 10nM of indicated transcription factors were incubated with H1-compacted arrays at room temperature followed by incubation with cBAF (6 nM) and ATP (0.5mM) for 30 minutes at 30°C.
DNase digestions were carried out by 2.5-10 ug/mL of DNase I diluted in 50 mM MgCl 2 , followed by incubation at room temperature for 1 min. MNase digestion was performed by addition of .075-0.6 U/mL MNase diluted in 30 mM CaCl2, followed by incubation at room temperature for 1 min. XbaI restriction enzyme digestion was performed by incubation with 0.25- 1 U/mL XbaI for 45 minutes at 30°C. Reactions were terminated by addition of 1 volume of stop buffer (20 mM Tris pH 7.5, 50 mM EDTA, 1% SDS, 0.5 mg/mL tRNA, and 0.2 mg/mL proteinase K) and incubated at 50C for 15 min. Digestion products are purified by ethanol precipitation and electrophoresed on 1% Agarose 1X TBE gels.

value: Plasmid-amplified sequence

tag: condition

value: Compacted Array with PU.1


title: Grad-seq E. faecium fraction 14


title: BAFexp_H1_PU1_BAF_BC06_Rep2

value: Compacted Array with PU.1+BAF


title: BAFexp_H1_PU1_BC03_Rep1


title: Sample 1 (MP-10-2H-1)

source_name: Immortalized Lung Epithelial cells (FE1)

value: MutaMouse

value: CuO Microparticle

value: 2 Hour

value: 11 mouse cell lines


title: Grad-seq E. faecium fraction 17


title: Stress H3K27Ac biological replicate 2

value: PDX MEFX 2090

tag: stress

value: glutamine deprivation


title: B11 H3K9me3

value: Cell Culture

value: Diagenode, C15410193


title: BAFexp_H1_PU1_BAF_BC05_Rep1


title: E5 input

value: late trophozoite-early schizont stage


title: Stress H3K27Ac biological replicate 1


title: B11 input


title: BAFexp_H1_NOTF_BC02_Rep2

value: Compacted Array


title: Grad-seq E. faecium fraction 12

value: wt

tag: growth state

value: OD 2


title: Input control


title: E5 H3K9me3


title: A7 input


title: Grad-seq E. faecium fraction 11


title: BAFexp_H1_NOTF_BC01_Rep1


title: BAFexp_free_DNA_MNase_digest_BC08_Rep2

value: Free DNA


title: NIPBL and CTCF double knockdown rep 2

first: Jennifer

middle: Mary

last: Luppino

state: Pennsylvania

address: 415 Curie Blvd., Room: 570

department: Genetics

institute: University of Pennsylvania

data_processing:
All custom scripts described herein are available on the AdelmanLab Github (https://github.com/AdelmanLab/NIH_scripts). Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10). R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the hg38 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl). Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end position at single nucleotide resolution.
For promoter reads, annotated transcription start sites were obtained from Ensembl v99 for hg38. After removing transcripts with {immunoglobulin, Mt_tRNA, Mt_rRNA} biotypes, PRO-seq signal in each sample was calculated in the window from the annotated TSS to +150 nt downstream, using a custom script, make_heatmap.pl.
Given good agreement between replicates (Spearman's rho ≥0.95) and similar return of spike-in reads, bedGraphs were merged within conditions, and depth-normalized, to generate bigWig files binned at 10bp.
To determine differentially expressed genes in PRO-seq analyses, the 5' ends from all PRO-seq reads were used to identify active transcription start sites using a custom script, proTSScall available on the NascentTranscriptionCore GitHub (https://github.com/NascentTranscriptionCore/proTSScall). Briefly, PRO-seq 3’ read bedGraphs for “+” and “-“ strands were separately combined across samples and the composite read counts were assigned to TSS-proximal windows (TSS to +150nt) using the same filtered TSS annotation described above.  TSSs with ≤9 counts in this window are deemed ‘inactive’ and the remaining TSSs, deemed ‘active’, are collapsed to yield 1 dominant TSS per gene, defined as the one with the highest TSS-proximal read count -- if the highest read count is shared amongst multiple transcripts, the TSS furthest upstream, in a strand-aware fashion, is called dominant.  Dominant TSSs sharing the same start position are deduplicated as follows: (1) if start positions are equal, the TSS with the longest associated annotated transcript is called dominant, (2) if start positions and transcript lengths are both equal, the TSS associated with the lowest Ensembl gene ID (numerical portion) is dominant.
Differential expression analysis was performed in R v3.6.1 with DESeq2 v1.30.1 (Love et al., 2014). Read counts were obtained over whole genes from TSS to TES as defined by proTSScall, distal dREG peaks, TSS proximal regions (dominant TSS to TSS+150bp), and gene bodies (dominant TSS+250 to TSS+2250bp) using the featureCounts function from Rsubread v1.34.7 (Liao et al., 2019). Defaults were used with the following exceptions: minMQS=10; countChimericFragments=FALSE; isPairedEnd=FALSE; strandSpecific=2 (or strandSpecific=0 for distal dREG peaks); nthreads=8. DESeq2 was run with defaults using the nbinomWaldTest function. The size factors obtained from whole gene bodies were applied to all other groups. Log fold change shrinkage was performed using the ‘apeglm’ algorithm (Zhu et al., 2019). Significant differentially expressed genes were filtered for a minimum adjusted p-value of 0.01 or less, removing NA values.
Assembly: hg38
Supplementary files format and content: bw: bigWig
Supplementary files format and content: txt: tab-delimined file containing differential expression analysis

growth_protocol: Cells were cultured in McCoy’s 5A media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100ug/ml streptomycin and filtered using a 0.22-μm PES membrane at 37°C with 5% CO2

extract_protocol:
RNAi was performed as previously described. Following 72 h knockdown, cells were rinsed with Dulbecco's phosphate buffered saline (DPBS) and treated with trypsin to detach them from the plate. Cells were resuspended in cold supplemented McCoy’s 5A media and three wells of a 6-well plate were pooled per replicate and placed on ice. From this point on, all steps were performed on ice, all buffers were pre-chilled, and samples were spun at 300xg for 10 min at 4ºC, unless otherwise noted. Cells were rinsed in PBS containing 1% Bovine Serum Albumin (BSA) to prevent cell clumping, and then resuspended in 1 ml Buffer W (10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 0.5 mM DTT, 10% glycerol, 1% BSA) then strained through a 35 μm nylon mesh filter. The tube was rinsed with an additional 1ml of Buffer W and passed through the same strainer. A 9X volume of Buffer P (Buffer W + 0.1% IGEPAL CA-630) was immediately added to each sample and nutated for 2 minutes at room temperature. Cells were resuspended in 500μl Buffer F (50 mM Tris-Cl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT, 1 μL/ml SUPERaseIn RNase inhibitor, 0.5% BSA) using a wide-bore P1000 tip and transferred to a low binding tube. The original tube was rinsed with another 500μl Buffer F and the samples were pooled. Samples were spun at 400xg and resuspended to 5 x 106 cells in 500μl Buffer F. Samples were flash frozen in liquid nitrogen and stored at −80°C
PRO-seq library construction and data analysis was performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA. Aliquots of frozen (-80°C) permeabilized cells were thawed on ice and pipetted gently to fully resuspend. Aliquots were removed and permeabilized cells were counted using a Luna II, Logos Biosystems instrument. For each sample, 1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run on assays and library preparation were performed essentially as described in Reimer et al. (Reimer et al., 2021)  with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 40uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/μl SuperaseIN (Thermo), 1% sarkosyl). Run-on reactions were performed at 37°C. Adenylated 3' adapter was prepared using the 5' DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturers instructions with 15% PEG-8000 final) and incubated at 16°C overnight. 180μl of betaine blocking buffer (1.42g of betaine brought to 10ml with binding buffer supplemented to 0.6 uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/)) was mixed with ligations and incubated 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads. After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash (0.25X T4 RNA ligase buffer (NEB), 0.3uM blocking oligo) solutions and resuspended in 5' adapter mix (10 pmol 5' adapter, 30 pmol blocking oligo, water). 5' adapter ligation was per Reimer but with 15% PEG-8000 final. Eluted cDNA was amplified 5-cycles (NEBNextµltra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Pooled libraries were sequenced using the Illumina NovaSeq platform.

treatment_protocol: The following siRNAs (Dharmacon) were used: Non-targeting control (D-001210-05-05), NIPBL (J-012980-08; target sequence: 5’-CAACAGAUCACAUAGAGUU-3’), WAPL (L-026287-01-0005; target sequences administered as a pool: 5’-GGAGUAUAGUGCUCGGAAU-3’, 5’-GAGAGAUGUUUACGAGUUU-3’, 5’-CAAACAGUGAAUCGAGUAA-3’, 5’-CCAAAGAUACACGGGAUUA-3’), and CTCF (L-020165-00-0010; target sequences administered as a pool: 5’-GAUGAAGACUGAAGUAAUG-3’, 5’-GGAGAAACGAAGAAGAGUA-3’, 5’-GAAGAUGCCUGCCACUUAC-3’, 5’-GAACAGCCCAUAAACAUAG-3’). siRNAs were incubated for 20 minutes at room temperature with RNAiMAX Lipofectamine transfection reagent (ThermoFisher) in Opti-MEM reduced serum media (ThermoFisher) and seeded into wells. HCT-116 cells were trypsinized and resuspended in antibiotic free media (McCoy’s 5A media supplemented with 10% FBS and 2 mM L-glutamine), then plated onto siRNA for a final siRNA concentration of 50 nM (non-targetting control and WAPL), 100 nM (NIPBL), or 150 nM (CTCF). For CTCF knockdowns, cells were retreated with 150nM CTCF siRNAs 24 hours after initial treatment. After 72h (NIPBL, WAPL, non-targeting control) or 96h from the initial RNAi treatment (CTCF), cells were harvested for experiments.

value: NIPBL and CTCF siRNA


title: Grad-seq E. faecium fraction 10


title: A7 H3K9me3

value: Yes


title: Grad-seq E. faecium fraction 13


title: BAFexp_free_DNA_MNase_digest_BC07_Rep1

value: Plasmid-amplified sequence


title: 10G input


title: NIPBL and CTCF double knockdown rep 1


title: NIPBL and WAPL double knockdown rep 2

value: NIPBL and WAPL siRNA


title: BAFexp_array_MNase_digest_BC10_Rep2

value: Nucleosome Array


title: Grad-seq E. faecium fraction 9


title: 10G H3K9ac

value: Diagenode, C15410004


title: Rat1_Proximal_Achilles

tag: region

value: tendon


title: 10G H3K9me3


title: BAFexp_array_MNase_digest_BC09_Rep1


title: NIPBL and WAPL double knockdown rep 1


title: TFexp_H1_PU.1_CEBPb_BC12_Rep2

value: Compacted Array with PU.1+CEBPb


title: Grad-seq E. faecium fraction 7


title: CTCF knockdown rep 2

value: CTCF siRNA


title: Grad-seq E. faecium fraction 6


title: 1.2B input


title: Grad-seq E. faecium fraction 5


title: CTCF knockdown rep 1


title: 1.2B H3K9ac


title: Grad-seq E. faecium fraction 8


title: WAPL knockdown rep 2

value: WAPL siRNA


title: 1.2B H3K9me3

value: Cell Culture


title: Grad-seq E. faecium fraction 4


title: TFexp_H1_PU.1_CEBPa_BC10_Rep2

value: Compacted Array with PU.1+CEBPa


title: WAPL knockdown rep 1


title: TFexp_H1_PU1_CEBPa_BC09_Rep1


title: Grad-seq E. faecium fraction 3


title: Embryo, E12.5,  visium

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: spatial transcriptomics

library_source: transcriptomic single cell

data_processing:
Raw data were pre-processed using SpaceRanger’s (v1.3.1)
Using 10X Genomics’ Loupe Browser (v6.0.0), we manually selected barcodes belonging to capture spots overlaying tissue and used these to filter the gene-barcode matrices obtained from SpaceRanger
Data for each section were merged and analyzed with Seurat (v4.1.0).
We normalized data and performed clustering following Signac (v1.6.0) standard workflow.
Assembly: mm10
Supplementary files format and content: h5 (feature-barcode matrix)
Supplementary files format and content: csv (metadata with spatial coordinates, sample, and clustering)
Supplementary files format and content: png/jpg (picture of the tissue section)

source_name: Embryo

extract_protocol:
Libraries were prepared according to Visium Spatial Gene Expression Slide and Reagents kit.
Libraries were dual indexed using Dual Index Kit TT Set A
Libraries were sequenced on Illumina NextSeq 550/2000 platform

value: Embryo

tag: age

value: WT


title: Grad-seq E. faecium fraction 2

value: wt