title: PBMC, NextGEM 3', sample F5B

city: Seattle

first: Anna

last: Elz

state: WA

address: 1201 Eastlake Ave E

institute: Fred Hutchinson Cancer Center

description: Library name: nextgem_3p_F5B

data_processing:
Sequencing Depth and Downsampling: Sample sequencing was conducted to achieve a depth exceeding 25,000 reads per cell for WT libraries except for FLEX which targeted 10,000 reads per cell.  TCR libraries all targeted for 5000 reads per cell. When sequencing surpassed the targets, FASTQs were downsampled to 25,000 reads per cell for the WT libraries and 5000 reads per cells for TCR libraries using seqtk version 1.3 with random seed 100 (Li, 2012).
Generating count matrices: The software provided by each kit vendor was utilized to generate UMI count matrices from the downsampled FASTQs. Pipelines were run with default parameters unless otherwise specified. For the 10x kits, CellRanger version 8.0.0 with the multi subcommand was employed with the reference version refdata-gex-GRCh38-2024-A. Parse data was processed with splitpipe v1.2.1 using parse’s hg38_V1.1.3 reference. Fluent data was processed with PIPseeker version 3.3.0 with reference gex-reference-GRCh38-2022.04. For each sample, PIPseeker generates 5 outputs of varying sensitivity for calling cells from background. We selected the sensitivity levels on a per-sample basis informed by the knee plots and vendor guidelines. Scale data was processed through scaleRNA version 1.5 with default parameters, library structure version 1.1 and the prebuilt GRCH38 reference genome provided by Scale. FASTQs were generated at the library level by passing raw BCL folders into the first scaleRNA run. We then ran Scale’s bc_parser (distributed with the nextflow pipeline) with the `--demux` flag and options to output 2 read files and 2 index files for each sample. These were downsampled and ran with default parameters to produce the filtered expression matrix.
Assembly: GRCh38
Supplementary files format and content: The first set of processed files are pipeline outputs from downsampled data. For WT/GEX libraries, processed files include files needed to construct the counts matrix. Either h5 files, or matrix + barcode + feature files. For VDJ/TCR libraries, the processed data files have the final clone assemblies.
Supplementary files format and content: The second set of processed files are the Seurat RDS files for each kit, with all samples for that kit merged. The datasets were processed to remove low quality cells and low-abundance genes. Data was clustered at the kit level and annotated manually using reference mapping and key gene expression. See the manuscript for full details.

source_name: PBMC

extract_protocol:
Benchmark I:  3’ Whole transcriptome comparison Multiple donor leukopak frozen aliquots were purchased from Bloodworks Northwest.  PBMCs from two healthy donors F1 and F5, stored in liquid nitrogen were thawed at 37 degrees C., transferred into 10ml prewarmed thawing media (Gibco RPMI 1640 + 10% FBS) and centrifuged at 500 x g for 5 minutes at 4 degrees. Cells were washed in 10ml cold 1XPBS -MgCl and -CaCl (Gibco), followed by subsequent centrifugation at 500 x g for 5 minutes and the pellet resuspended in 10ml 1X PBS.  The CellacaMX (Revvity) live-dead assay was used to count AOPI stained cells. Viability was 83% and 88% respectively.  Each cell suspension was aliquoted for use in the 10X Genomics GEM-X and NextGEM assays in which the cell suspensions were loaded in replicate, with a targeted recovery of 20,000 and 10,000 cells, respectively.  The remaining cell suspensions were aliquoted out in technical replicates of 1 million cells and fixed using Parse’s Cell Fixation v3 User Manual (UM0027 v1.1), Fluent’s Demonstrated Protocol DSP-Methanol Fixation for Cells (FB0004708), and 10x Demonstrated Protocol Fixation of Cells and Nuclei for Chromium Fixed RNA Profiling (FLEX) (CG000478 Rev C). Separate aliquots of F1 and F5 donors were processed as above except with PBS 1% BSA for the final resuspension.  One set was fixed in technical replicates of 1 million cells following the Scale’s standard fixation kit protocol Rev. B.  The second set of aliquots was processed as above with PBS + 0.04% BSA and Promega RNase Inhibitor resuspension and no fixation for Fluent’s PIPseq V.  Benchmark II:  5’ WT, TCR single cell comparison Frozen PBMCs from four healthy donors (F1, F2, F4, and F5) of mixed sex (3 males, 1 female) and ethnicity (3 persons of Caucasian descent and 1 person of Asian descent) supplied by Bloodworks Northwest were processed in two batches one week apart (F1, F2 followed by F4, F5). Cells were thawed in a 37°C water bath before transfer to thawing media (Gibco RPMI 1640 + 10% FBS). Samples were then centrifuged at 400 x g for 10 minutes at 4°C. The supernatant was decanted, and the pellet resuspended in 10 mL of sorting media (cold Gibco 1X PBS + 1% BSA), followed by an additional centrifugation at 400 x g for 10 minutes. Each sample was next resuspended in 200 µL of stain media. Cells were stained to enrich for T-cells and to remove as many B-cells as possible. We stained the samples with human CD3, CD45, and CD19 (citation for antibodies). 7AAD was used to assess the in-flight viability of the cells during the sort. We sorted T cells using the Becton-Dickenson Symphony S6 cytometer. The final population was CD3+, CD45+, and CD19-. An aliquot of the sorted T-cells was stained with AOPI and assessed for viability and cell counts using the Nexcelom CellacaMX (Revvity).  Viabilities ranged from 88-90 % (F1 and F2) and 83-87% (F4 and F5).  An aliquot of the of each donor T-cells was utilized for 10x Genomics GEM-X 5′ v3 (CG000733 RevA) and NextGEM 5′ v2 (CG000331 RevE) assays, in which 20,000 and 10,000 cells were targeted for recovery, respectively. The remaining cell suspension, ~1.5 million cells, was fixed following Parse Evercode Cell Fixation v2 (UM0039 v2.3). Cells were frozen and later processed as directed by Evercode TCR Human WT + TCR v1 (UM0018).
Benchmark I:  3’ Whole transcriptome comparison 10x Genomics FLEX Fixed RNA profiling Per the 10x Genomics CG000527 Rev E protocol, fixed cells were incubated overnight with mRNA transcript probes targeting ~18K genes, with the left handle containing a sample specific barcode. Following probe hybridization, samples were counted and pooled equally before a series of washes to remove unbound probes.  After counting the pool, a volume targeting a recovery of 40,000 cells was combined with a master mix that contains enzymes that ligate and extend the probes during GEM incubation. This mixture was then loaded into the NEXT GEM Chip Q with gel beads and partitioning oil. Following microfluidic GEM generation on the ChromiumX, the GEMs were recovered and amplified to generate product to put into library preparation.  A portion of the amplified material was re-amplified with library specific P5 and P7 indices. 10x Genomics GEM-X 3’v4 and NextGEM v3.1 Following the 10X Genomics GEM-X 3’v4 (CG000731) and NextGEM v3.1 (CG000315) protocols, PBMCs from donor F1 and donor F5 were combined with a reverse transcript mastermix and loaded on to a microfluidic chip (Chromium GEM-X 3’ chip and NextGEM Chip G) along with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads using the ChromiumX instrument and subsequently underwent reverse transcription. The cDNA was recovered, cleaned, and amplified to create enough material for library preparation. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final amplification. Fluent Biosciences PIPseq v.4 Fixed cells were partitioned, and libraries generated using the PIPseq T20 3’ Single Cell RNA Kit v4.0PLUS User Guide (FB0002130 Rev 8.3). To target a recovery of 20,000 cells per sample, 8uls of a cell suspension at a concentration of approximately 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices.  Fluent Biosciences PIPseq V Sample replicates of live cells (40,000 each) were loaded into PIPs for capture and barcoding as described in PIPseq V T20 3’ Single Cell RNA kit User Guide (FB0005261). To target a recovery of 20,000 cells per sample, 8ul of 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices. Parse Evercode v3 Following the Parse protocol UMWT3300, fixed and permeabilized PBMCs were thawed, and counted using trypan blue and a hemocytometer, diluted and added to 12 wells per replicate of Plate 1 as directed by the sample loading table (48 wells total across all replicates). Following reverse transcription, cells were pooled and split an additional two times, the last of which added a barcode containing R2 and Biotin for magnetic bead enrichment Cells were pooled again, counted, and distributed into eight sublibraries each targeting under 12,500 cells where they were lysed and the biotin labelled cDNA recovered with binder beads. cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned. A portion of this cleaned product was fragmented, adapter ligated and had p5 and p7 indices added in a final PCR. Scale Biosciences Following the Scale 1020796 Rev A protocol, fixed cells at a concentration of approximately 2000 cells/ul were added to 96 wells of barcode plate 1 and well IDs documented to map back cells to their sample of origin. The cells underwent reverse transcription and were then pooled by centrifugation into a funnel. Cells were washed and then split across a 384 well ligation plate where cells were barcoded. Cells were again pooled by centrifugation, washed, and counted to assess for recovery. The cell stock was diluted to approximately 460 cells/ul and 4uls loaded into each well of the final distribution plate, with the remainder saved at -80 degrees. In the final distribution plate, the cell membrane is broken down, cDNA is tagmented with a transposase, and the library specific P5 and P7 indexes added.  Benchmark II:  5’ WT, TCR single cell comparison 10X Genomics GEM-X 5’v3 and Next GEM 5’v2 Following the 10X Genomics GEM-X 5’v3 (CG000733) and NextGEM 5’v2 (CG000331) protocols, sorted T cells were added to a reverse transcription mastermix and loaded on to a microfluidic chip (Chromium GEM-X 5’ chip and NextGEM Chip K respectively) with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads (GEMS) and subsequently underwent reverse transcription.  The cDNA was recovered and cleaned before being amplified to create enough material for library preparation for gene expression and TCR. To generate TCR libraries, a small amount of cDNA underwent 2 rounds of PCR with a set of TCR specific primers. A portion of the PCR product was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR.  Parse Evercode TCR Fixed and permeabilized T cells were thawed, counted using trpyan blue and a hemocytometer, following Parse protocol UMIT2300.  Each sample was diluted according to the sample loading table and recounted before dispensing into 12 wells per sample of Plate 1 (48 wells total). Following reverse transcription, cells were pooled and split an additional two times to add barcodes, the last pool and split also adding the R2 and biotin. Cells were pooled, counted, and distributed into eight sublibraries each targeting 12,500 cells. Cells were lysed and biotin labelled cDNA recovered with binder beads.  cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned to be usable in TCR and whole transcriptome library preparation. Whole transcription libraries undergo library preparation as described in Evercode TCR Human WT + TCR v1 (UM0018), which utilized the Parse v2 WT chemistry. The TCR library is generated from a subset of the WT cDNA in a PCR reaction targeting the V(D)J segments of the CDR3 region of the T cell.

value: PBMC

value: 10x Genomics' Chromium NextGEM 3' v3.1


title: Patient Sample, 004-059_d28_cd4

status: Public on May 27 2025

type: SRA

city: Boston

first: Alal

last: Eran

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

description: Library name: 004-059_d28_cd4

library_source: transcriptomic

data_processing:
Sequence data were demultiplexed using bcl2fastq v2 and the resulting FASTQ files were trimmed using Trimommatic version 0.39 and aligned to the human genome (GRCh38.p14) using STAR version 2.7.10a.
GENCODE 40 gene abundance was calculated using RSEM version 1.3.3, and normalized using the trimmed mean of M values (TMM) approach in edgeR version 3.40.1.
Assembly: GRCh38.p14
Supplementary files format and content: Tab delimited text files include log TMM-normalized expression for each sample.
Supplementary files format and content: CD8_8_8_PBO_logTMM_expression.txt includes samples from GSE157280 labeled according to their GSM IDs.

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
CD4+ and CD8+ T cells were sorted from blood samples obtained from hematopoietic cell transplant patients in the placebo-control arm of the ABA2 clinical trial (NCT# NCT01743131). RNA was isolated from CD4+ and CD8+ sorted T cells for each patient using the RNeasy Micro kit (Qiagen) with on-column DNase digestion, and RNA quality was assessed using an Agilent Bioanalyzer..
Two nanograms of total RNA were used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Illumina NexteraXT DNA Library Preparation kit. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq3000, yielding on average 25 million 100bp single end reads per sample.

tag: tissue

value: Blood

tag: patient id

tag: cell type

value: CD4+ T cells

tag: time

value: 28_cd4 days post hematopoietic cell transplant


title: MuMT, FFS, biol repl 2

city: PITTSBURGH

first: Leigh

middle: M

last: Miller

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: University of Pittsburgh

description:
Library name: MuMT_FFS2
Column in 2006932_FPKM.xlsx

data_processing:
Data processing was performed by MedGenome
Sequence reads were trimmed when necessary using fastq-mcf (v1.05) program and cutadapt (v2.5)
Contamination removal was performed using Bowtie2 (v2.5.1)
Raw read counts were estimated using HTSeq (v0.11.2)
Assembly: Trimmed sequences were mapped to GRCm38 reference sequence using STAR (2.7.3a)
Supplementary files format and content: Read count normalized via DESeq2 and reported as FPKM and TPM

organism: Mus musculus

source_name: Lung

extract_protocol:
Lungs were perfused priior to extraction and dissociated using collagenase media with Dnase for 1 hour followed by filtering in a 70uM filter to get a single cell suspension. Cells were rinsed with PBS and strained in a 40uM filter.  Dead cell removal was performed via negative selection using the EasySep Mouse Dead Cell Removal (Annexin V) kit. The flow through was centrifuged and resuspended in PBS (10% FBS, 1mM EDTA) and CD8+ T cells were isolated using the CD8+ T cell Isolation Kit as directed. RNA was extracted from isolated lung CD8+ T cells using TRI reagent (Zymo Research, Irvine, CA). Samples were digested on ice for 5 minutes with mechanical agitation of samples occurring 2-3 times. RNA was further extracted from samples using the Direct-zol Mini Prep kit as directed.
RNA was shipped to MedGenome for sequencing via Takara SMART-Seq mRNA kit (100 read length).

treatment_protocol: Mice were infected with 0.5-1 x 10^5 PFU of mouse-adapted influenza virus A/HKx31 H3N2 (X31) or PBS vehicle. After 54 days, the mice were rechallenged with 10^3 PFUs of a heterotypic strain of mouse-adapted influenza virus A/PR/8/34 H1N1 (PR8) or PBS vehicle. Six days after influenza virus rechallenge (day 60), the mice were challenged with 5 x 10^7 CFUs of USA300 MRSA suspended in PBS or vehicle and harvested a day later. All infections were given via oropharyngeal instillation and tissues were harvested 24 hours after MRSA challenge.

value: Lung

value: CD8 T cell

tag: genotype

value: uMT

tag: treatment

value: FFS


title: PBMC, NextGEM 3', sample F5A

description: Library name: nextgem_3p_F5A

library_source: transcriptomic single cell

molecule: polyA RNA


title: Tumor (AT3-OVA) and draining lymph node, TCR sequences

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

description:
10x Genomics
AK_AT3o_VDJ

data_processing:
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the multi subcommand to align reads to the transcriptome and obtain gene counts (GEX), align reads to a custom hashtag reference and count hastag sequences (CSP), align reads to the alpha/beta TCR reference and assemble and count clonotypes (VDJ)
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome), 10x TCR reference GRCm38-alts-ensembl-5.0.0 (VDJ)
Supplementary files format and content: Tar file of outputs from cellranger multi containing gene and antibody counts (sample_filtered_feature_bc_matrix), TCR sequences (VDJ), and hashtag reference

source_name: Tumor, LN

extract_protocol:
Tumors from untreated or anti-PDL1 and CTLA4-treated (day 12, 14, 16 after tumor inoculation) mice were harvested 18 days after tumor inoculation and finely minced using scalpel blades. Tumors were then digested enzymatically in RPMI with 1 mg/mL collagenase IV and 0.01 μg/mL DNase I for 45 minutes on a shaker at 37°C, vortexing samples midway. Digestion was stopped using cold PBS supplemented with 2% FCS. Tumor suspensions were gently mashed and filtered through a 70-μm nylon cell strainer. Lymphocytes were isolated by a 40:80 discontinuous percoll gradient centrifugation (500g, 20 minutes at 20 °C). Cells at the interface were collected and washed once prior to further use. To obtain single-cell suspensions, harvested swollen LNs (axillary and inguinal) were gently mashed and filtered through a 70-μm nylon cell strainer. CD4+ and CD19+ cell microbeads (Miltenyi Biotech) were used for negative selection and enrichment of CD8+ T cells, performed according to the manufacturer’s instructions. Single cell suspensions of CD8+ T cells from tumors and lymph nodes were stained and FACS sorted.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, tumoral and draining lymph node CD8+T cells with or without cehckpoint treatment were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM) after staining hashtag. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), the 10x Barcode and template switch oligo. And DNA from cell surface protein feature barcode conjugated to the antibody are generated simultaneously in In the same partition. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8+T cells

value: Tumor, LN

tag: strain

tag: age

value: 17-18 weeks


title: Neurons_control_3

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

description: Library name: 1-20-74

data_processing:
Sequenced reads were mapped to the Rnor6.0 version of rat genome using STAR (v. 2.7.9a) with default parameters.
For each dataset, raw read counts were obtained using FeatureCounts (v 2.0.1) with GTF file for Rnor 6.0, taken from ENSEMBL ftp. Used parameters: -T 8 -p -a Rattus_norvegicus.Rnor_6.0.101.gtf -s 0
Counts from both datasets were combined in single matrix,  normalized by “median-of-ratios” method from DESeq2 (v 1.29) R-package.
Assembly: Rnor6.0
Supplementary files format and content: tab-delimited text file, that includes normalized expression values for each sample (column).

organism: Rattus norvegicus

source_name: Primary neuron cultures

growth_protocol: Cell cultures were prepared as previously described (Borodinova et al., 2019). Briefly, Wistar rat pups were euthanized by decapitation with sharp scissors. The cortices were isolated in chilled DMEM medium supplemented with glutamine and glucose (Paneco), and gently cut into pieces with a sharp blade. Tissue fragments were treated with warm trypsin solution for 15 min at 37 °C to release the cells. To stop trypsin activity, the samples were centrifuged and washed with chilled DMEM solution. The pellet was then re-suspended in Neurobasal medium (Gibco) supplemented with 2% B-27 serum (Gibco) and alanyl-glutamine (Paneco) followed by series of mild trituration to isolate brain cells. The final concentration of isolated cells in the suspension was calculated manually in a Goryaev chamber. Approximately 0.25-0.3 million of isolated cells were plated into individual wells coated with poly-D-lysine hydrobromide (Sigma). Culture media was refreshed one hour later. Primary cortical neuron cultures were grown for two weeks in CO2 incubator (5% CO2, 37 °C), culture medium was partially refreshed every 2-3 days. HDAC inhibitors were applied on the 14th day in vitro (DIV) without washout.

extract_protocol:
total RNA was extracted using ExtractRNA reagent (Evrogen, Russia) following manufacturer’s protocol.
mRNA was purified from a total RNA mixture using oligo(dT)-coated magnetic beads, followed by mRNA fragmentation and cDNA synthesis. The synthesized cDNA was then subjected to end repair, 3’-adenylation and adapter ligation. Following amplification of cDNA fragments, the PCR products were purified using Ampure XP Beads (AGENCOURT) and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were then heat denaturated and circularized using splint oligo sequence to generate a final library of single-stranded circular DNA molecules. The library was amplified using phi29 DNA polymerase to create a DNA nanoball containing more than 300 copies of a single DNA molecule.

treatment_protocol: Two broad-spectrum histone deacetylase (HDAC) inhibitors with different chemical structures were used in the study. The HDAC inhibitor trichostatin A (TSA, 100 nM, Sigma) was applied for 19 hours as previously described (Borodinova et al., 2019). The HDAC inhibitor sodium butyrate (NaB, 5 μМ, Sigma-Aldrich) was applied for a longer time of 24 hours. Both inhibitors were applied without washout.

value: Primary neuron cultures

tag: condition

value: Wistar

tag: sample


title: MuMT, FF, biol repl 2

description:
Library name: MuMT_FF2
Column in 2006932_FPKM.xlsx

value: FF


title: MuMT, FFS, biol repl 1

description:
Library name: MuMT_FFS1
Column in 2006932_FPKM.xlsx


title: FT_SD_biol_rep3

city: Oxford

first: Raffaele

last: Sarnataro

address: 13 Mansfield Road

department: Centre for neural circuits and behaviour

country: United Kingdom

institute: University of Oxford

data_processing:
Raw transcriptomic data were pre-processed with a custom command line script {Macosko et al., 2015}{Satija et al., 2015}{Croset et al., 2018}, which extracted cell barcodes and aligned associated reads to a combination of the Drosophila melanogaster genome release BDGP6.22 and the reference sequences of the GAL4 and EGFP-p10 3’UTR transgenes, using STAR2.7 with default settings. Flybase version FB2018_03 gene names were used for annotation. The cumulative fraction of reads as a function of cell barcodes, arranged in descending order of the number of reads, was inspected, and only cells with a high number of reads, up to a clearly visible shoulder, were retained {Macosko et al., 2015)
Assembly: Drosophila melanogaster genome release BDGP6.22
Supplementary files format and content: Txt files. Digital expression matrices, with one dimension indicating individual cells, the other dimension indicating genes, and cell values indicating corresponding UMIs per cell per gene.

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Fly brains were dissected, dissociated mechanically and enzymatically, FACS sorted between the EGFP positive and negative fractions, and submitted for scRNA-sequencing
3' 10X RNA

value: Brain

value: Sleep-deprived, EGFP negative


title: FT_Rested_biol_rep3

value: Rested, EGFP negative


title: Patient Sample, 004-056_d28_cd4

description: Library name: 004-056_d28_cd4


title: PBMC, NextGEM 3', sample F1B

description: Library name: nextgem_3p_F1B

value: PBMC

value: 10x Genomics' Chromium NextGEM 3' v3.1


title: Patient Sample, 004-049_d21_cd4

description: Library name: 004-049_d21_cd4

value: Blood

value: CD4+ T cells

value: 21_cd4 days post hematopoietic cell transplant


title: MuMT, FF, biol repl 3

description:
Library name: MuMT_FF3
Column in 2006932_FPKM.xlsx

value: Lung

value: CD8 T cell


title: EGFP_SD_biol_rep3

value: Sleep-deprived, EGFP positive


title: PBMC, NextGEM 3', sample F1A

description: Library name: nextgem_3p_F1A


title: PBMC, GEM-X 3', sample F5B

description: Library name: gemx_3p_F5B

value: 10x Genomics' GEM-X 3' v4


title: FT_SD_biol_rep2


title: Patient Sample, 004-055_d21_cd4

description: Library name: 004-055_d21_cd4


title: Patient Sample, 004-046_d21_cd4

description: Library name: 004-046_d21_cd4


title: MuMT, FF, biol repl 1

description:
Library name: MuMT_FF1
Column in 2006932_FPKM.xlsx

value: uMT


title: PBMC, GEM-X 3', sample F5A

description: Library name: gemx_3p_F5A


title: EGFP_SD_biol_rep2


title: Patient Sample, 004-037_d28_cd4

description: Library name: 004-037_d28_cd4

value: 28_cd4 days post hematopoietic cell transplant


title: FT_Rested_biol_rep2


title: PDL015_slide2

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

hyb_protocol: A total of 343 unique genes were included in the analysis of this dataset. 246 genes came from an early version of the Xenium human lung base panel (PD_336) and 97 genes from a custom designed panel (CVEVZD). The custom panel was curated based on human lung single cell analysis data (Habermann et al. 2020), selecting for genes useful in cell type identification and/or with suspected involvement in IPF. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta.

data_processing: Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data in this paper was acquired on instrument software version 1.6.1.0 and analysis version xenium-1.6.0.8. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

molecule: other

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a clinician who identified areas of interest. One core from each sample was manually punched out using a puncher from the “Quick-Ray Manual Tissue Microarrayer Full Set” and a custom square-shaped 3mm tip. A custom square recipient block mold was created, and paraffin wax (VWR 76548-194) was poured to mold empty core spaces for each core in a 3x6 sample layout with one empty core for orientation. Once complete, blocks are placed face down on a clean glass slide and briefly heated in a warm drawer (~60°C) to slightly melt the paraffin together and even the block face. TMA blocks were then cooled to room temperature overnight, removed from the slide, sealed, and stored at 4°C.

extract_protocol: Sectioning was performed at 5um on a Leica RM2135 with a water float temperature of 40°C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were baked the next day at 42°C for 3 hours, then stored in a sealed dessicator at room temperature for a maximum of 10 days. Two adjacent sections were placed on Xenium slides to serve as technical replicates.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

value: 33 weeks

value: 0 weeks

value: Pulmonary hypoplasia


title: Patient Sample, 004-037_d21_cd4

description: Library name: 004-037_d21_cd4


title: PBMC, GEM-X 3', sample F1B

description: Library name: gemx_3p_F1B


title: EGFP_Rested_biol_rep3

value: Brain

value: Rested, EGFP positive


title: PBMC, GEM-X 3', sample F1A

description: Library name: gemx_3p_F1A


title: PBMC, Flex, sample F5B

description:
Library name: flex_F5B
Flex files are processed all together through cellranger to split samples. All files listed for Flex samples should be processed together

value: 10x Genomics' Fixed RNA Profiling


title: FT_SD_biol_rep1

value: Sleep-deprived, EGFP negative


title: EGFP_Rested_biol_rep2


title: PBMC, Flex, sample F5A

description:
Library name: flex_F5A
Flex files are processed all together through cellranger to split samples. All files listed for Flex samples should be processed together

value: PBMC


title: Patient Sample, 004-029_d21_cd4

description: Library name: 004-029_d21_cd4

value: Blood


title: Patient Sample, 004-046_d28_cd4

description: Library name: 004-046_d28_cd4

value: CD4+ T cells


title: Patient Sample, 004-028_d21_cd4

description: Library name: 004-028_d21_cd4

value: 21_cd4 days post hematopoietic cell transplant


title: PBMC, Flex, sample F1B

description:
Library name: flex_F1B
Flex files are processed all together through cellranger to split samples. All files listed for Flex samples should be processed together


title: Patient Sample, 004-028_d28_cd4

description: Library name: 004-028_d28_cd4


title: EGFP_SD_biol_rep1


title: EGFP_Rested_biol_rep1


title: PBMC, Flex, sample F1A

description:
Library name: flex_F1A
Flex files are processed all together through cellranger to split samples. All files listed for Flex samples should be processed together


title: PDL009_slide2

value: 28 weeks

value: 3 weeks

value: 31 weeks

value: E. coli sepsis & congenital heart disease


title: Patient Sample, 004-023_d28_cd4

description: Library name: 004-023_d28_cd4


title: Patient Sample, 004-013_d21_cd4

description: Library name: 004-013_d21_cd4


title: Patient Sample, 002-016_d28_cd4

description: Library name: 002-016_d28_cd4


title: MCF7_plusDOX_E2_ER-ChIP

city: Houston

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

library_source: genomic

data_processing:
ChIP-seq:  Reads were aligned to hg19 (GRCh37) reference genome using Bowtie2
ChIP-seq:  Spike-in normalization as previously described in Chen et al., 2015 and Egan et al., 2016 as noted in manuscript methods.
ChIP-seq:  Peaks were called by MACS v.1.4.2 with a cutoff p <= 10e-8, clonal peaks removed and any peaks overlapping "negative peaks" were also discarded
Assembly: hg19
Supplementary files format and content: Bigwig files

molecule: genomic DNA

source_name: Luminal breast carcinoma epithelial MCF-7 cells

growth_protocol: MCF7 cells were maintained in high glucose DMEM supplemented with 10% FBS.

extract_protocol:
Cells were grown in hormone-deprived media for 48 hrs before treatment for 45 min.  Crosslinking was then performed followed by chromatin extraction, sonication, and ChIP.  Crosslink reversal and chromatin isolation was performed before sequencing.
Rubicon ThruPlex DNA-Seq library preparation system (publication number R400523, protocol QAM-108-002)

treatment_protocol: DOX-inducible NF1 knock-down MCF-7 cells were seeded in phenol-red-free RPMI1640 and 10% charcoal-stripped FBS (hormone-deprived media) for 48 hrs before treatment for 45 min. Dox was added when seeding.

tag: cell line

value: Doxycycline inducible NF1 knockdown model

tag: chip antibody

value: ER (Santa Cruz, sc-8002, clone F-10)

tag: dox

value: plusDOX

value: Hormone-deprived media + E2


title: MCF7_plusDOX_E2_Input-ChIP

value: Luminal breast carcinoma epithelial MCF-7 cells


title: Sorted T-cells from PBMC, NextGEM 5' VDJ/TCR, sample F2

description: Library name: nextgem_5p_tcr_F2

value: Sorted T-cells

value: 10x Genomics' Chromium NextGEM 5′ v2


title: MCF7_plusDOX_Veh_ER-ChIP

value: Hormone-deprived media


title: Patient Sample, 002-016_d21_cd4

description: Library name: 002-016_d21_cd4


title: FT_Rested_biol_rep1

value: Brain

value: Rested, EGFP negative


title: MCF7_minusDOX_E2_ER-ChIP

value: minusDOX


title: Sorted T-cells from PBMC, NextGEM 5' VDJ/TCR, sample F1

description: Library name: nextgem_5p_tcr_F1

value: PBMC


title: Patient Sample, 002-006_d28_cd4

description: Library name: 002-006_d28_cd4

value: Blood

value: CD4+ T cells

value: 28_cd4 days post hematopoietic cell transplant


title: MCF7_plusDOX_Veh_Input-ChIP


title: Sorted T-cells from PBMC, GEM-X 5' VDJ/TCR, sample F2

description: Library name: gemx_5p_tcr_F2

value: 10x Genomics' GEM-X 5′ v3


title: Patient Sample, 002-004_d28_cd4

description: Library name: 002-004_d28_cd4


title: MCF7_minusDOX_Veh_ER-ChIP


title: Patient Sample, 002-002_d21_cd4

description: Library name: 002-002_d21_cd4

value: 21_cd4 days post hematopoietic cell transplant


title: MCF7_minusDOX_Veh_Input-ChIP

value: Doxycycline inducible NF1 knockdown model


title: Patient Sample, 004-013_d28_cd4

description: Library name: 004-013_d28_cd4


title: Patient Sample, 001-031_d28_cd4

description: Library name: 001-031_d28_cd4


title: GS.0865 (3DD-UA-GSC)_p16

city: Rotterdam

first: Martine

last: Lamfers

address: Dr. Molewaterplein 40

department: Neurosurgery

country: Netherlands

institute: Erasmus MC

description:
SORTseq
ERA-MC-27

data_processing:
Read alignment and count matrix was performed by Single Cell Discoveries, Utrecht. The poisson counting statistics corrected and UMI corrected counts were used for the analysis
Annotation of the count data with the per cell information was performed based on the FACS sorting layout of the 384-well plates
Assembly: hg38
Supplementary files format and content: Tab-separated raw counts

growth_protocol: Cells were grown in serum-free medium. Cell cultures were grown in Dulbecco’s modified Eagle’s medium-F12, supplemented with 1% Penicillin/Streptomycin, 2% B27, 20 ng/mL bFGF, 20 ng/mL EGF, and 5 μg/mL Heparin.

extract_protocol:
Cell cultures were washed with PBS and incubated with Accutase (Gibco) for 10-15 minutes, and collected in HBSS. Cells were centrifuged and resuspended in HBSS (Gibco), and subsequently sorted with FACSAria II (BD Biosciences) into 384-well plates based on single cells selection gating. Cells were then subjected to single cell transcriptomic sequencing (SORT-seq)
The libraries were constructed according to the SORTseq protocol. Briefly, single cells sorted into 384-well plates were submitted for scRNAsequencing at Single Cell Discoveries, Utrecht. Libraries were constructed based on a semi-robotized implementation of the CELseq2 library protocol, and submitted for paired-end sequencing

treatment_protocol: Untreated

value: patient-derived

value: glioblastoma

value: IDH-wildtype

tag: passage


title: GS.0865 (3DD-GSC)_p1_p5

description:
SORTseq
ERA-MC-26

value: p1 and p5


title: Patient Sample, 001-039_d28_cd4

description: Library name: 001-039_d28_cd4


title: PDL017_slide1

value: 28 weeks

value: 30 years

value: BPD (explant of adult with BPD)


title: GS.0865 (3DD-UA-GSC)_p1_p5

description:
SORTseq
ERA-MC-25

value: Brain


title: Sorted T-cells from PBMC, GEM-X 5' VDJ/TCR, sample F1

description: Library name: gemx_5p_tcr_F1

value: Sorted T-cells


title: Patient Sample, 001-031_d21_cd4

description: Library name: 001-031_d21_cd4


title: Sorted T-cells from PBMC, NextGEM 5' GEX/WT, sample F2

description: Library name: nextgem_5p_gex_F2

value: 10x Genomics' Chromium NextGEM 5′ v2


title: Patient Sample, 001-024_d21_cd4

description: Library name: 001-024_d21_cd4


title: GS.0865 (3DD-GSC)_p16

description:
SORTseq
ERA-MC-19


title: GS.0865 (3DD-UA-GSC)_p11

description:
SORTseq
ERA-MC-18


title: Patient Sample, 001-023_d28_cd4

description: Library name: 001-023_d28_cd4


title: Patient Sample, 001-026_d21_cd4

description: Library name: 001-026_d21_cd4


title: GS.0865 (3DD-GSC)_p11

description:
SORTseq
ERA-MC-17


title: PDL015_slide1

value: 33 weeks

value: 0 weeks

value: Pulmonary hypoplasia


title: MCF7_minusDOX_E2_Input-ChIP

value: Luminal breast carcinoma epithelial MCF-7 cells

value: minusDOX

value: Hormone-deprived media + E2


title: Patient Sample, 002-002_d28_cd4

description: Library name: 002-002_d28_cd4

value: Blood

value: CD4+ T cells

value: 28_cd4 days post hematopoietic cell transplant


title: PDL006_slide2

value: 24 weeks

value: Prematurity


title: Patient Sample, 001-018_d28_cd4

description: Library name: 001-018_d28_cd4


title: Sorted T-cells from PBMC, GEM-X 5' GEX/WT, sample F2

description: Library name: gemx_5p_gex_F2

value: PBMC

value: 10x Genomics' GEM-X 5′ v3


title: Patient Sample, 001-018_d21_cd4

description: Library name: 001-018_d21_cd4

value: 21_cd4 days post hematopoietic cell transplant


title: PDL009_slide1

value: 28 weeks

value: 3 weeks

value: 31 weeks

value: E. coli sepsis & congenital heart disease


title: Patient Sample, 001-017_d21_cd4

description: Library name: 001-017_d21_cd4


title: GS.0906 (3DD-UA-GSC) [ERA-MC-75]

description:
SORTseq
ERA-MC-75

value: Brain

value: patient-derived

value: glioblastoma

value: IDH-wildtype

value: p2 and p16


title: GS.0906 (3DD-GSC) [ERA-MC-74]

description:
SORTseq
ERA-MC-74

value: p1 and p16


title: Resistant HCC827 Renilla knockout cells, (HCC827-OsiR Ren KO), replicate 2

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
RNA-seq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for all samples

growth_protocol: Knockout cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Nucleospin RNA mini kit (MN).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R Kit by Macrogen company

value: lung adenocarcinoma

value: Renilla Control


title: Patient Sample, 001-015_d28_cd4

description: Library name: 001-015_d28_cd4

value: Blood

value: CD4+ T cells

value: 28_cd4 days post hematopoietic cell transplant


title: GS.0906 (3DD-UA-GSC) [ERA-MC-73]

description:
SORTseq
ERA-MC-73

value: p5 and p11


title: Resistant HCC827 JUN g2 knockout cells, (HCC827-OsiR JUN g1 KO), replicate 2

value: JUN KO


title: Patient Sample, 001-015_d21_cd4

description: Library name: 001-015_d21_cd4

value: 21_cd4 days post hematopoietic cell transplant


title: GS.0906 (3DD-GSC) [ERA-MC-72]

description:
SORTseq
ERA-MC-72


title: Resistant HCC827 Renilla knockout cells, (HCC827-OsiR Ren KO), replicate 1


title: Resistant HCC827 JUN g2 knockout cells, (HCC827-OsiR JUN g1 KO), replicate 1


title: Patient Sample, 001-013_d21_cd4

description: Library name: 001-013_d21_cd4


title: PDL005_slide1

value: 24 weeks

value: 0 weeks

value: Prematurity


title: 3D_bioreactor 3

city: Los Angeles

first: Brandon

middle: Justin

last: Blau

state: California

address: 2011 Zonal Avenue

department: Department of Surgery, Keck School of Medicine

institute: University of Southern California

data_processing:
Raw sequencing reads were firstly trimmed 2 nucleotides (nt) from the 5’ end and then secondly trimmed from both ends using a Quality Score method, in which bases with a quality score below 20 were trimmed from both ends.
Trimmed reads shorter than 25 nt were excluded from downstream analyses.
The adequate quality trimmed reads were then mapped to the human genome hg38 using STAR version 2.4.1d with default parameter settings.
Gencode v26 was used to quantify the aligned reads using the Partek E/M method. Genes with fewer than 10 reads in any sample among a data set were excluded from the analysis.
Finally, read counts per gene in all samples were offset by 1 then normalized using Upper Quartile normalization nd analyzed for differential expression using the Partek Gene Specific Analysis method.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw read counts for all samples

source_name: HepG2 cell line

growth_protocol: The cells in the bioreactor were cultured in a medium comprised of a 1:1 mixture of EMEM and DMEM from Gibco (Waltham, MA) with 10% FBS, 1% Penicillin-Streptomycin, and 1% GlutaMAX. Cultures were maintained at 37 °C, the medium recirculation rate was 23.5 mL/min, and the feed rate was 2 mL/hour. A mixture of 95% air and 5% CO2 was supplied at a flow rate of 200 mL/min. CO2 perfusion rates were adjusted, if required, to maintain a stable pH between 7.2 and 7.4. The cells in 2D culture were seeded at a density of 2.0x105 cells/cm2 in 6-well plates from BD Biosciences (Franklin Lakes, NJ). Cells were cultivated using EMEM medium. Cultures were maintained in a humidified atmosphere with 5% CO2 at 37 °C and culture medium was refreshed every two days.

extract_protocol:
Total RNA was isolated using TRIzol from Thermo Fisher Scientific (Waltham, MA) and RNA Clean & Concentrator-5 from Zymo Research (Irvine, CA) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture


title: PDL006_slide1


title: Resistant HCC827 JUN g1 knockout cells, (HCC827-OsiR JUN g1 KO), replicate 2


title: Patient Sample, 001-008_d21_cd4

description: Library name: 001-008_d21_cd4


title: 3D_bioreactor 1


title: Patient Sample, 001-005_d28_cd4

description: Library name: 001-005_d28_cd4


title: Patient Sample, 001-005_d21_cd4

description: Library name: 001-005_d21_cd4


title: 3D_bioreactor 2


title: 2D_plate 3


title: 2D_plate 2


title: Resistant HCC827 FOSL1 g2 knockout cells, (HCC827-OsiR FOSL1 g1 KO), replicate 2

value: FOSL1 KO


title: Resistant HCC827 FOSL1 g2 knockout cells, (HCC827-OsiR FOSL1 g1 KO), replicate 1


title: Patient Sample, 001-002_d28_cd4

description: Library name: 001-002_d28_cd4


title: 2D_plate 1


title: Resistant HCC827 FOSL1 g1 knockout cells, (HCC827-OsiR FOSL1 g1 KO), replicate 2


title: Chip4 Subpool4 RNA Rep 2

first: Xinshu

middle: Grace

last: Xiao

state: CA

address: 610 Charles E. Young Drive South

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description: Library name: C4Sp4R2

data_processing:
Read sequences and adaptors were extracted using UMItools (v 0.5.5). The library sequences were then aligned to the designed reference sequences using Botwtie2 (version 2.3.5), allowing up to 1 mismatch per alignment. We only retained perfectly mapped reads or reads with 1 mismatch at positions other than the designed SNPs. PCR duplicates were removed by retaining only one read with the same UMI that mapped to the same reference sequence. The UMIs were then counted in the DNA- and RNA-seq libraries, respectively. The counts were quantile-normalized across the 3 biological replicates. Sequencing data of the plasmid DNA and mRNA were compared to identify sites associated with significant expression differences between the two alleles using MPRAnalyze.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contain MPRAnalyze results

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Gibco, Cat# 11995065) with 10% FBS (Gibco, Cat# 26140079) and antibiotic-antimycotic reagent (Gibco, Cat# 15240062) at 37 °C with 5% CO2 supply.

extract_protocol:
24 hours after electroporation, HeLa cells were lysed using TRIzol (Thermo Fisher Scientific, Cat# 15596026). Each 500 μl TRIzol-lysed solution was mixed with 100 μl chloroform (Fisher Chemical, Cat# C298-500) to allow phase separation. The upper aqueous phase was transferred and mixed with equal volume ethanol (200 proof, Fisher BioReagents). The mixture was loaded to the column supplied by the Direct-zol RNA Miniprep Plus kit (Zymo Research, Cat# R2072) to isolate total RNA following the manufacturer’s protocol. PolyA selection was carried out to isolate mRNA from total RNA using Dynabeads™ Oligo(dT)25 (Thermo Fisher Scientific, Cat# 61002).
custom DNA-Seq and RNA-Seq

treatment_protocol: HeLa cells were transfected with MapUTR plasmid library via electroporation and incubated in growth media at 37 °C for 24 hours before extraction.

value: HeLa


title: tissues of  intrauterine adhesion 3

type: RNA

city: Nanjing

first: Xing

last: Chen

state: Jiangsu

address: 368 Jiangdong North Road

department: Gynecology

country: China

institute: The First Affiliated Hospital with Nanjing Medical University

description: Biological replicate 3 of 3 tissues of  intrauterine adhesion

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies)

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data
The probes detected with at least 75.0 percent in any group were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: tissues of  intrauterine adhesion

label_protocol: Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: Totally three paired IUA samples and adjacent normal samples were selected under hysteroscopy

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Tissues were immediately immersed in liquid nitrogen

value: intrauterine adhesion


title: Chip4 Subpool4 RNA Rep 3

description: Library name: C4Sp4R3


title: HeLa, shKDM4A.5, H3K9me3, ChIP

city: Montréal

first: Frédérick

middle: Antoine

last: Mallette

state: Québec

address: 5415 boul. de l'Assomption

country: Canada

institute: Université de Montréal / Hôpital Maisonneuve-Rosemont

description: Library name: HeLa_H3K9me3_shKDM4A.5

data_processing:
Raw fastq sequencing data were analyzed using FastQC (version 0.11.9). Raw reads were quality trimmed and filtered using cutadapt (version 3.5; parameters: -q 10 -m 15). Only uniquely mapping reads were used for further analysis. Reads were aligned to the human hg19 genome using BWA (v0.7.16a).
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Uterus; Cervix

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min at room temperature and quenched with 125 mM glycine. Nuclei were isolated, lysed and chromatin was sheared on a Bioruptor sonicator (Diagenode). Immunoprecipitation was performed by incubating chromatin overnight with 1.5 μg antibody at 4°C with rotation. To isolate antibody-chromatin complexes, Dynabeads (Thermo Fisher) were added to the ChIP reaction and incubated for 2 hours at 4°C with rotation. Following washes, immunoprecipitates were eluted in 1% SDS, 0.1M NaHCO3 with gentle mixing and incubation at 65°C for 1 hour. Immunoprecipitated DNA was reverse crosslinked with overnight incubation at 65°C in the presence of 0.2 M NaCl, followed by treatment with RNase A for 30 min at 37°C and with proteinase K for an additional 2 hours in the same tube. ChIP DNA was recovered by phenol-chloroform and ethanol precipitation.
Libraries were generated robotically with 10 ng of fragmented DNA (range 100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold and the size selection step was done after the PCR step. Adapters and PCR primers were purchased from Integrated DNA Technologies). Size selection was performed on a Pippin Prep instrument (SAGE Biosciences Inc).  Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip (PerkinElmer) instrument. The libraries were normalized at 2nM and pools were generated with 5 libraries per pool. The pools were denatured in 0.1N NaOH and then were diluted to 9pM using HT1 buffer. The clustering was done on a Illumina cBot and the flowcell was run on a HiSeq 2000 for 1x50 cycles (single-end mode) following the manufacturer's instructions. A phiX library was used as a control and mixed with libraries at 1% level. The Illumina control software was HCS 2.2.58, the real-time analysis program was RTA v. 1.18.64. Demultiplexing and generation of fastq reads was performed using bcl2fastq v1.8.4.

value: Uterus; Cervix

value: epithelial cell


title: Resistant HCC827 FOSL1 g1 knockout cells, (HCC827-OsiR FOSL1 g1 KO), replicate 1


title: Resistant HCC827 cells, (HCC827-OsiR), replicate 2

data_processing:
nf-core ATAC-seq pipeline was followed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for all samples

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Genomic DNA was extracted using ActiveMotif ATAC-Seq Kit following manufacturer's protocol.
ATAC libraries for ATAC-seq were prepared using ActiveMotif ATAC-Seq Kit following manufacturer's protocol.

value: Res


title: HeLa, shcontrol, H3K9me3, ChIP

description: Library name: HeLa_H3K9me3_shcontrol


title: tissues of  intrauterine adhesion 2

description: Biological replicate 2 of 3 tissues of  intrauterine adhesion


title: HeLa, shKDM4A.3, H3K9me3, ChIP

description: Library name: HeLa_H3K9me3_shKDM4A.3


title: Chip4 Subpool4 RNA Rep 1

description: Library name: C4Sp4R1


title: Resistant HCC827 JUN g1 knockout cells, (HCC827-OsiR JUN g1 KO), replicate 1

value: lung adenocarcinoma


title: Chip4 Subpool4 Pre-transfection DNA Rep 2

description: Library name: C4Sp4D2

library_source: other


title: HCC827 cells, control, replicate 2

value: WT


title: Resistant HCC827 cells, (HCC827-OsiR), replicate 1


title: HCC827 cells, control, replicate 1


title: HeLa, Input, ChIP

description: Library name: HeLa_Input


title: normal endometrium 3

description: Biological replicate 3 of 3 normal endometrium

source_name: tissues of normal endometrium

value: endometrium


title: smc5-aid HiC

status: Public on May 26 2025

city: Toulouse

first: christophe

last: chapard

address: 118 route de Narbonne

department: CBI - MCD

country: France

institute: CNRS

data_processing:
HiCstuff (www.github.com/koszullab/hicstuff) version 3.0.1; Chromosight (www.github.com/koszullab/chromosight) v1.3.1 36; Bowtie2 (version 2.3.4.1 available online at http://bowtie-bio.sourceforge.net/bowtie2/); Samtools (version 1.9 available online at http://www.htslib.org/download/); Bedtools (version 2.29.1 available online at https://bedtools.readthedocs.io/en/latest/content/installation.html); Cooler (version 0.8.7- 0.8.11 available online at https://cooler.readthedocs.io/en/latest/); bamCoverage (version 3.4.1 https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html)
Processing of the reads, computation of contact matrices, and generation of contact maps:  Reads were aligned and the contact data processed using Hicstuff, available on Github (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012). PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded. Contact maps from independent replicates were generated with the “view” function of Hicstuff, merged and normalized using the merge and balance functions of Cooler. Bins were set at 1, exp0.2 transformed, and rendered.
Computation of the contact probability as a function of genomic distance:  Computation of the contact probability as a function of genomic distance P(s) and its derivative have been determined using the “distance law” function of Hicstuff with default parameters, averaging the contact data of entire chromosome arms. P(s) from two independent replicates were determined and plotted.
For ChIP-seq analysis: Bowtie2 was used for two rounds of alignments, first on C.glabrata (CBS138) and then on S. cerevisiae allowing the generation of an alignment of IP and WCE that exclusively mapped on S. cerevisiae (an vice-versa for C.glabrata). The obtained SAM file was converted into a BAM file, sorted and indexed using Samtools. ChIP-seq profiles were then normalised by the number of million sequences and converted into BigWig using bamCoverage. Profiles were multiplied by the ORi factor (WCEglabrataIPcerevisiae / WCEcerevisiaeIPglabrata, in which WCE glabrata and IPglabrata correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads) using Integrated Genome Browser
Loop detection and scoring with Chromosight: Chromosight 1.3.1 36 was used to call loops de novo from contact maps binned at 1 kb and balanced with Cooler. Matrices were subsampled to contain the same total number of contacts.  De novo loop calling was computed using the “ detect ”  mode of Chromosight, with minimum loop length set at 2kb, percentage undetected set at 25 and pearson correlation threshold set at 0.315. Loop strength was quantified for each loop using the quantify mode of Chromosight and the mean loop score was calculated for each condition. Loop pile-up of averaged 17kb windows were generated with Chromosight. De novo loop calling and scoring were performed on independent HiC replicates, where indicated, which were subsampled independently for each experiment, using the number of contacts of the least covered map or subsampling to 20M reads. Loop score is shown as mean ± standard deviation.
Assembly: S.  cerevisiae W303: Telomere to telomere assembly, Gift from O’Donnell et al., BioRxiv 2022 ; C. glabrata: http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/current/
Supplementary files format and content: bigWig
Supplementary files format and content: cool

organism: Saccharomyces cerevisiae W303

source_name: Unicellular eukaryote

growth_protocol: cells were grown overnight in YPD

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Samples were sonicated using Covaris (DNA 300bp). For ChIP seq data: The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transfer in tubes 2mL containing glass beads before mechanical cells lysis.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

value: Unicellular eukaryote

value: smc5-aid HiC


title: smc3-aid HiC

value: smc3-aid HiC


title: HeLa, Interferon gamma, ChIP

description: Library name: HeLa_IFNg


title: WT HiC

value: WT HiC


title: Patient Sample, 001-002_d21_cd4

description: Library name: 001-002_d21_cd4

value: Blood

value: CD4+ T cells

value: 21_cd4 days post hematopoietic cell transplant


title: normal endometrium 2

description: Biological replicate 2 of 3 normal endometrium


title: tissues of  intrauterine adhesion 1

description: Biological replicate 1 of 3 tissues of  intrauterine adhesion


title: normal endometrium 1

description: Biological replicate 1 of 3 normal endometrium


title: Chip4 Subpool4 Pre-transfection DNA Rep 3

description: Library name: C4Sp4D3


title: FB219-2a, scc1-pk-aid, sys oe +IAA +oestradiol HiC

data_processing:
Reads were aligned and the contact data processed using Hicstuff, available on Github (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered
PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded.
Contact maps from independent replicates were generated with the “view” function of Hicstuff, merged and normalized using the merge and balance functions of Cooler. Bins were set at 1, exp0.2 transformed, and rendered.
For ChIP seq: Bowtie2 was used for two rounds of alignments, first on C. glabrata (CBS138) and then on S. cerevisiae allowing the generation of an alignment of IP and WCE that exclusively mapped on S. cerevisiae (an vice-versa for C. glabrata).  The obtained SAM file was converted into a BAM file, sorted and indexed using Samtools.  ChIP-seq profiles were then normalised by the number of million sequences and converted into BigWig using bamCoverage.  Profiles were multiplied by the ORi factor
Assembly: W303
Supplementary files format and content: bigwig and cool

source_name: yeast

growth_protocol: cells were grown overnight in rich media as appropriate

treatment_protocol: Cells were synchronised in G1 thanks to α-factor during 2h30. Auxin (2mM final) was added to the media for depletion when necessary. oestradiol was added for GAL genes activation where indicated. After G1 arrest cells were washed twice in fresh medium and released in appropriate rich medium containing Nocodazole and either oestradiol and or IAA where indicated for 2h. For ChIP-seq experiments: Cells were grown exponentially to OD600 = 0.5. In triplicates, 15 OD600 units of S. cerevisiae cells were mixed with 3 OD600 units of C. glabrata to a total volume of 45 mL and fixed with 4mL of fixative solution (50 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA; 30% (v/v) formaldehyde) for 30 min at room temperature (RT) with rotation. The fixative was quenched with 2mL of 2.5M glycine (RT, 5 min with rotation). The cells were then harvested by centrifugation at 3,500 rpm for 3 min and washed with ice-cold PBS

value: yeast

tag: treatments


title: Chip4 Subpool4 Pre-transfection DNA Rep 1

description: Library name: C4Sp4D1


title: HeLa, KDM4A, ChIP

description: Library name: HeLa_KDM4A


title: FB219-2a, scc1-pk-aid, sys oe +IAA HiC

description: FB219-2a, scc1-pk-aid, sys oe +IAA HiC

value: scc1-pk-aid, sys oe +IAA HiC


title: WT Pol2 Chip-seq G2 IP

description: WT Pol2 Chip-seq G2 IP

value: WT Pol2 Chip-seq G2 IP


title: PDS5-aid, Pol2 Chip-seq G2 Input

description: PDS5-aid, Pol2 Chip-seq G2 Input

value: PDS5-aid, Pol2 Chip-seq G2 Input


title: BEN15 sys oe noco HiC

description: BEN15 sys oe noco HiC

value: sys oe noco HiC


title: FB219-2a nocodazole +IAA + oestradiol from G1 HiC


title: WT Pol2 Chip-seq G2 Input

description: WT Pol2 Chip-seq G2 Input

value: WT Pol2 Chip-seq G2 Input


title: FB2456 2h cdc20 Glu HiC

description: FB2456 2h cdc20 Glu HiC

value: 2h cdc20 Glu HiC


title: FB218-4a Noco Scc1-HA IP ChIP-seq

description: FB218-4a Noco Scc1-HA IP ChIP-seq

value: Noco Scc1-HA IP ChIP-seq


title: PDS5-aid, Pol2 Chip-seq G2 IP

description: PDS5-aid, Pol2 Chip-seq G2 IP

value: PDS5-aid, Pol2 Chip-seq G2 IP


title: BEN15 sys oe noco HiC +oestradiol

description: BEN15 sys oe noco HiC +oestradiol

value: sys oe noco HiC +oestradiol


title: FB220-8c_Pds5-pk-aid, syst oe, HiC, T90

description: FB220-8c_Pds5-pk-aid, syst oe, HiC, T90

value: Pds5-pk-aid, syst oe, HiC, T90


title: W303-1A WT noco HiC +oestradiol

description: W303-1A WT noco HiC +oestradiol

value: WT noco HiC +oestradiol


title: FB2456 2h cdc20 Gal HiC

description: FB2456 2h cdc20 Gal HiC

value: 2h cdc20 Gal HiC


title: FB218-8d Noco Scc1-HA IP ChIP-seq

description: FB218-8d Noco Scc1-HA IP ChIP-seq


title: W303-1A WT noco HiC

description: W303-1A WT noco HiC

value: WT noco HiC


title: FB218-8d Noco Scc1-HA Input ChIP-seq +oestradiol

value: Noco Scc1-HA Input ChIP-seq +oestradiol


title: FB218-4a Noco Scc1-HA Input ChIP-seq +oestradiol


title: FB218-8d Noco Scc1-HA Input ChIP-seq

description: FB218-8d Noco Scc1-HA Input ChIP-seq

value: Noco Scc1-HA Input ChIP-seq


title: FB218-4a Noco Scc1-HA Input ChIP-seq

description: FB218-4a Noco Scc1-HA Input ChIP-seq


title: FB218-8d Noco Scc1-HA IP ChIP-seq +oestradiol

value: Noco Scc1-HA IP ChIP-seq +oestradiol


title: FB220-8c_Pds5-pk-aid, syst oe, HiC, T0

description: FB220-8c_Pds5-pk-aid, syst oe, HiC, T0

value: yeast

value: Pds5-pk-aid, syst oe, HiC, T0


title: FB220-2a_Pds5-pk-aid HiC, T90

description: FB220-2a_Pds5-pk-aid HiC, T90

value: Pds5-pk-aid HiC, T90


title: FB218-4a Noco Scc1-HA IP ChIP-seq +oestradiol


title: FB220-2a_Pds5-pk-aid HiC, T60

description: FB220-2a_Pds5-pk-aid HiC, T60

value: Pds5-pk-aid HiC, T60


title: FB220-2a_Pds5-pk-aid HiC, T0

description: FB220-2a_Pds5-pk-aid HiC, T0

value: Pds5-pk-aid HiC, T0


title: FB220-8c_Pds5-pk-aid, syst oe, HiC, T120

value: Pds5-pk-aid, syst oe, HiC, T120


title: ChIP-seq Input Pds5-pk-aid, syst oe, T30


title: FB220-8c_Pds5-pk-aid, syst oe, HiC, T60

description: FB220-8c_Pds5-pk-aid, syst oe, HiC, T60

value: Pds5-pk-aid, syst oe, HiC, T60


title: ChIP-seq Input Pds5-pk-aid, syst oe, T0

description: ChIP-seq Input Pds5-pk-aid, syst oe, T0

value: ChIP-seq Input Pds5-pk-aid, syst oe, T0


title: FB220-8c_Pds5-pk-aid, syst oe, HiC, T30

description: FB220-8c_Pds5-pk-aid, syst oe, HiC, T30

value: Pds5-pk-aid, syst oe, HiC, T30


title: ChIP-seq Input Pds5-pk-aid, T30

description: ChIP-seq Input Pds5-pk-aid, T30

value: ChIP-seq Input Pds5-pk-aid, T30


title: ChIP-seq Input Pds5-pk-aid, T90

description: ChIP-seq Input Pds5-pk-aid, T90

value: ChIP-seq Input Pds5-pk-aid, T90


title: ChIP-seq Input Pds5-pk-aid, T60

description: ChIP-seq Input Pds5-pk-aid, T60

value: ChIP-seq Input Pds5-pk-aid, T60


title: ChiP-seq IP Pds5-pk-aid, syst oe, T30

description: ChiP-seq IP Pds5-pk-aid, syst oe, T30

value: ChiP-seq IP Pds5-pk-aid, syst oe, T30


title: ChiP-seq IP Pds5-pk-aid, syst oe, T90

description: ChiP-seq IP Pds5-pk-aid, syst oe, T90

value: ChiP-seq IP Pds5-pk-aid, syst oe, T90


title: ChiP-seq IP Pds5-pk-aid, T0

description: ChiP-seq IP Pds5-pk-aid, T0

value: ChiP-seq IP Pds5-pk-aid, T0


title: FB220-2a_Pds5-pk-aid HiC, T120

description: FB220-2a_Pds5-pk-aid HiC, T120

value: Pds5-pk-aid HiC, T120


title: FB218-4a nocodazole +oestradiol from G1 Input Scc1-HA ChIP


title: FB220-2a_Pds5-pk-aid HiC, T30

description: FB220-2a_Pds5-pk-aid HiC, T30

value: Pds5-pk-aid HiC, T30


title: FB218-8d nocodazole +oestradiol from G1 IP pol2 ChIP

value: yeast


title: ChiP-seq IP Pds5-pk-aid, T30

description: ChiP-seq IP Pds5-pk-aid, T30

value: ChiP-seq IP Pds5-pk-aid, T30


title: FB218-4a nocodazole +oestradiol from G1 IP Scc1-HA ChIP


title: ChIP-seq Input Pds5-pk-aid, syst oe, T90


title: ChIP-seq Input Pds5-pk-aid, syst oe, T60


title: W303-1A nocodazole +IAA + oestradiol from G1 HiC


title: ChIP-seq Input Pds5-pk-aid, T0

description: ChIP-seq Input Pds5-pk-aid, T0

value: ChIP-seq Input Pds5-pk-aid, T0


title: G2 Scc1 IP Gal ChIP

description: G2 Scc1 IP Gal ChIP

value: G2 Scc1 IP Gal ChIP


title: ChiP-seq IP Pds5-pk-aid, syst oe, T60

description: ChiP-seq IP Pds5-pk-aid, syst oe, T60

value: ChiP-seq IP Pds5-pk-aid, syst oe, T60


title: yLD116-1a Pol2 Gal IP ChIP

description: yLD116-1a Pol2 Gal IP ChIP

value: Pol2 Gal IP ChIP


title: ChiP-seq IP Pds5-pk-aid, syst oe, T0

description: ChiP-seq IP Pds5-pk-aid, syst oe, T0

value: ChiP-seq IP Pds5-pk-aid, syst oe, T0


title: ChiP-seq IP Pds5-pk-aid, T90

description: ChiP-seq IP Pds5-pk-aid, T90

value: ChiP-seq IP Pds5-pk-aid, T90


title: ChiP-seq IP Pds5-pk-aid, T60

description: ChiP-seq IP Pds5-pk-aid, T60

value: ChiP-seq IP Pds5-pk-aid, T60


title: yLD116-1a Pol2 Glu IP ChIP

description: yLD116-1a Pol2 Glu IP ChIP

value: Pol2 Glu IP ChIP


title: FB218-8d nocodazole +oestradiol from G1 Input pol2 ChIP


title: RWIS-BDEV_1

city: Tokorozawa

first: Yusuke

last: Mizohata

address: Namiki 3-2

country: Japan

institute: National Defense Medical College

description: Mouse miRNA Oligo chip Ver.21 (3D-Gene, TORAY, Tokyo, Japan)

hyb_protocol: No hybridization.

scan_protocol: According to the protocol of Mouse miRNA Oligo chip (3D-Gene, TORAY, Tokyo, Japan). (This was performed by contract analysis.)

data_processing:
In each of the RWIS group (n=2) and control group (n=2), the global normalization values of the two samples that changed in the same direction and increased or decreased more than the other group were considered as candidates for microRNAs that were altered by RWIS.
Global normalization value (each value when corrected so that the median signal intensity (sum) is 25).

source_name: microRNAs obtained from BDEV

label_protocol: No labeled.

growth_protocol: Eight-week-old male C57BL/6J mice were purchased from CLEA Japan (Tokyo, Japan). Breeding conditions were 23 ± 1°C, 55 ± 10% relative humidity, light period of 5:00-19:00, free feeding and drinking. All of the mice were used after acclimatisation to the breeding environment for one week.

extract_protocol:
Extraction of BDEV-derived total RNA was performed using the miRNeasy Serum/Plasma Kit (217184, Qiagen) according to the manufacturer’s instructions. The extraction procedure was similar to the method described above, with exceptions of performing the final column wash using 80% ethanol and quality-checking of miRNAs through a bioanalyzer (2100, Agilent Technologies, Santa Clara, CA, United States) using an RNA6000 Pico Kit (5067-1513, Agilent Technologies).
First, 2.5 mL of pooled serum from eight mice was centrifuged (10,000 g, 10 min, 4 °C) to remove cell debris. The supernatant was transferred to ultracentrifuge tubes (344090, Beckman Coulter, Brea, CA, United States). Total EVs were precipitated using an Optima MAX ultracentrifuge (Beckman Coulter, Brea, CA, United States) with an MLS-50 swinging rotor at 110,000 g for 70 min at 4 °C. A pellet of whole EVs was resuspended in 250 µL of PBS containing a protease/phosphatase inhibitor (78440, Thermo, Waltham, MA, United States). Then, 100 µL of 3% BSA/PBS with 5 µg of biotinylated anti-human CD171 antibody (13-1719, eBioscience, San Diego, CA, United States) was added to the suspension of total EVs, followed by shaking (1 h, 4 °C). Subsequently, 50 µL of 3% BSA/PBS plus 125 µL of streptavidin agarose resin (20347, Thermo) was added and shaken (30 min, 4 °C). Then 500 µL of PBS was added and the supernatant was removed after centrifugation (200 g, 10 min, 4 °C). The pellet was mixed with 50 µL of 0.05 M glycine-HCl (pH 2.8) for 10 s by a mixer. Then 5 µL of 1 M Tris-HCl (pH 8.0) was added and neutralised by mixing for a few seconds. After centrifugation (200 g, 5 min, 4 °C), the supernatant was collected.

treatment_protocol: Restraint water immersion stress was used for exposing mice to acute stress. Mice were confined in 25 mL tubes and submerged chest-deep in a 37°C water bath for 1 h (7:00-8:00). Control mice were transferred to a newly prepared cage where they were allowed free movement for 1 h during the same period.

value: Brain-derived extracellular vesicles

value: water immersion


title: FB218-4a nocodazole +oestradiol from G1 IP pol2 ChIP


title: FB218-8d nocodazole +oestradiol from G1 IP Scc1-HA ChIP


title: FB220-1b nocodazole +IAA + oestradiol from G1 HiC


title: G2 Scc1 Input Gal ChIP

description: G2 Scc1 Input Gal ChIP

value: G2 Scc1 Input Gal ChIP


title: yLD116-1a Pol2 Gal Input ChIP

description: yLD116-1a Pol2 Gal Input ChIP

value: Pol2 Gal Input ChIP


title: HEK293 and NIH/3T3 cells, fomamide, no, rep1

city: qingdao

first: Xue

last: Dong

address: 238 songling road

institute: Ocean University of China

description:
Library name: sample47
mix cell, formamide (no), rep1

data_processing:
Drop-seq software
Assembly: hg38, mm10
Supplementary files format and content: GETD.summary

source_name: cell line

extract_protocol:
After tissue enzymatic digestion, the biotinylated cDNA was enriched using streptavidin-coated magnetic beads. The enriched cDNA was then amplified and prepared for sequencing
smart-seq2

value: cell line

value: HEK293 and NIH/3T3

value: wide

value: in situ reaction

tag: batch


title: FB2456 G1 Glu HiC

description: FB2456 G1 Glu HiC

value: yeast

value: G1 Glu HiC


title: FB218-4a nocodazole +oestradiol from G1 Input pol2 ChIP


title: Hela cell, nuclear,rep1

description:
Library name: sample35
Resolution, nuclear,rep1

tag: tissue

value: Hela


title: Hela cell, nuclear,rep2

description:
Library name: sample36
Resolution, nuclear,rep2


title: WM, CD4, POOL2

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

institute: Netherlands Institute for Neuroscience

description:
Library name: 105842-001-146
105842-001-146

data_processing:
Adapter sequences were trimmed using using fastp (version 0.23.2) was performed in the second dataset.
Reads were mapped to the human GRCh38.p13 genome using STAR2 (version 2.7.10) on default settings.
Feature counts of reads mapped to genes were  determined using HTSeq (version 2.0.2).
Three samples were removed due to low library size, and aberrant expression of CD4 and CD8.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited tekst file includes raw counts for each sample

source_name: WM

extract_protocol:
Primary cells were isolated, with an additional step of incubating homogenized samples before enzymatic digestion with the transcriptional inhibitor triptolide (10 μM), anisomycin (27.1 μg/ml), and actinomycin D (5 μg/ml). Sorted cells were lysed in 350 ml buffer RLT plus 1% β-mercaptoethanol and stored at -80°C until further processing. Total RNA was isolated with the RNeasy MicroKit according to the manufacturers’ instructions, and RNA sequencing was performed (GenomeScan).
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420L)

value: WM

tag: donor

value: POOL

tag: cellnr

tag: diagnosis

value: Control

tag: sekse

tag: pmd

tag: ph

tag: rqn


title: Control-BDEV_2

tag: treatment

value: control


title: FB218-8d nocodazole +oestradiol from G1 Input Scc1-HA ChIP

tag: cell type

tag: strain


title: WM, CD4, 2

description:
Library name: 105842-001-141
105842-001-141

tag: age

value: M


title: FB2456 G1 Gal HiC

description: FB2456 G1 Gal HiC

value: G1 Gal HiC


title: Control-BDEV_1

value: Brain-derived extracellular vesicles


title: WM, CD8, 2

description:
Library name: 105842-001-129
105842-001-129


title: RWIS-BDEV_2

value: water immersion


title: HEK293 and NIH/3T3 cells, fomamide, yes, rep3

description:
Library name: sample52
mix cell, formamide (yes), rep3

tag: cell line

tag: genotype


title: WM, CD8, 3

description:
Library name: 105842-001-122
105842-001-122


title: HEK293 and NIH/3T3 cells, fomamide, yes, rep2

description:
Library name: sample51
mix cell, formamide (yes), rep2


title: HEK293 and NIH/3T3 cells, fomamide, yes, rep1

description:
Library name: sample50
mix cell, formamide (yes), rep1


title: CSF, CD8, POOL

description:
Library name: 105842-001-116
105842-001-116

source_name: CSF

value: CSF


title: WM, CD8, 1

description:
Library name: 105842-001-121
105842-001-121


title: HEK293 and NIH/3T3 cells, fomamide, no, rep2

description:
Library name: sample48
mix cell, formamide (no), rep2


title: WM, CD4, 4

description:
Library name: 105842-001-109
105842-001-109

value: F


title: yLD116-1a Pol2 Glu Input ChIP

description: yLD116-1a Pol2 Glu Input ChIP

value: Pol2 Glu Input ChIP


title: TEM, CD8, 6

description:
Library name: 105842-001-108
105842-001-108

source_name: TEM

value: TEM


title: CSF, CD8, 8

description:
Library name: 105842-001-093
105842-001-093


title: TEM, CD4, 4

description:
Library name: 105842-001-082
105842-001-082


title: Hela cell, nuclear,rep3

description:
Library name: sample37
Resolution, nuclear,rep3

value: cell line

value: wide


title: CSF, CD8, 4

description:
Library name: 105842-001-083
105842-001-083


title: Hela cell, cytoplasm,rep3

description:
Library name: sample40
Resolution, cytoplasm,rep3

value: in situ reaction


title: Hela cell, cytoplasm,rep2

description:
Library name: sample39
Resolution, cytoplasm,rep2


title: TEM, CD8, POOL

description:
Library name: 105842-001-084
105842-001-084


title: Hela cell, cytoplasm,rep1

description:
Library name: sample38
Resolution, cytoplasm,rep1


title: CSF, CD4, 8

description:
Library name: 105842-001-139
105842-001-139


title: CSF, CD8, 7

description:
Library name: 105842-001-051
105842-001-051


title: TEM, CD8, 2

description:
Library name: 105842-001-048
105842-001-048


title: CSF, CD4, POOL

description:
Library name: 105842-001-079
105842-001-079


title: TEM, CD4, 5

description:
Library name: 105842-001-062
105842-001-062


title: WM, CD4, POOL1

description:
Library name: 105842-001-125
105842-001-125


title: CSF, CD8, 5

description:
Library name: 105842-001-066
105842-001-066


title: TEM, CD8, 8

description:
Library name: 105842-001-140
105842-001-140


title: TEM, CD4, POOL

description:
Library name: 105842-001-045
105842-001-045


title: HEK293 and NIH/3T3 cells, fomamide, no, rep3

description:
Library name: sample49
mix cell, formamide (no), rep3

value: HEK293 and NIH/3T3


title: WM, CD8, 5

description:
Library name: 105842-001-092
105842-001-092


title: WM, CD8, 7

description:
Library name: 105842-001-038
105842-001-038


title: TEM, CD4, 2

description:
Library name: 105842-001-044
105842-001-044


title: TEM, CD4, 6

description:
Library name: 105842-001-030
105842-001-030


title: TEM, CD8, 5

description:
Library name: 105842-001-114
105842-001-114


title: TEM, CD4, 8

description:
Library name: 105842-001-016
105842-001-016


title: CSF, CD4, 4

description:
Library name: 105842-001-068
105842-001-068


title: TEM, CD8, 4

description:
Library name: 105842-001-027
105842-001-027


title: WM, CD8, 4

description:
Library name: 105842-001-008
105842-001-008


title: TSA-seq_HeLa_HS_input_rep1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
The 150-nt paired-end sequencing was performed by NovaSeq 6000 Sequencing System. Low quality reads were trimmed by Trimmomatic (v.038), then clean reads were aligned to the human reference genome (CHM13 T2T V2.0) using Bowtie2 (v2.1.0) with default parameters. Potential PCR duplicates in the alignment were removed with the rmdup command from SAMtools (v1.5). Then the alignment files were used as the input files for TSA-seq normalization. TSA-seq normalization and TSA-seq enrichment score were calculated as proposed in the previous paper (PMID: 33355299).
Assembly: CHM13 T2T v2.0
Supplementary files format and content: bigWig

extract_protocol:
HeLa cells were grown in 15 cm dish and performed SA or HS treatments, then fixed by quickly pouring away growth media, adding freshly made 0.5 mg ml-1 DSP (Sigma-Aldrich) in PBS, and incubating at RT for 30-45 min. Cells were permeabilized with 0.5% PBST at RT for 15 min. Free aldehyde groups were quenched with 20 mM glycine in PBS at RT for 10 min. Cells were then incubated with 1.5% H2O2 in PBS at RT for 1 h. Cells were blocked with 10% formamide/2×SSC at RT for 10 min and then incubated with Digoxigenin (DIG) labeled probes targeting SatⅢ RNA at 37°C overnight. Cells were incubated with HRP conjugated anti-Dig monoclonal antibody (Abcam, 1:2,500 dilution) in 0.1% PBST at 4°C for 10-12 h. Cells were TSA-labeled with a working solution of 50% sucrose/PBS containing 0.0015% H2O2 and 25 µM tyramide-biotin at RT for 30 min. For each staining, a small portion of attached cells were scraped off and loaded onto coverslips for immunostaining to visualize the TSA labeling. Cells were briefly air-dried on the coverslip and fixed. IF of tyramide-biotin and SatⅢ RNA were performed by Streptavidin-Alexa Fluor 568 (Thermo Fisher Scientific) and Anti-Digoxigenin/Digoxin (DIG) Antibody, DyLight-488 (Vector Lab). Coverslip was mounted in mounting medium and checked by fluorescence microscopy. Cells were scrapped and transferred for subsequent processing. Cells were incubated at 37°C for 30 min to reverse the DSP crosslinks. Cell lysis was done at 55°C with 500 μg ml-1 proteinase K for 6-12 h. DNA was extracted using an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) and with an equal volume of chloroform/isoamyl alcohol (24:1). Tubes were kept at 55°C for 1 h with the cap off to evaporate phenol residues, and then were treated with 25 μg ml-1 RNaseA at 37°C for 1 h and extracted again. DNA was then precipitated with 1:10 volume of 3 M Na acetate, pH 5.2, and two volumes of 100% ethanol at -20°C for 2 h. DNA was dissolved in double-distilled H2O and sonicated to 300-500 bp. DNA was then precipitated with 1:10 volume of 3 M Na acetate, pH 5.2, and two volumes of 100% ethanol at -20°C for 2 h. DNA was dissolved in double-distilled H2O, DNA concentration was measured by NanoDrop (Thermo Fisher Scientific). 150 μl streptavidin beads were washed in 1 mL W&B buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) by rotating for 1 min. Beads were resuspended with DNA solution and rotated for 30 min at RT, then overnight at 4°C. Beads were washed with W&B buffer, TSE 500 buffer (20 mM Tris-HCl pH 8.0, 1% (v/v) Triton-X100, 0.1% (w/v) SDS, 2 mM EDTA, 500 mM NaCl), high TE buffer (10 mM Tris-HCl, 10 mM EDTA pH 8.0). Sequentially, each time removing the previous wash after immobilization of the beads on a magnetic stand. After the final wash, beads were resuspended in digestion mixture (10 mM Tris,10 mM EDTA, 0.5% SDS, 1 mg ml-1 proteinase K) overnight at 55°C with rotation. DNA was then extracted using ChIP DNA Clean & Concentrator kit (Qiagen).
The quality of the DNA samples was checked using Agilent 2100 Bioanalyzer (Agilent), after which libraries were constructed according to the Illumina TruSeq ChIP Sample Preparation guide.

value: HeLa

value: HeLa cells

value: HS stressed


title: WM, CD4, 1

description:
Library name: 105842-001-088
105842-001-088

value: WM

value: Control


title: WM, CD8, 8

description:
Library name: 105842-001-025
105842-001-025


title: CSF, CD4, 5

description:
Library name: 105842-001-005
105842-001-005


title: TSA-seq_HeLa_HS_pulldown_rep2


title: CSF, CD4, 7

description:
Library name: 105842-001-010
105842-001-010


title: Citeseq, MLN, GEX + ADT

city: Montreal

first: Laurence

last: Chapuy

state: QC

address: 3175 chemin de la Cote Sainte-Catherine

institute: Université de Montréal

description:
Library name: SAR19144
Rhapsody BD

data_processing:
FASTQ files were uploaded on the SevenBridges platform and run through the BD Rhapsody WTA pipeline to align, annotate and de-multiplex. The DBEC_MolsPerCell.csv output file was imported into Seurat (version 4.3.0.1) and normalized using sctransform with default parameters except for variables genes which were set to 4000. Genes expressed in less than 5 cells were excluded. Cells that formed clusters based on a high percentage of mitochondrial genes expressed (> 40%) were removed. No other cell nor gene filter was used. The sample identity of the cells that remained undetermined after demultiplexing was recovered using vireo algorithm (vireoSNP-0.5.727) and the identity of 96% of the undetermined cells could be recovered. Global clustering of the whole dataset (all the cell types together) was performed on the SCT assay according to the Seurat pipeline for dimensionality reduction. Specific parameters were as followed: 50 PCs, 30 neighbors with dimensions 1:20, clustering using Louvain algorithm with resolution = 1, and umap.method = umap-learn with 1:20 dimensions. Cluster annotation of the general cell types was based on common known markers. Then refined clustering of each cell type was performed by subsetting all clusters for a given type, and the raw counts of the subsetted cells were sctransform-normalized using the same parameters as described above. After conversion to an .h5ad object, the refined clustering was performed in scanpy  (except for monocytes-dendritic cells) because of the possibility to perform nested clustering without disturbing the previous satisfactory clusters. PCA was performed on centered, unscaled, SCT normalized data, with 50 PCs computed from highly variable genes computed by sctransform. The neighborhood graph was computed based on 50 PCs and 30 neighbors, and clustering was done using the leiden algorithm with a resolution =1. Based on the gene expression profile, clusters that needed to be refined were further split using the “restrict_to” parameter of the scanpy.tl.leiden( ) function. For the monocytic-dendritic population, multimodal refined clustering was performed in Seurat rather than scanpy using the combined RNA-protein expression data, because we found that the Seurat multimodal pipeline put more emphasis on the protein component than scanpy, which in the case of this particular cell type allowed for a better cluster resolution. The protein data (ADT assay of the Seurat object) was normalized using the CLR method, and then principal components (50) were computed. The multimodal neighborhood graph was computed using a combination of the SCT assay (RNA expression) and ADT assay (protein expression) computed PCs. Resulting clusters were visualized based on a umap computed from the resulting weighted.nn graph. DEGs were calculated using MAST28 and the data slot of the SCTransformed Seurat object.
Assembly: Human GRCh38/hg38
Supplementary files format and content: Comma-separated values files
Library strategy: CITE-seq

source_name: colonic mesenteric lymph nodes

extract_protocol:
Cell suspensions from fresh MLNs draining the inflamed colon were prepared by shredding MLNs as previously described26 and immediately cryopreserved in FCS, DMSO 2%.Frozen MLN samples from UC (n=3) and CD (n=3) were thawed. Cell count for viability was performed by Trypan blue exclusion and 3.5 x 106 cells from each sample were labelled with Sample Tags using the BD Single-Cell Multiplexing Kit according to the manufacturer’s protocol. After tagging, cells were pooled and labelled with FACS antibodies (Table S2) before sorting. FACS-sorted CD3+ T cells and CD19-CD3- non-B, non-T cells were pooled at a 1:2 ratio. Next, the bar-coded pooled sample was labeled with nine BD Abseq antibodies (2μl/antibody; Table S3) according to the BD protocol, washed twice and resuspended in cold BD Sample Buffer for a total of 45,000 cells in 650 μL. For whole transcriptomics experiment, the BD Rhapsody Express system was used.Cell count was performed on the BD Rhapsody Express system to check for viability before cell loading for single cell capture and cDNA synthesis. After priming the nanowell cartridge, the pooled sample was loaded onto one BD Rhapsody cartridge and incubated at room temperature for 20 minutes. Preparation, loading and washing of Cell Capture Beads, cell lysis and retrieval of Cell Capture Beads was performed according to the BD protocol. Quality control (QC) analysis by the BD Rhapsody scanner indicated a total of 8489 wells with viable cells and a bead, and a cell multiplet rate of 2%.
Libraries were prepared for 3’ whole transcriptome (WT) analysis, AbSeq and Sample Tag according to the BD mRNA WTA, AbSeq and Sample Tag library preparation protocol. Index PCRs for WTA mRNA, AbSeq and Sample Tag were performed to prepare final libraries for sequencing. After library preparation and indexing steps, PCR product cleanup was done using the Agencourt AMPure XPbeads (Beckman Coulter Life Sciences) with bead and PCR product ratios recommended by BD. QC control before sequencing was performed on the 2100 Agilent Bioanalyzer. Sample bioanalyzer trace showed PCR product size and peak in the expected range for the three libraries. Sequencing was performed at The Centre for Applied Genetics (Hospital for SickKids, Toronto, Canada). The libraries were pooled for paired-end (100bp) sequencing on the NovaSeq Illumina platform with 40,000 reads/cell for WT mRNA, 120 reads/cell for Sample Tag and 9000 (9 AbSeq x1000) reads/cell for AbSeq libraries.

value: colonic mesenteric lymph nodes


title: ICI.LP_016

city: New York

first: Madeline

last: Kim

state: NY

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

description: Library name: ICI.LP_016

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genomic features with <10 counts in at least 7 (n of smallest group) samples were filtered out (filterByExpr [edgeR R package] default parameters)
Data was then transfomed to log2-counts per million by voom-transform
Fold changes (FCHs) vs. normals and between LS (lesional) and NL (non-lesional) were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Assembly: GRCh37
Supplementary files format and content: expression matrix (csv file) of voom-transformed counts in log2 counts per million

source_name: Skin tape strip

extract_protocol:
Total RNA was extracted from skin tape stip samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 5ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragmented mRNA by reverse transcription, second strand synthesis and ligation of specific adapters.

value: Skin tape strip

tag: patient id

tag: disease

tag: tissue type

value: Non-Lesional


title: TSA-seq_HeLa_HS_input_rep2


title: ICI.LP_015

description: Library name: ICI.LP_015

tag: tissue

value: Lesional


title: ICI.LP_24NL

description: Library name: ICI.LP_24NL


title: TEM, CD4, 1

description:
Library name: 105842-001-034
105842-001-034

tag: donor

value: M


title: ICI.LP_24LS

description: Library name: ICI.LP_24LS


title: TSA-seq_HeLa_HS_pulldown_rep1


title: ATAC-seq_THP-1_UN_rep2

data_processing:
The 150-nt paired-end sequencing was performed by NovaSeq 6000 Sequencing System. Raw read qualities were evaluated by FastQC. Low quality reads from ATAC-seq were trimmed by Trimmomatic (v.038), then clean reads were mapped to the human reference genome (CHM13 T2T V2.0) using Bowtie2 (v2.3.5) with default parameters. The duplicates were eliminated by MarkDuplicates in Picard (https://broadinstitute.github.io/picard/). Tn5 offset was then adjusted using deepTools (v3.2.1) with the command “alignmentSieve --ATACshift.” Peaks were called for individual replicate using MACS2 (v2.1.2) subcommand callpeak with the following parameter combination: “callpeak -g hs --nomodel --shift -100 --extsize 200.” In these peaksets, the closest peak to TSS of each protein coding gene was selected to perform downstream analysis. DiffBind (v3.10.0) were utilized to derive consensus peaksets and conduct differential analysis between control and treatment replicates. The consensus peaks of control and treatment replicates were annotated by ChIPseeker (v1.36.0) providing information about genomic regions and flanking genes associated with each peak. After filtering out the peaks annotated as intergenic regions, the peak at promoter region is selected to represent the accessibility of each gene to profile accessibility change after treatment.
Assembly: CHM13 T2T v2.0
Supplementary files format and content: bigWig

extract_protocol:
THP-1 cells were seeded at a density of 5×105 cells ml-1 in 6-well plates and exposing the cells to 200 ng ml-1 PMA) for 24 h. After SA, HS and control treatment, cells were centrifuged for 10 min at 1,000 g (4 °C) using a swinging-bucket rotor, and the supernatant was carefully removed to avoid disturbing the cell pellet. The cells were lysed for 5 min in 50 μl of cold resuspension buffer (RS buffer, 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin). The nuclei were pelleted for 10 min at 1,000g (4 °C). The supernatant was carefully removed resuspended in 50 μl of transposition mix (16.5 μl TW buffer, 4 μl TTE Mix V50, 10 μl 5×TTBL, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween-20 and 18.5 μl double-distilled water) and incubated for 30 min at 37 °C on a thermomixer. The DNA was then purified using ATAC DNA Extract Beads according to the manufacturer’s instructions and eluted in 21 μl of elution buffer.
ATAC-seq was performed with Hyperactive ATAC-seq Library Prep Kit (Vazyme).The DNA was then purified using ATAC DNA Extract Beads according to the manufacturer’s instructions and eluted in 21 μl of elution buffer. Libraries were amplified as originally described and the final preparations were purified using ATAC DNA Clean Beads.

value: THP-1  cells

value: untreated


title: TSA-seq_HeLa_SA_input_rep2

value: SA stressed


title: ICI.Ecz_22LS

description: Library name: ICI.Ecz_22LS


title: TSA-seq_HeLa_SA_input_rep1


title: ICI.LP_006

description: Library name: ICI.LP_006


title: TSA-seq_HeLa_SA_pulldown_rep1


title: TSA-seq_HeLa_SA_pulldown_rep2


title: ICI.LP_005

description: Library name: ICI.LP_005


title: ATAC-seq_THP-1_SA_rep1


title: ATAC-seq_THP-1_HS_rep1


title: ICI.Ecz_014

description: Library name: ICI.Ecz_014


title: ATAC-seq_THP-1_UN_rep1


title: WM, CD8, 6

description:
Library name: 105842-001-013
105842-001-013

tag: cellnr


title: ICI.Ecz_23NL

description: Library name: ICI.Ecz_23NL


title: ICI.Ecz_23LS

description: Library name: ICI.Ecz_23LS


title: RNA-seq_THP-1_SA_rep2

data_processing:
The 150-nt paired-end sequencing was performed by NovaSeq 6000 Sequencing System. Raw read qualities were evaluated by FastQC. RNA-seq reads were first processed by using trimmomatic (v0.39) to remove low quality bases and adaptor sequences, and then mapped by using HISAT2 (v2.1.0, parameters: -no-softclip-score-min L, -16,0-mp 7, 7-rfg 0, 7-rdg 0,7-dta -k 1-max-seeds 20) to CHM13 T2T human reference genome with the gene annotation. The HISAT2-mapped sam files were transferred to bam format by SAMtools (v1.5). Gene expression levels were calculated with FPKM (Fragments Per Kilobase of transcript per Million mapped reads) by normalizing gene counts from featureCounts (version 1.5.1, parameters: -fraction -O -T 10 -t exon -g gene_id). Averaged FPKM of two biological replicates were used for comparison across different conditions.
Assembly: CHM13 T2T v2.0
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

extract_protocol:
HeLa, THP-1 cells and HUVEC cells were plated in 6-well plates. The next day, cells were performed untreated (UN), SA and HS treatments. Cells were washed in DPBS and prepared for RNA extraction according to the RNeasy protocol (Qiagen).
The quality of the RNA samples was checked using Agilent 2100 Bioanalyzer (Agilent), after which libraries were constructed according to the Illumina TruSeq RNA sample preparation guide.


title: ATAC-seq_THP-1_SA_rep2


title: ICI.Ecz_22NL

description: Library name: ICI.Ecz_22NL


title: RNA-seq_THP-1_SA_rep1


title: ATAC-seq_THP-1_HS_rep2


title: ICI.Ecz_018

description: Library name: ICI.Ecz_018


title: ICI.Ecz_017

description: Library name: ICI.Ecz_017


title: ICI.Ecz_012

description: Library name: ICI.Ecz_012


title: ICI.Ecz_013

description: Library name: ICI.Ecz_013


title: RNA-seq_THP-1_UN_rep1


title: Control_99

description: Library name: Control_99


title: RNA-seq_THP-1_HS_rep1


title: Control_97

description: Library name: Control_97


title: Control_87

description: Library name: Control_87


title: Control_91

description: Library name: Control_91


title: RNA-seq_HUVEC_SA_rep1

source_name: HUVEC

value: HUVEC


title: RNA-seq_HUVEC_SA_rep2


title: RNA-seq_HUVEC_HS_rep2


title: Control_81

description: Library name: Control_81


title: Control_85

description: Library name: Control_85


title: Control_77

description: Library name: Control_77


title: RNA-seq_HUVEC_HS_rep1


title: RNA-seq_THP-1_HS_rep2


title: ICI.Ecz_011

description: Library name: ICI.Ecz_011


title: RNA-seq_HUVEC_UN_rep2


title: RNA-seq_HUVEC_UN_rep1


title: Control_67

description: Library name: Control_67


title: RNA-seq_HeLa_SA_rep2


title: RNA-seq_HeLa_SA_rep1


title: RNA-seq_THP-1_UN_rep2


title: AD_58

description: Library name: AD_58

value: AD


title: AD_60

description: Library name: AD_60


title: AD_54

description: Library name: AD_54


title: RNA-seq_HeLa_HS_rep1


title: RNA-seq_HeLa_HS_rep2


title: AD_51

description: Library name: AD_51


title: AD_52

description: Library name: AD_52


title: AD_49

description: Library name: AD_49


title: RNA-seq_HeLa_UN_rep2


title: RNA-seq_HeLa_UN_rep1