title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_17

description:
Library name: FDM__01cd58__240229_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_Dechor_sample_X4
re-sequenced on Illumina NovaSeqX

data_processing:
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed using trimgalore, corrected to a whitelist allowing 1 mismatch (in PUMATAC pipeline, nextflow version: nextflow-21.04.3), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
For all samples (mouse (in house generated and commercial), fly and barnyard cell lines): Reads were mapped to reference genomes using bwa-mem2 and fragemnet files were created with create_fragments_file by the (in PUMATAC pipeline, nextflow version: nextflow-21.04.3)
For mouse samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing the Otsu threshold in PUMATAC (nextflow version: nextflow-21.04.3) were included.
For Drosophila samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing  the trhshold of TSS_enrichment >2 and number of unique fragments > 800 in PUMATAC (nextflow version: nextflow-21.04.3) were included.
Assembly: For mouse samples: mm10, for hybrid samples in the barnyard: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary files format and content: For mouse and Drosophila samples: standard tab-separated fragments files, count matrix and metadata inforamtion for cell data (barcode) and region data in tsv format
Supplementary files format and content: For barnyard: standard tab separated fragment file

extract_protocol:
Mouse: The nuclei were extracted from mouse cortex samples that were snap-frozen in liquid nitrogen and stored at -80 °C. We transferred ~1 cm3 of frozen mouse cortex to 500 μL of ice-cold homogenization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 0.1% IGEPAL CA-630, 1× complete protease inhibitor, and 1 mM DTT) in a Dounce Homogenizer. The tissue was left to thaw for 2 min before the tissue was homogenized with 10 strokes of the loose pestle and 5 strokes of the tight pestle. Before the end of a 5-minute incubation, the homogenate was filtered through a 70 μm cell strainer (Corning), and the homogenizer and strainer were washed with homogenization buffer to obtain a final volume of 1 mL. The filtrate was transferred to a 1.5 mL DNA LoBind tube (Eppendorf) and centrifuged at 500 xg for 5 minutes. The supernatant was discarded, and the pellet was topped up to 520 μL with wash buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 1× complete protease inhibitor, and 1 mM DTT) and resuspended. Next, we added 520 μL gradient medium (50% Optiprep, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 5 mM MgCl2, 75 mM sucrose, 1× complete protease inhibitor, and 1 mM DTT) and mixed the entire volume by gentle pipetting. In a 2 mL DNA LoBind tube we layered 790 μL Optiprep cushion (29% Optiprep, 31 mM Tris-HCl pH 8, 77.5 mM KCl, 15.5 mM MgCl2, 129.2 mM sucrose) at the bottom and 1040 μL of the sample on top, gently without disrupting the cushion. The tube was then centrifuged at 9000 xg for 20 minutes at 4 °C. After the centrifugation the debris on top was carefully removed with a 1 mL tip and the rest of the supernatant was also carefully removed until 50 μL was left in the tube. The pellet was gently resuspended before we mixed it with 50 μL 0.2× permeabilization buffer (20 mM Tris-HCl pH 7.5, 20 mM NaCl, 6 mM MgCl2, 0.2% Tween-20, 0.02% IGEPAL CA-630, 0.02% Digitonin, 2% BSA, and 2 mM DTT) and left the nuclei suspension for 2 minutes on ice before we stopped the permeabilization by mixing it with 1 mL of wash buffer 2 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA). The nuclei were pelleted by centrifugation at 500 xg for 5 minutes at 4 °C. The nuclei were resuspended in PBS with 0.04% BSA. For Drosophila, the nuclei were isolated by using an adapted protocol based on the nuclei isolation protocol for single-cell ATAC sequencing (10x Chromium CG000169-RevE).  Similar to mouse, for the barnyard, the cell lines were mixed to equal parts and a pellet of one million dissociated cells or fewer was incubated on ice in 200 μL of ATAC lysis buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 μM Pitstop in DMSO, 0.01% digitonin) for 5 minutes. 1 mL of ATAC nuclei wash buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm strainer (Flowmi).
Nuclei, resuspended in PBS (supplemented with 0.04% BSA), were tagmented for one hour at 37 °C in 15 μL ATAC reaction mix (10% DMF, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/µL Tn5, 70 µM Pitstop in DMSO, 0.1% Tween-20, 0,01% Digitonin). Tagmented nuclei were placed on ice and 95 µL of PCR mix (1.25× Phusion HF buffer, 15% Optiprep, 1.25 mM dNTPs, 75 mM DTT, 0.0625 U/µL Phusion HF polymerase, 0.0625 U/μL Deep Vent polymerase, 0.0125 U/μL ET SSB) was added. Next, 110 μL of nuclei mixed in PCR mix was co-encapsulated with 45 μL of HyDrop-ATACv2 beads in HFE-7500 Novac oil with EA-008 surfactant (RAN Biotech) using the Onyx microfluidics platform (Droplet Genomics). The resulting emulsion was split over two PCR tubes and was placed in a thermocycler with the following program: 72 °C – 15 mins, 98 °C – 3 mins, 12 cycles of 98 °C – 10 s; 55 °C – 30 s; 72 °C – 1 min; 72 °C – 5 mins, and finally the amplification products were cooled to 4 °C. To break the emulsion and remove excess oil, 125 μL of recovery agent (20% PFO in HFE) was added and the PCR tubes were inverted 10 times to mix before the oily phase was removed. Next, we added 180 μL GITC mix (5M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4), 10 μL Dynabeads, and 10 μL 2.4 M DTT to each of the aliquots, and mixed everything by pipetting up and down 10 times and incubating for 10 minutes. Dynabeads were pelleted on a magnet and washed twice with 80% ethanol. Elution was done in 50 μL of EB-DTT-Tween (24 mM DTT, 0.1% Tween-20 in EB (10 mM Tris-HCl pH 8.5)). Next, a 1.2× Ampure bead purification was performed according to manufacturer’s recommendations. Elution was done with 40 μL of EB-DTT (10 mM DTT in EB). The library was completed by amplifying the eluate in a total volume of 100 μL PCR mix (1× KAPA HiFi, 1 μM index i7 primer, 1 μM Universal P5 primer) with the following program: 95 °C – 3 mins, 12 cycles of 98 °C – 10 s; 63°C – 30 s; 72 °C – 1 min; 72 °C – 1 min, and finally a hold stage at 4 °C. The final libraries were subjected to 0.4×–1.2× doublesided Ampure purification and eluted in 20 μL elution buffer.

value: whole embryo

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

tag: Sex

value: pooled male and female

tag: age

value: 38 to 20h after egg laying, pooled samples


title: SYO1I_MS67_D2_RNA_R2

status: Public on Apr 02 2025

type: SRA

city: Durham

first: Yao

last: Yu

state: North Carolina

address: Medical Science Res Bldg III, 3 Genome Court

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
For samples added with spike-in controls, the fastq files were mapped to both main reference genome and spike-in genome using STAR (v.2.7.11a). Then non-primary alignment and PCR duplicates alignments were removed respectively by Samtools (v.1.10) (-F 256) and Picard ‘MarkDuplicates’ function (v.2.18.2). The scale factor used for normalization was calculated by comparing the total number of spike-in alignment reads among different groups.
For differential gene expression, the raw read counts were used and followed by DESeq analysis.
Assembly: hg38
Supplementary files format and content: Log2 fold change of gene expression using Deseq analysis and filtered by q-val<0.05

molecule: total RNA

organism: Homo sapiens

source_name: Synovial Sarcoma

growth_protocol: HSSY II and SYO1 synovial sarcoma cells were grown in DMEM high glucose medium plus 10% of FBS and 1% of antibiotics.

extract_protocol:
RNA was prepared by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
Equal amount of ERCC RNA Spike-In Mix (Thermo, 4456740) was added into all samples as spike-in control before library preparation. NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used for library preparation.

treatment_protocol: Cells were treated with 2.5 uM of DMSO or MS67 for two or four days before collection.

tag: tissue

value: Synovial Sarcoma

tag: cell line

tag: treatment

value: Treated by MS67 for 2 days


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_16

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
Library name: FDM__ff0cf3__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS2
re-sequenced on Illumina NovaSeqX

library_source: genomic single cell

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol:
Barnyard cell culture: cultured in RPMI1640 (ThermoFisher 11875093) medium supplemented with 10% FBS (ThermoFisher 10270–106), 1% penicillin/streptomycin (Life Technologies 15140122), and 10 ug/mL insulin (Sigma Aldrich I9278) and passaged twice per week. Melanoma cell lines were derived by physical resection of primary cutaneous lesions. Mouse melanoma cells were cultured in DMEM (ThermoFisher 13345364) supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. All cell lines tested negative for mycoplasma prior to use.
Mouse: The mice were housed under standard housing conditions in a pathogen-free facility with a 14 hr light, 10 hr dark light cycle from 7 to 21 hr. Mice used in the study were 60 days old.
Drosophila: All flies were raised on a yeast-based medium and kept at 25 °C on a 12h/12h day/night light cycle. For embryo collection, flies were transferred to cages fixed to a plate with a normal yeast-based medium 24 hours before embryo collection. On the day of embryo collection, the plate was exchanged for a juice plate. The juice was prepped by adding 20 g agar and 22 g sucrose to 300 ml distilled water, boiling, and then mixing in 100 ml apple juice, 10 ml 95% ethanol, and 5 ml 100% glacial acetic acid. The flies laid eggs for four hours. Sixteen hours later, the embryos aged between 16 to 20 hours were collected from the juice plate with a small brush and transferred to a 70 µm nylon mesh filter.

tag: cell type

tag: genotype

value: 37 to 20h after egg laying, pooled samples

tag: batch


title: UOK109 cells, NONO::TFE3-KO, Rep1

city: Baltimore

first: Wanlu

last: Chen

state: MD

address: 615 N. Wolfe Street

institute: Johns Hopkins University

description: i7 Index Name: v2_Ad2.1_TAAGGCGA

library_source: genomic

data_processing:
Initial steps involved trimming raw fastq files using fastp.
Subsequently, reads were aligned to the hg38 genome assembly using bowtie2 v2.5.2.
Duplicate reads in ATAC-seq data were removed using PICARD’s MarkDuplicates.
Bigwigs were generated using bedtools.
Peak calling was performed using MACS2.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak

source_name: UOK109 cells

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM, 15-013-CV, Corning) supplemented with 10% v/v fetal bovine serum (FBS, 26140079, Gibco), 1% v/v Penicillin-Streptomycin (10,000 U/mL) (15140122, Thermo Fisher), 1% v/v GlutaMAX Supplement (35050061, Thermo Fisher), and 1% v/v Mem Non Essential Amino Acids Solution (100X) (11140050, Thermo Fisher). Cells were grown at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
We used the Illumina Tagment DNA Enzyme and Buffer Kit (20034197, Illumina). We used 50,000 cells for each reaction. Upon transposition, we cleaned up the reaction using a Zymo DNA Clean and Concentrator-5 Kit (D4014, Zymo) according to the manufacturer’s protocol.
We amplified the eluted DNA using 2x NEBNext Q5 Hotstart HiFi PCR Master Mix (M0543L, NEB) for 11 cycles. We purified the amplified libraries using the Zymo DNA Clean and Concentrator-5 Kit.

treatment_protocol: Media was changed 6h before sample isolation.

value: UOK109 cells

value: Patient-derived cells harboring NONO::TFE3 fusion

value: NONO::TFE3 KO

value: baseline culturing conditions


title: b_subtilis_Z4225957206_rep3

city: Chapel Hill

first: Kevin

middle: M

last: Weeks

state: NC

address: 250 Bell Tower Drive

department: Chemistry

institute: UNC – Chemistry

data_processing:
ShapeMapper (v2.1.5) was used to align reads to the 23S rRNA (LSU) and calculate per nucleotide reactivities using the --random-primer-len option.
Assembly: ASM904v1
Supplementary files format and content: Tab-delimited file with Shapemapper profile data
Supplementary files format and content: Shapemapper 2 log data
Library strategy: Frag-Map

organism: Bacillus subtilis

growth_protocol: Bacillus subtilis subsp. subtilis strain 168 (ATCC) was grown on LB agar plates at 30 ºC. A 5 mL culture was inoculated with a single colony and grown overnight in LB media at 30 ºC, 225 rpm. A 2 mL aliquot of the culture was diluted (1:25) with LB media to create a subculture that was grown at 30 ºC, 225 rpm to OD600 ~0.5.

extract_protocol:
Cells were collected and pelleted at 3,000 xg for 10 minutes, resuspended in 250 μL lysis buffer (30 mM Tris pH 7.0, 10 mM EDTA, 10 mg/mL lysozyme), and incubated at 25 ºC for 30 minutes. Total RNA was then extracted (1 mL of TRIzol; Invitrogen) and purified with on-column DNase treatment (Monarch Total RNA Miniprep; NEB).
Click labeling and RNA enrichment. Total RNA was chemically fragmented at 94 ºC for 2 minutes to yield an average size of ~200 nucleotides (Magnesium RNA Fragmentation Module; NEB). RNA fragments were purified (silica-based SPE, using Monarch RNA Cleanup Kit; NEB).  The cross-linked RNA fragments were then labeled with magnetic azide click beads via Cu(I)-catalyzed azide–alkyne cycloaddition. The cycloaddition was generally performed with 0.5 µM of heat-denatured RNA, 0.5 µM medium magnefy azide click beads (Bang Laboritories, Inc.), 240 µM Copper(II)-TBTA complex (Lumiprobe), 500 µM fresh ascorbic acid (Sigma), and 50% v/v DMSO, in a final reaction volume of 50 µL. All reactions were sparged with nitrogen, incubated at 40 °C for 30 minutes, and finally quenched with 1 µL of 0.5 M EDTA. The cross-link RNA was enriched by resuspending the RNA four times with wash buffer (1M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.01% TWEEN-20) and a final time in nuclease-free water, the supernatant from each wash was removed via pipette after immobilizing the bead-conjugated RNA using a magnetic separation rack (NEB). MaP reverse transcription. RNA was subjected to mutational profiling reverse transcription with random nonamer primers, with the addition of robust denaturation step for rRNA analysis . Bead-conjugated RNA was mixed with 100 ng of random nonamer primer (NEB), and 20 nmol of dNTPs (NEB) and then denatured at 90 ˚C for 5 minutes followed by incubation at 4 ˚C for 2 minutes. MaP-RT buffer (6 mM MnCl2, 1 M betaine, 50 mM Tris (pH 8.0 at 25 ˚C), 75 mM KCl, and 10 mM fresh DTT) was added to the RNA solution and incubated at 25 ˚C for 2 minutes. SuperScript II Reverse Transcriptase (1 μL, 200 units; Invitrogen) was added and the reverse transcription reaction was performed according to the following temperature program: 25 °C for 10 min, 42 °C for 90 min, 10 × [50 °C for 2 min, 42 °C for 2 min], 72 °C for 10 min (Smola et al., 2015). The resulting cDNA was purified via magnetic pull-down using a magnetic separation rack (NEB). Library preparation and sequencing. Double-stranded DNA was prepared from the reverse transcription reaction product (NEBNext Ultra II Non-directional RNA Second Strand Synthesis Module; NEB) and DNA sequencing libraries were prepared using the manufacturer protocol (NEBNext Ultra II DNA Library Prep with Sample Purification; NEB). Libraries were then quantified (Qubit high-sensitivity dsDNA assay; Invitrogen and High sensitivity D1000 screentape; Agilent) and pooled as an equimolar sequencing library. The library was sequenced using 2x110 paired-end sequencing on an Illumina NextSeq 1000 instrument (P2 200 cycle sbs reagents; Illumina).

treatment_protocol: The cells were pelleted at 3,000 xg for 10 minutes, washed once with PBS, pelleted again, and then resuspended in a final volume of 25 mL PBS. Resuspended cells (5 mL) were then incubated with 200 µM fully functionalize fragment (FFF)probe for 30 minutes in the dark at 30 ºC, 225 rpm. Treated cells (5 mL) were then transferred to 6-well plates, placed on ice, and exposed to 3 J/cm2 of 365-nm-wavelength UV light over 9 minutes (Analytik Jena UVP CL-1000 equipped with five 8-W F8T5 black lights) at 10 cm from the light source.

value: Enamine Z4225957206 FFF 200 uM


title: 10% gfm-1_RNAi_rep1

city: Hangzhou

first: Xuanxuan

last: Guo

state: Zhejiang

address: No 600 Dunyu Road

country: China

institute: westlake university

data_processing:
Web-based RNA-Seq analysis platform of  WestLake University
Assembly: C.elegans WS274
Supplementary files format and content: text file inculdes raw counts for each sample
Supplementary files format and content: text file inculde RPKM values for each sample

organism: Caenorhabditis elegans

source_name: worm

extract_protocol:
RNA was harvested by TRIzol,1ug of total RNA was uesd for the construction of secquencing libraries.
RNA libraries for mRNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit following manfacturer's protocol.

value: worm

value: WT

value: 10% gfm-1 RNAi


title: SYO1_MS67_D2_RNA_R1


title: Lib2_INPUT

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
demultiplexed, filtered by transposon tag (up to 1 mismatch)
Adapter removal: BBDuk (BBMap v38.94)
Alignment/Quantification: Bio-TraDIS pipeline (v1.4.5) for each fastq file separately.
Assembly: CP037923.1, CP037924.1
Supplementary files format and content: shigella_infections_counts_neg_meta.csv.gz: count table with all non-zero insertion sites in the negative strand (summed over all fastq files), insertion sites are assigned to genes
Supplementary files format and content: shigella_infections_counts_pos_meta.csv.gz: count table with all non-zero insertion sites in the positive strand (summed over all fastq files), insertion sites are assigned to genes

organism: Shigella flexneri

growth_protocol: The Shigella flexneri Tn5 Library #2 comprising 43 sub-libraries were used to infect replicate wells containing ~800 basal-out enteroids at MOI 40 as described above. After infection, enteroids were lysed in 0.1% Na-deoxycholate by extensive pipetting. Intracellular bacterial populations were enriched ON at 30°C in 2ml LB. A diluted culture of the inoculum was also enriched and used as the input reference. A 1.5ml portion of the bacterial culture was used to extract genomic DNA.

extract_protocol:
gDNA isolation was performed using the GenElute Bacterial gDNA kit (Sigma; NA2110-1KT). 1.5ug of gDNA was cleaned with Ampure XP beads to remove EDTA. 500ng of cleaned gDNA was used as input for the sequencing library preprarations.
TraDIS library (Barquist et al., 2016 Bioinformatics)

tag: strain

value: pool of EZ-Tn5 transposase mutants

value: enriched input


title: 10% gfm-1_RNAi_rep2


title: SYO1_DMSO_D2_RNA_R1

value: Treated with DMSO for 2 days as controls


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_15

description:
Library name: FDM__48e432__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS3
no resequencing

value: whole embryo

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

value: 36 to 20h after egg laying, pooled samples


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_14

description:
Library name: FDM__af277c__240229_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_Dechor_sample_X2
re-sequenced on Illumina NovaSeqX

value: pooled male and female

value: 35 to 20h after egg laying, pooled samples


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_12

description:
Library name: FDM__79eb57__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS1
re-sequenced on Illumina NovaSeqX

value: 33 to 20h after egg laying, pooled samples


title: b_subtilis_Z4225957206_rep2


title: b_subtilis_Z4225957206_rep1


title: 10% gfm-1_RNAi_rep3


title: b_subtilis_quinoxaline_rep6

value: 6-aminoquinoxaline FFF 200 uM


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_10

description:
Library name: FDM__23c6d3__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS6
re-sequenced on Illumina NovaSeqX

value: 31 to 20h after egg laying, pooled samples


title: SYO1_DMSO_D2_RNA_R2

value: Synovial Sarcoma


title: HSSYII_MS67_D4_RNA_R2

value: HSSY II

value: Treated by MS67 for 4 days


title: b_subtilis_quinoxaline_rep5


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_9

description:
Library name: FDM__4ae8ee__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS4
no resequencing

value: 30 to 20h after egg laying, pooled samples


title: crtl_RNAi_rep2

value: worm

value: WT

value: control


title: HSSYII_DMSO_D4_RNA_R2

value: Treated by DMSO for4 days as controls


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_8

description:
Library name: FDM__5d36d3__240208_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleV1
re-sequenced on Illumina NovaSeqX

value: whole embryo

value: 27 to 20h after egg laying, pooled samples


title: b_subtilis_quinoxaline_rep4


title: PFC A46, Cohort 14, Age 5.23, 6 month EtOH 2.33

city: Winston-Salem

first: Kip

middle: D

last: Zimmerman

address: Medical Center Blvd

institute: Wake Forest School of Medicine

description:
Library name: S10251
DNA methylation

data_processing:
FastQC
Alignment to Mmul10
Bismark
PQLSeq
Assembly: Mmul10
Supplementary files format and content: Ratio of Methylated Reads over Total Reads

organism: Macaca mulatta

source_name: Prefrontal Cortex A46

extract_protocol:
Qiagen AllPrep DNA Universal Kit
SureSelect XT Human Methyl-Seq library preparation

value: Prefrontal Cortex A46

value: EtOH Naïve Tissue, Cohort 14, Age 5.23, 6 month EtOH 2.33


title: PFC A46, Cohort 14, Age 5.27, 6 month EtOH 4.31

description:
Library name: S10252
DNA methylation

value: EtOH Naïve Tissue, Cohort 14, Age 5.27, 6 month EtOH 4.31


title: HSSYII_DMSO_D4_RNA_R1

value: Treated by DMSO for 4 days as controls


title: crtl_RNAi_rep3


title: Drosophila_melanogaster_embryo_10x_v2_beads_inhouse_4

description:
Library name: FDM__440342__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS7
re-sequenced on Illumina NovaSeqX

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

value: pooled male and female

value: 25 to 20h after egg laying, pooled samples


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_7

description:
Library name: FDM__cc46ab__240208_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleV2
re-sequenced on Illumina NovaSeqX

value: 26 to 20h after egg laying, pooled samples


title: b_subtilis_linezolid_rep3

value: linezolid FFF 200 uM


title: HSSYII_MS67N2_D2_RNA_R2

value: Synovial Sarcoma

value: HSSY II

value: Treated by MS67N2 for 2 days


title: PFC A46, Cohort 14, Age 5.29, 6 month EtOH 2.98

description:
Library name: S10249
DNA methylation

value: EtOH Naïve Tissue, Cohort 14, Age 5.29, 6 month EtOH 2.98


title: b_subtilis_linezolid_rep2


title: PFC A46, Cohort 14, Age 5.39, 6 month EtOH 3.61

description:
Library name: S10248
DNA methylation

value: EtOH Naïve Tissue, Cohort 14, Age 5.39, 6 month EtOH 3.61


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_6

description:
Library name: FDM__a436c1__240208_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleV3
re-sequenced on Illumina NovaSeqX

value: whole embryo

value: 24 to 20h after egg laying, pooled samples


title: crtl_RNAi_rep1

value: worm

value: WT

value: control


title: PFC A46, Cohort 14, Age 5.25, 6 month EtOH 3.27

description:
Library name: S10247
DNA methylation

value: Prefrontal Cortex A46

value: EtOH Naïve Tissue, Cohort 14, Age 5.25, 6 month EtOH 3.27


title: PFC A46, Cohort 14, Age 5.18, 6 month EtOH 1.69

description:
Library name: S10246
DNA methylation

value: EtOH Naïve Tissue, Cohort 14, Age 5.18, 6 month EtOH 1.69


title: Drosophila_melanogaster_embryo_10x_v2_beads_inhouse_3

description:
Library name: FDM__4805c2__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS8
re-sequenced on Illumina NovaSeqX

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

value: pooled male and female

value: 23 to 20h after egg laying, pooled samples


title: HSSYII_MS67N1_D2_RNA_R2

value: Synovial Sarcoma

value: Treated with MS67N1 for 2 days


title: b_subtilis_methyl_rep6

value: methyl FFF 200 uM


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_4

description:
Library name: FDM__15d2ea__240116_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleS5
re-sequenced on Illumina NextSeq2000

value: 21 to 20h after egg laying, pooled samples


title: HSSYII_MS67_D4_RNA_R1

value: HSSY II

value: Treated by MS67 for 4 days


title: b_subtilis_methyl_rep5


title: b_subtilis_linezolid_rep1

value: linezolid FFF 200 uM


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_3

description:
Library name: FDM__8521d7__240208_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_sampleV4
re-sequenced on Illumina NovaSeqX

value: whole embryo

value: 19 to 20h after egg laying, pooled samples


title: HSSYII_MS67N1_D2_RNA_R1


title: PFC A46, Cohort 14, Age 5.33, 6 month EtOH 2.85

description:
Library name: S10244
DNA methylation

value: EtOH Naïve Tissue, Cohort 14, Age 5.33, 6 month EtOH 2.85


title: HSSYII_MS67_D2_RNA_R2

value: Treated with MS67 for 2 days


title: b_subtilis_quinoxaline_rep1

value: 6-aminoquinoxaline FFF 200 uM


title: HSSYII_MS67_D2_RNA_R1


title: PFC A46, Cohort 14, Age 5.20, 6 month EtOH 3.21

description:
Library name: S10242
DNA methylation

value: Prefrontal Cortex A46

value: EtOH Naïve Tissue, Cohort 14, Age 5.20, 6 month EtOH 3.21


title: b_subtilis_methyl_rep4


title: b_subtilis_methyl_rep3


title: HSSYII_MS67N2_D2_RNA_R1

value: Treated by MS67N2 for 2 days


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_2

description:
Library name: FDM__9d9712__240229_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_Dechor_sample_X1
re-sequenced on Illumina NovaSeqX

value: divers cells of whole Drosophila embryo

value: three DGRP fly lines (DGRP-639, DGRP-502, DGRP-409) mixed after collection for genetic diversity

value: pooled male and female

value: 18 to 20h after egg laying, pooled samples


title: Drosophila_melanogaster_embryo_10x_v2_beads_inhouse_1

description:
Library name: FDM__3a8f3b__20230622_Dros_DGRP_scATAC_sample4_16_20hAEL_Embryo
re-sequenced on Illumina NovaSeq6000 and NextSeq2000

value: 17 to 20h after egg laying, pooled samples


title: Drosophila_melanogaster_embryo_HyDrop_v2_beads_1

description:
Library name: FDM__0a2768__240229_HyDropATAC_Dros_DGRP_Embryo_16_20AEL_Dechor_sample_X3
re-sequenced on Illumina NovaSeqX

value: 16 to 20h after egg laying, pooled samples


title: HSSYII_DMSO_D2_RNA_R2

value: Synovial Sarcoma

value: HSSY II

value: Treated with DMSO for 2 days as controls


title: HSSYII_DMSO_D2_RNA_R1


title: PFC A46, Cohort 10, Age 5.02, 6 month EtOH 2.11

description:
Library name: S10211
DNA methylation

value: EtOH Naïve Tissue, Cohort 10, Age 5.02, 6 month EtOH 2.11


title: b_subtilis_methyl_rep2

value: methyl FFF 200 uM


title: PFC A46, Cohort 10, Age 5.08, 6 month EtOH 3.19

description:
Library name: S10215
DNA methylation

value: EtOH Naïve Tissue, Cohort 10, Age 5.08, 6 month EtOH 3.19


title: YO2_counts

status: Public on Apr 01 2025

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description: steady state (spf)

library_source: transcriptomic single cell

data_processing:
Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).
Rhapsody pipeline cwl runner (Alignment, quantification and quality filter)
Assembly: mm10
Supplementary files format and content: count matrix for both samples

organism: Mus musculus

source_name: Multiple tissues

extract_protocol:
Up to 60.000 sorted mouse neutrophils from different tissues were  labelled with BD® AbSeq Ab-Oligos and Sample Tags. Cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions. Basically, cells are isolated into nanowells by gravity, then cells are lysed and mRNA, AbSeq oligos and Sample tags oligos are released and captured by beads present in the nanowells. Each bead contains a unique oligo named “cell label” to identify each individual bead. All beads present in the cartridge are collected and cDNA synthesis takes place in a single reaction. At this point each cDNA, AB-Seq oligo and Sample Tag oligo is attached to its corresponding “cell label” oligo.
Three separated indexed libraries were prepared for whole transcriptome analysis, Ab-Seq analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit® fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

value: 10 weeks and 20 Months old


title: YO2_tags

description: steady state (spf)


title: YO1_tags

description: steady state (spf)


title: YO1_unidentified

description: steady state (spf)


title: complement strain (FK6768-ΔluxS-pluxS) rep3

city: wenzhou

first: Changrui

last: Qian

state: zhejiang

address: wenzhou medical university

institute: wenzhou medical university

data_processing:
The RNA-seq data of 9 samples was filtered with fastp.
The clean reads were mapped to the reference genome using HISAT2.
Expression level of gene was calculated by featureCounts.
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: FK6768 (ASM1599962v1)
Supplementary files format and content: gene_counts_matrix.txt

organism: Klebsiella pneumoniae

source_name: Bacterial cells

growth_protocol: Klebsiella pneumoniaei FK6768, FK6768-ΔluxS and  FK6768-ΔluxS-pluxS were cultured in LB medium at 37℃ with constant shaking (200 rpm) for 16 h.

extract_protocol:
Bacterial cells were pelleted and flash frozen on dry ice. Pellets were shipped to Genewiz for RNA extraction, Illumina Ribo-Zero rRNA removal, Illumina library construction, and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: b_subtilis_methyl_rep1


title: YO1_counts

description: steady state (spf)


title: luxS gene knockout strain (FK6768-ΔluxS)  rep2


title: luxS gene knockout strain (FK6768-ΔluxS)  rep1


title: luxS gene knockout strain (FK6768-ΔluxS)  rep3


title: wild type FK6768 rep3

value: wild type


title: wild type FK6768 rep2


title: complement strain (FK6768-ΔluxS-pluxS) rep1


title: PFC A46, Cohort 14, Age 5.44, 6 month EtOH 2.21

description:
Library name: S10243
DNA methylation

value: Prefrontal Cortex A46

value: EtOH Naïve Tissue, Cohort 14, Age 5.44, 6 month EtOH 2.21


title: wild type FK6768 rep1


title: I16R043h06: frontalCortex_TG_12m_4

city: Saarbrüecken

first: Julia

last: Schulze-Hentrich

address: Campus A2.4

department: Genetics/Epigenetics

institute: Saarland University

data_processing:
Sequencing data were processed with the Nf-core RNA-seq Pipeline (v3.13.0).
Read counts for all genes were determined using Rsubread (v2.12.3).
Assembly: Custom-build reference genome of the ensembl Rattus norvegicus genome (mRatBN7.2) including the human SNCA transgene
Supplementary files format and content: CSV file with raw read counts per gene identified by Ensembl gene ID

molecule: polyA RNA

organism: Rattus norvegicus

source_name: frontal cortex

extract_protocol:
Total RNA, miRNA, and DNA were simultaneously extracted using the DNA/RNA/microRNA Universal Kit (Qiagen) using the manufacturer protocol
Using the TruSeq RNA Sample Prep Kit (Illumina) and 100 ng of total RNA for each sequencing library, poly-A selected paired-end sequencing libraries (125 bp read length) were generated according to the manufacturer’s instructions.
Libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 20-35 mio reads each.

treatment_protocol: Striatal, frontocortical and, cerebellar tissue was incubated in RNAlater before storage at -80°C

value: frontal cortex

value: TG

value: 12 months


title: I16R043h05: frontalCortex_TG_12m_3


title: I16R043h07: frontalCortex_TG_12m_5


title: I16R043h02: frontalCortex_TG_12m_1


title: I16R043g07: frontalCortex_WT_12m_5

value: WT


title: I16R043g06: frontalCortex_WT_12m_4


title: I16R043g01: frontalCortex_WT_12m_1


title: I16R043g04: frontalCortex_WT_12m_2


title: I16R043h03: frontalCortex_TG_12m_2


title: I16R043f07: cerebellum_TG_12m_5

source_name: cerebellum

value: cerebellum


title: complement strain (FK6768-ΔluxS-pluxS) rep2


title: I16R043f04: cerebellum_TG_12m_2


title: I16R043f01: cerebellum_TG_12m_1


title: I16R043g05: frontalCortex_WT_12m_3


title: I16R043e03: cerebellum_WT_12m_3


title: I16R043e04: cerebellum_WT_12m_4


title: I16R043e02: cerebellum_WT_12m_2


title: I16R043f05: cerebellum_TG_12m_3


title: I16R043d04: striatum_TG_12m_3

source_name: striatum

value: striatum


title: I16R043c07: striatum_WT_12m_5


title: I16R043f06: cerebellum_TG_12m_4


title: I16R043d01: striatum_TG_12m_1


title: I16R043c06: striatum_WT_12m_4


title: I16R043d02: striatum_TG_12m_2


title: I16R043c05: striatum_WT_12m_3


title: I16R043d07: striatum_TG_12m_5


title: I16R043e06: cerebellum_WT_12m_5


title: I16R043c01: striatum_WT_12m_1


title: I16R043c02: striatum_WT_12m_2


title: I16R020h05: striatum_TG_5m_4

value: 5 months


title: I16R020h04: striatum_TG_5m_3


title: I16R020h03: striatum_TG_5m_2


title: I16R020h06: striatum_TG_5m_5


title: I16R020h02: striatum_TG_5m_1


title: I16R043d05: striatum_TG_12m_4


title: I16R020g03: striatum_WT_5m_3


title: I16R020g02: striatum_WT_5m_2


title: I16R020d04: frontalCortex_TG_5m_4


title: I16R020g01: striatum_WT_5m_1


title: I16R020d06: frontalCortex_TG_5m_5


title: I16R043e01: cerebellum_WT_12m_1


title: I16R020c04: frontalCortex_WT_5m_3


title: I16R020d01: frontalCortex_TG_5m_1


title: I16R020b04: cerebellum_TG_5m_3


title: I16R020b01: cerebellum_TG_5m_1


title: I16R020d02: frontalCortex_TG_5m_2


title: I16R020b06: cerebellum_TG_5m_5


title: I16R020a06: cerebellum_WT_5m_5


title: I16R020a05: cerebellum_WT_5m_4


title: I16R020c03: frontalCortex_WT_5m_2


title: I16R020b02: cerebellum_TG_5m_2


title: I16R020b05: cerebellum_TG_5m_4


title: I16R020a04: cerebellum_WT_5m_3


title: I16R020a02: cerebellum_WT_5m_2


title: KO2_2

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
RNA-seq reads were aligned to the rnor_6_0_gca_000001895_4 genome assembly using HISAT2
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: kidney

growth_protocol: The cells maintained in DMEM(Invitrogen) containing 10% fetal calf serum, penicillin (100 units/ml) and streptomycin (100 μg/ml). All cells were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from NRK-52E subline cells with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To knock out Erbin in NRK-52E cells, single-guide RNA (sgRNA) constructs were designed using the online CRISPR design tool (http://crispr.mit.edu/). The sgRNA expression constructs were cloned into the LentiGuide-Puro plasmid respectively. To obtain lentivirus, 293T cells were transfected with LentiGuide-Puro, the packaging plasmid psPAX2 and the VSV-G envelope plasmid pMD2.G using the Lipofectamine 2000 reagent. After infection with the lentivirus capable of expressing Cas9, the NRK-52E cell lines overexpressing Cas9 were selected using blasticidin. The Erbin knockout cell lines were then obtained after infecting with lentivirus expressing sgRNA and selecting by blasticidin and puromycin. The clones were screened at the mRNA and protein level.

value: kidney

value: proximal tubular epithelial cell

value: Erbin knockout

value: untreated


title: KO2_3


title: I16R020g05: striatum_WT_5m_5


title: I16R020g04: striatum_WT_5m_4


title: I16R020a01: cerebellum_WT_5m_1


title: I16R020c06: frontalCortex_WT_5m_5


title: NC3


title: I16R020c05: frontalCortex_WT_5m_4


title: A7r5 cells, siRNALemd3, replicate 3

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: School of Basic Medical Sciences, Peking University

data_processing:
RNA-seq raw reads were mapped to the rat genome version rn7 using TopHat (v2.1.1)73, and expression value (number of raw reads) for each gene was determined by the software HTSeq2 (v2.2.1). Normalized (using the upperquartile method) expression values and differentially expressed genes were determined by edgeR. Genes with |logFC| >1 and adjusted p-value < 0.05 in both were considered differential expressed genes (DEGs). We used the function bamCoverage in deepTools (3.5.1)74, normalized the bam files by scaling factor, Reads Per Kilobase per Million mapped reads (RPKM), to generate a BigWig file that contains RNA-seq signal (read density) at each base pair across the genome.
Assembly: rn7
Supplementary files format and content: There are the raw counts of RNA-seq and the results of edgeR.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Vazyme Biotech Co., Nanjing, China). Total RNA (1 µg) was reverse transcribed into cDNA using a reverse transcription system (Vazyme Biotech Co., Nanjing, China).
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina following manufacturers's protocols.

value: aortic thoracic smooth muscle cells

value: LEMD3 knockdown


title: I16R020d03: frontalCortex_TG_5m_3


title: NC2


title: A7r5 cells, siRNALemd3, replicate 1


title: A7r5 cells, siRNALemd3, replicate 2


title: L30_NON_RECURRENT

city: Hwasun-gun

first: S. M. ABDUS

last: SALAM

state: Jeollanam-do

address: 322 Seoyang-ro

department: Pathology

country: South Korea

institute: Chonnam National University Hwasun Hospital

description: Library name: L30

data_processing:
Illumina NovaSeq 6000 platform with paired-end reads (2 × 101 bp) using Illumina's SBS technology.Data quality was evaluated with metrics such as Q20/Q30 scores and GC content, achieving an average Q30 >95%.
Low quality reads and adapter sequence were trimmed by Trimmomatic (version 0.39)
Quantified gene were counted by FeatureCounts function from subread (version 2.0.8) package
Assembly: GRCh38
Supplementary files format and content: csv file include raw counts for each paired fastq sample

source_name: LMS

extract_protocol:
Tissue samples were sectioned at a thickness of 10-μm from FFPE blocks and mounted on glass slides for RNA extraction and analysis by Macrogen (Seoul, Republic of Korea).
Libraries were prepared with the SureSelectXT RNA Direct Reagent Kit for strand-specific RNA-Seq

value: LMS

value: cisplatin


title: L32_NON_RECURRENT

description: Library name: L32


title: A7r5 cells, siRNAscramble, replicate 3


title: A7r5 cells, siRNAscramble, replicate 2


title: L31_RECURRENT

description: Library name: L31

source_name: LMS Bx

value: LMS Bx


title: KO2_1


title: L27_NON_RECURRENT

description: Library name: L27

source_name: LMS biopsy

value: LMS biopsy


title: L24_NON_RECURRENT

description: Library name: L24


title: L28_NON_RECURRENT

description: Library name: L28

source_name: biopsy

value: biopsy


title: L26_RECURRENT

description: Library name: L26

source_name: Tracheal fenestration, tracheal mass excision, laryngeal mass diagnostic esophagoscopy, LN excision


title: L23_RECURRENT

description: Library name: L23

value: cisplatin, FP


title: NC1


title: L16_NON_RECURRENT

description: Library name: L16


title: L22_NON_RECURRENT

description: Library name: L22


title: L20_NON_RECURRENT

description: Library name: L20


title: L25_RECURRENT

description: Library name: L25


title: L17_NON_RECURRENT

description: Library name: L17


title: L18_RECURRENT

description: Library name: L18

source_name: LMS, R)partial parotidectomy

value: LMS, R)partial parotidectomy


title: L14_RECURRENT

description: Library name: L14

value: cetuximab, docetaxel, cisplatin


title: L21_NON_RECURRENT

description: Library name: L21

source_name: LMS(laser)

value: LMS(laser)


title: L12_RECURRENT

description: Library name: L12


title: A7r5 cells, siRNAscramble, replicate 1

value: WT


title: L15_NON_RECURRENT

description: Library name: L15


title: L19_NON_RECURRENT

description: Library name: L19

source_name: LMS(biopsy)

value: LMS(biopsy)

value: cetuximab


title: L11_NON_RECURRENT

description: Library name: L11

source_name: LMS Bx, stripping

value: LMS Bx, stripping

value: cisplatin, TP


title: L29_NON_RECURRENT

description: Library name: L29


title: L9_NON_RECURRENT

description: Library name: L9


title: I16R020c01: frontalCortex_WT_5m_1

value: frontal cortex

value: 5 months


title: L8_RECURRENT

description: Library name: L8


title: L7_NON_RECURRENT

description: Library name: L7


title: L5_NON_RECURRENT

description: Library name: L5


title: L4_RECURRENT

description: Library name: L4

source_name: Partial laryngectomy(laser)

value: Partial laryngectomy(laser)


title: L6_NON_RECURRENT

description: Library name: L6


title: L3_NON_RECURRENT

description: Library name: L3

value: LMS


title: L2_NON_RECURRENT

description: Library name: L2

value: cisplatin


title: L1_RECURRENT

description: Library name: L1

source_name: Total laryngectomy both neck Dissection

value: Total laryngectomy both neck Dissection


title: PBMC, OSAHS S4

city: Dali

first: Guangming

last: Wang

state: Yunnan Province

address: Center of Genetic Testing, The First Affiliated Hospital of Dali University

department: Center of Genetic Testing

description: Library name: S4

data_processing:
A series of processes were performed on the data in the FASTQ format file, such as removing low-quality sequences, removing connection contaminated sequences, removing sequences with unknown base ratios greater than 5%, and removing rRNA.
Assembly: Using the HiSAT2 alignment results, the base sequences were further assembled into transcripts using StringTie software for subsequent analysis.
Supplementary files format and content: Processed data file contains the TPM values for each sample.

source_name: peripheral blood mononuclear cell

extract_protocol:
RNA was extracted using a centrifugal column method. The E.Z.N.A.™ PX RNA Kit (omega biologics, USA) is designed for the isolation and purification of total RNA from blood samples in PAXgene whole blood RNA tubes. A Kaio K5500 Spectrophotometer (Kaio, Beijing, China) and an Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA) were used to check the purity, concentration and integrity of the RNA.
Extract 3 ug of total RNA from each sample as the starting amount to construct strand specific libraries and small RNA libraries. Ribosomal RNA was removed from the samples using the Ribo-Zero™ Magnetic Kit. The constructed library was subjected to Illumina sequencing (NEB, USA).

value: peripheral blood mononuclear cell


title: PBMC, OSAHS S3

institute: The First Affiliated Hospital of Dali University

description: Library name: S3


title: PBMC, OSAHS S5

description: Library name: S5


title: PBMC, healthy subjects Z5

description: Library name: Z5


title: PBMC, OSAHS S2

description: Library name: S2


title: PBMC, healthy subjects Z4

description: Library name: Z4


title: PBMC, OSAHS S1

description: Library name: S1


title: PBMC, healthy subjects Z2

description: Library name: Z2


title: PBMC, healthy subjects Z1

description: Library name: Z1


title: H3k4me1_3_dox_r2

city: Boston

first: Danyang

state: Massachusetts

address: 300 longwood ave

department: Cardiology

institute: Boston Children's Hospital

description: Library name: Sample62

data_processing:
Raw paired-end reads were trimmed and uniquely aligned to the reference genome hg38 using Bowtie2 (v2.3.4.3).
The mapped reads were filtered to retain reads with mapping quality of at least 30 and remove mitochondrial reads by samtools (v1.13).
After removal of PCR duplication reads by Picard tools MarkDuplicates (v 2.27.4), peaks were identified using MACS2 (v2.1.1).
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&Run

source_name: iPSC

extract_protocol:
For CUT&RUN, 500,000 cells per reaction were harvested followed by two washes in the RT Wash Buffer. Cells were incubated with concanavalin A beads then resuspend in a cold Antibody Buffer.  Cells were incubated with 1 μg of Primary Antibody. For ATAC-seq, 100,000 cells were used.
CUT&RUN was performed following the EpiCypher CUTANA protocol. ATAC-seq was performed following the Omni-ATAC protocol.

value: iPSC

value: induced pluripotent stem cells

value: Dox


title: H3k27ac_dox_c_r2

description: Library name: Sample59


title: endo_prog_en_r_r2

description: Library name: Sample57

value: no Dox


title: H3k27ac_3_dox_r2

description: Library name: Sample60


title: V5_tag_dox_cr_r2

description: Library name: Sample56


title: PBMC, healthy subjects Z3

description: Library name: Z3


title: L10_RECURRENT

description: Library name: L10


title: L13_NON_RECURRENT

description: Library name: L13

value: biopsy


title: Etv2_dox_group_r2

description: Library name: Sample55


title: H3k4me3_3_dox_r1

description: Library name: Sample53


title: H3k4me1_3_dox_r1

description: Library name: Sample54


title: H3k27ac_3_dox_r1

description: Library name: Sample52


title: V5_tag_dox_cr_r1

description: Library name: Sample50


title: D3_dox_group_c_r2

description: Library name: Sample58

data_processing:
Raw paired-end reads were trimmed and uniquely aligned to the reference genome hg38 using Bowtie2 (v2.3.4.3).
The mapped reads were filtered to retain reads with mapping quality of at least 30 and remove mitochondrial reads by samtools (v1.13).
After removal of PCR duplication reads by Picard tools MarkDuplicates (v 2.27.4), peaks were identified using MACS2 (v2.1.1).
Assembly: hg38
Supplementary files format and content: BigWig


title: H3k27ac_dox_c_r1

description: Library name: Sample48


title: Etv2_dox_group_r1

description: Library name: Sample49


title: mes_prog_r_cr_r1

description: Library name: Sample46


title: H3k27ac_3_ctrl_r2

description: Library name: Sample43


title: H3k4me1_3_ctrl_r2

description: Library name: Sample45


title: D3_dox_group_r_r1

description: Library name: Sample47


title: H3k4me3_3_dox_r2

description: Library name: Sample61


title: H3k27ac_dox_g_r2

description: Library name: Sample42


title: mes_prog_g_cr_r2

description: Library name: Sample40


title: V5_no_dox_cr_r2

description: Library name: Sample39


title: Etv2_nodox_cr_r2

description: Library name: Sample38


title: D3_nodox_ig_g_r2

description: Library name: Sample37


title: H3k27ac_dox_g_r1

description: Library name: Sample36


title: D3_dox_group_g_r2

description: Library name: Sample41


title: endo_prog_oe_r_r1

description: Library name: Sample51


title: D3_dox_group_c_r1

description: Library name: Sample35


title: H3k4me1_3_ctrl_r1

description: Library name: Sample34


title: H3k27ac_3_ctrl_r1

description: Library name: Sample32


title: Etv2_nodox_cr_r1

description: Library name: Sample29


title: V5_no_dox_cr_r1

description: Library name: Sample30


title: H3k4me3_3_ctrl_r1

description: Library name: Sample33


title: D3_dox_ig_g_r1

description: Library name: Sample31


title: NF2

city: Guangzhou

first: Yinghui

last: Zhu

state: Guangzhou

address: 651 Dongfeng Road East, Yuexiu District

institute: Sun Yat-sen University Cancer Center

description:
Library name: NF2
N2

data_processing:
After sequencing, nucleotides where the Phred score fell below 25 were trimmed and reads shorter than 36 bp were removed using trim_galore. Then, the trimmed reads were mapped to the human reference genome (hg38) using HISAT2, and gene counts were produced with featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: adjacent normal tissues

growth_protocol: Primary fibroblasts were isolated from surgically resected ESCC and adjacent normal tissues. Briefly, freshly collected tissues were promptly minced into 1 mm3 pieces and digested with 1 mg/mL collagenase IV. Following digestion, the cell suspension was washed with PBS and seeded in DMEM supplemented with 10% FBS and penicillin/streptomycin. Approximately 5 days post-seeding, cells were able to grow out from the tissue clumps. The culture medium was refreshed every three days. All cells were incubated at 37°C in a humidified 5% CO2 atmosphere. Upon reaching confluence, cells were trypsinized and passaged 1:3.

extract_protocol:
Total RNA of NFs and CAFs were extracted using TRIzol reagent. mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X).First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: adjacent normal tissues

value: primary fibroblasts


title: CAF2

description:
Library name: CAF2
T2

source_name: ESCC tissues

value: ESCC tissues


title: NF3

description:
Library name: NF3
N3


title: CAF1

description:
Library name: CAF1
T1


title: CAR1_NT_WT

first: Xinran

last: Ma

address: 28 Fuxing Road

institute: Chinese general PLA hospital

description:
Library name: Sample 10
CAR1_NT_WT

data_processing:
CLC Genomics workbench
Assembly: We aligned reads of all samples to the homo sapiens reference genome using HISAT2
Supplementary files format and content: xlsx file include counts and FKPM values for each sample

source_name: CAR-T

extract_protocol:
Total RNA was extracted from samples using Trizol reagent (Thermo Fisher) following the manufacturer’s protocol.
mRNA was enriched from 5 µg of total RNA using Dynabeads Oligo(dT) (Thermo Fisher) through two rounds of purification. The purified mRNA was fragmented using divalent cations (Magnesium RNA Fragmentation Module, NEB) at 94°C for 5–7 minutes. First-strand cDNA synthesis was performed with SuperScript™ II Reverse Transcriptase (Invitrogen), followed by second-strand synthesis using E. coli DNA polymerase I (NEB), RNase H (NEB), and dUTP Solution (Thermo Fisher) to generate U-labeled double-stranded cDNA. After A-tailing and adapter ligation (dual-indexed adapters), size selection was performed with AMPureXP beads. UDG enzyme (NEB) treatment removed U-labeled strands, and PCR amplification (8 cycles) generated the final cDNA libraries with an average insert size of 300 ± 50 bp. Paired-end sequencing (2 × 150 bp) was conducted on an Illumina Novaseq™ 6000 platform (LC-Bio Technology).

value: CAR-T

value: Ctrl

value: WT


title: CAR3_NT_CD58KO

description:
Library name: Sample 9
CAR3_NT_CD58KO


title: CAR3_NT_WT

description:
Library name: Sample 12
CAR3_NT_WT


title: CAR2_NT_WT

description:
Library name: Sample 11
CAR2_NT_WT


title: H3k4me3_3_ctrl_r2

description: Library name: Sample44


title: CAR3_DKO_CD58KO

description:
Library name: Sample 3
CAR3_DKO_CD58KO


title: CAR1_DKO_WT

description:
Library name: Sample 4
CAR1_DKO_WT


title: CAR3_DKO_WT

description:
Library name: Sample 6
CAR3_DKO_WT


title: CAR2_DKO_CD58KO

description:
Library name: Sample 2
CAR2_DKO_CD58KO


title: CAR2_DKO_WT

description:
Library name: Sample 5
CAR2_DKO_WT


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 34

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

institute: Georgia Institute of Technology

description:
Library name: GCA_92_Ce
10X genomics 3' single cell assay

data_processing:
The demultiplexing, barcoded processing and gene counts were made using Cell Ranger software count v 6.1.2
Assembly: GRCh38
Supplementary files format and content: Tab-separed values files and matrix files

source_name: cecum

extract_protocol:
Single cells were isolated from Ileum, colon and rectal biopsies of each patient using a  cold protease protocol. The biopsies were digested twice in an enzyme mix   (with Rho kinase and Caspase inhibitors in DPBS with 0.5M EDTA) for 15 mins each, followed by filtration through a 40 µm filter. Then washed with Benzonase buffer, then a second wash without Benzonase buffer filtered through 20 um filter and centrifuged at 400 g for 5 minutes. The cells were then resuspended in 200-300 µL of RPMI with 10% FBS and counted.
Single-cell encapsulation was performed using the 10X reagent mix, followed by loading the Chromium microfluidic device according to the manufacturer's instructions.
The Chromium Next GEM Single Cell 3? Reagent Kit v3.1 Dual Index was used, with a target of 10,000 cells. The barcoded libraries, made from amplified cDNA were sequenced using the Illumina NOVA S4 kit with a target of 50,000 reads per cell.

value: cecum

value: Crohn's disease

value: treatment naïve


title: CAR1_NT_CD58KO

description:
Library name: Sample 7
CAR1_NT_CD58KO


title: CAR1_DKO_CD58KO

description:
Library name: Sample 1
CAR1_DKO_CD58KO


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 34

description:
Library name: GCA_92_I
10X genomics 3' single cell assay

source_name: ileum

value: ileum


title: CAF3

description:
Library name: CAF3
T3


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 34

description:
Library name: GCA_92_R
10X genomics 3' single cell assay

source_name: rectum/rectal sigmoid

value: rectum/rectal sigmoid


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 33

description:
Library name: GCA_89_Ce
10X genomics 3' single cell assay


title: NF1

description:
Library name: NF1
N1


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 32

description:
Library name: GCA_87_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 31

description:
Library name: GCA_86_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 31

description:
Library name: GCA_86_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 32

description:
Library name: GCA_87_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 30

description:
Library name: GCA_84_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 30

description:
Library name: GCA_84_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 30

description:
Library name: GCA_84_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 29

description:
Library name: GCA_79_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 29

description:
Library name: GCA_79_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 28 sample 1

description:
Library name: GCA_77_ICV
10X genomics 3' single cell assay

source_name: ileocecal valve

value: ileocecal valve


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 28

description:
Library name: GCA_77_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 28 sample 2

description:
Library name: GCA_77_Ce
10X genomics 3' single cell assay


title: CAR2_NT_CD58KO

description:
Library name: Sample 8
CAR2_NT_CD58KO


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 27

description:
Library name: GCA_74_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 27

description:
Library name: GCA_74_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 27

description:
Library name: GCA_74_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 26

description:
Library name: GCA_72_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 26

description:
Library name: GCA_72_SC
10X genomics 3' single cell assay

source_name: sigmoid colon

value: sigmoid colon


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 24

description:
Library name: GCA_68_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 25

description:
Library name: GCA_71_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 31

description:
Library name: GCA_86_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 25

description:
Library name: GCA_71_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 23

description:
Library name: GCA_67_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 23

description:
Library name: GCA_67_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 22

description:
Library name: GCA_66_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 26

description:
Library name: GCA_72_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 24

description:
Library name: GCA_68_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 33

description:
Library name: GCA_89_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 21

description:
Library name: GCA_64_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 21

description:
Library name: GCA_64_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 21

description:
Library name: GCA_64_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 24

description:
Library name: GCA_68_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 22

description:
Library name: GCA_66_SF
10X genomics 3' single cell assay

source_name: splenic flexture

value: splenic flexture


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 20

description:
Library name: GCA_63_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 18

description:
Library name: GCA_60_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 19

description:
Library name: GCA_62_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 18

description:
Library name: GCA_60_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 29

description:
Library name: GCA_79_AC
10X genomics 3' single cell assay

source_name: ascending colon

value: ascending colon


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 18

description:
Library name: GCA_60_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 33

description:
Library name: GCA_89_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 17

description:
Library name: GCA_58_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 17

description:
Library name: GCA_58_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 17

description:
Library name: GCA_58_T
10X genomics 3' single cell assay

source_name: transverse colon

value: transverse colon


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 16 sample 2

description:
Library name: GCA_56_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 16 sample 1

description:
Library name: GCA_56_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 16

description:
Library name: GCA_56_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 15

description:
Library name: GCA_54_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 15 sample 2

description:
Library name: GCA_54_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 20

description:
Library name: GCA_63_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 14

description:
Library name: GCA_53_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 14

description:
Library name: GCA_53_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 15 sample 1

description:
Library name: GCA_54_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 13

description:
Library name: GCA_52_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 13

description:
Library name: GCA_52_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 12

description:
Library name: GCA_51_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 13

description:
Library name: GCA_52_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 20

description:
Library name: GCA_63_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 19

description:
Library name: GCA_62_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 11

description:
Library name: GCA_50_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 14

description:
Library name: GCA_53_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 11

description:
Library name: GCA_50_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 11

description:
Library name: GCA_50_C
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 12

description:
Library name: GCA_51_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 12

description:
Library name: GCA_51_Ce
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 10

description:
Library name: GCA_45_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 9

description:
Library name: GCA_49_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 10

description:
Library name: GCA_45_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 9

description:
Library name: GCA_49_DC
10X genomics 3' single cell assay

source_name: descending colon

value: descending colon


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 8

description:
Library name: GCA_48_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 9

description:
Library name: GCA_49_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 8

description:
Library name: GCA_48_T
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 8

description:
Library name: GCA_48_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 7

description:
Library name: GCA_44_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 7

description:
Library name: GCA_44_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 7

description:
Library name: GCA_44_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 6

description:
Library name: GCA_43_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 6

description:
Library name: GCA_43_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 5

description:
Library name: GCA_42_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 4

description:
Library name: GCA_40_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 4

description:
Library name: GCA_40_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 5

description:
Library name: GCA_42_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 5

description:
Library name: GCA_42_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 10

description:
Library name: GCA_45_C
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 6

description:
Library name: GCA_43_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 2

description:
Library name: GCA_32_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 1

description:
Library name: GCA_31_R
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 4

description:
Library name: GCA_40_I
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 3

description:
Library name: GCA_33_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric colon, donor 1

description:
Library name: GCA_31_A
10X genomics 3' single cell assay


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 3

description:
Library name: GCA_33_I
10X genomics 3' single cell assay


title: normal cell N8

city: Seoul

first: Seo Yeon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: Yonsei universtiy

description: Library name: N8

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to hg19 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 1.3.4d, with parameter --rf -l -o -G -A -e
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: normal cell

extract_protocol: RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold standard protocols

value: human epithelial cell

value: 8822 infection


title: normal cell N6

description: Library name: N6

value: 60190 infection


title: Rheu

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

description: Library name: Rheu

data_processing:
HTO-demultiplexed multiome data was obtained via BD Rhapsody pipeline ver. 2.2 from R1 and R2 FASTQ files and an AbSeq_TNFRSF1AB.fasta ADT reference file
Assembly: RhapRef_Human_WTA_2023-02.tar.gz
Supplementary files format and content: BD Rhapsody mRNA and ADT combined output files for each sample: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

source_name: Peripheral blood

extract_protocol:
We collected the peripheral blood into tubes containing EDTA. We isolated PBMCs using density gradient centrifugation with a density of 1.077 g/mL at 266 RCF for 30 min.
The CITE-seq was performed using the BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA), AbSeq, and Sample Tag Library Preparation Protocol

treatment_protocol: To study the effects of TNF on PBMCs, we incubated 500.000 cells with TNF at the concentration of 5 ng/µl for 6h in the complete RPMI culture medium.

value: Peripheral blood

value: PBMCs

tag: condition

value: Rheumatiod Arthritis

tag: library type

value: mRNA + ADT + HTO

tag: hto

value: BD Sample Tag 1-6 (see demultiplex data)


title: Norm

description: Library name: Norm

value: Control


title: single cell RNA seq of Homo sapiens: pediatric ileum, donor 1

description:
Library name: GCA_31_I
10X genomics 3' single cell assay

value: ileum

value: Crohn's disease

value: treatment naïve


title: normal cell N-delta

description: Library name: N-delta

value: delta CagA infection


title: normal cell NV

description: Library name: NV

value: CagA vector trasfection


title: cancer cell C8

description: Library name: C8

source_name: cancer cell

value: AGS


title: normal cell NX

description: Library name: NX

value: Empty vector transfection


title: cancer cell C6

description: Library name: C6


title: cancer cell C-delta

description: Library name: C-delta


title: cancer cell CV

description: Library name: CV


title: GBM Tumorsphere 15-88, control

first: Kibyeong

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei University

description: Library name: TS15-88_control

data_processing:
First, the raw fastqs are trimmed for adapter sequences using skewer.
Then, the trimmed read files are mapped to hg38 with STAR aligner.
Raw count table is then generated with featureCounts.
Transcrips per million (TPM) is calculated with R.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files containing transcripts per million (TPM)

source_name: Cultured glioblastoma tumorsphere

extract_protocol:
TSs were then harvested and treated with Trizol for RNA extraction. Total RNA samples were assessed using Agilent 2100 Bioanalyzer
The libraries of the samples are prepared with Illumina TruSeq RNA Library Prep Kit v2, following the manufacturer's protocol.

value: Cultured glioblastoma tumorsphere

value: control vehicle


title: single cell RNA seq of Homo sapiens: pediatric rectum, donor 3

description:
Library name: GCA_33_R
10X genomics 3' single cell assay

value: rectum/rectal sigmoid


title: GBM Tumorsphere 15-88, SPA8009-Treated

description: Library name: TS15-88_NO_5


title: GBM Tumorsphere 13-64, control

description: Library name: TS13-64_control


title: GBM Tumorsphere 13-64, SPA8009-Treated

description: Library name: TS13-64_NO_5


title: GBM Tumorsphere 15-88, SPA8007-Treated

description: Library name: TS15-88_NO_4


title: GBM Tumorsphere 13-64, SPA8007-Treated

description: Library name: TS13-64_NO_4


title: GBM Tumorsphere 13-30, control

description: Library name: TS13-30_control


title: GBM Tumorsphere 13-30, SPA8009-Treated

description: Library name: TS13-30_NO_5


title: N59, non-tumor

city: Suwon-si

first: Ji-Hye

last: Choi

state: Gyeonggi-do

address: World cup-ro

institute: Ajou university

description: Library name: N59

data_processing:
Low-quality sequence reads with PHRED scores < 30 and adapter sequences were trimmed using the Trim Galore tool and then mapped to the mouse reference genome (hg38). RNA abundance was estimated as the FPKM values using TopHat2/Cufflinks according to the GENCODE database (version v27) with default parameters.
Assembly: hg38
Supplementary files format and content: comma-deliminated txt file includes FPKM values for each sample

source_name: non-tumor

extract_protocol:
RNA was isolated from the cells using TRIzol reagent (Invitrogen).
We used 100 ng total RNA from all subjects to prepare sequencing libraries with by using the TruSeq stranded mRNA sample preparation kit(Illumina, CA, USA). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×101bp) using Illumina NovaSeq6000 platfrom.

value: non-tumor

value: head and neck cancer


title: N43, non-tumor

description: Library name: N43


title: N31, non-tumor

description: Library name: N31


title: N51, non-tumor

description: Library name: N51


title: N57, non-tumor

description: Library name: N57


title: N38, non-tumor

description: Library name: N38


title: N26, non-tumor

description: Library name: N26


title: N21, non-tumor

description: Library name: N21


title: N30, non-tumor

description: Library name: N30


title: N22, non-tumor

description: Library name: N22


title: N09, non-tumor

description: Library name: N09


title: cancer cell CC

description: Library name: CC

value: human epithelial cell


title: N06, non-tumor

description: Library name: N06


title: N07, non-tumor

description: Library name: N07


title: N04, non-tumor

description: Library name: N04


title: cancer cell CX

description: Library name: CX


title: N08, non-tumor

description: Library name: N08


title: normal cell NC

description: Library name: NC


title: N03, non-tumor

description: Library name: N03


title: C59, tumor

description: Library name: C59

source_name: tumor

value: tumor


title: C51, tumor

description: Library name: C51


title: C43, tumor

description: Library name: C43


title: C57, tumor

description: Library name: C57


title: C38, tumor

description: Library name: C38


title: C26, tumor

description: Library name: C26


title: C31, tumor

description: Library name: C31


title: C30, tumor

description: Library name: C30


title: GBM Tumorsphere 13-30, SPA8007-Treated

description: Library name: TS13-30_NO_4


title: C22, tumor

description: Library name: C22


title: C03, tumor

description: Library name: C03


title: C08, tumor

description: Library name: C08


title: C07, tumor

description: Library name: C07


title: C04, tumor

description: Library name: C04


title: 293AAV cells, sgRNA g6 9

city: Sacramento

first: Jennifer

last: Waldo

state: CA

address: 2921 Stockton Blvd

institute: UC Davis

description: Library name: G623

data_processing:
Trim galore to trim adapters
bismark was used to align bisulfite-converted genomes to hg38
samtools was used to sort the genome
Methylkit was used to analyze aligned reads
Assembly: hg38
Supplementary files format and content: csv file with filtered normalized methylation counts

growth_protocol: 293 AAV cells were maintained in DMEM supplemented with 10% FBS and 5% L-glut in a 5% CO2 incuabtor at 37C

extract_protocol:
gDNA was harvested using DNA miniprep kit (Qiagen)
Library was constructed via the UC Davis sequencing core using

treatment_protocol: Cells were transfected with CRISPRoff and an empty sgRNA vector or lead sgRNA 6, media was changed after 24hrs and cells were taken down 72hrs post-transfection

value: Human embryonic kidney cell

value: WT

value: CRISPRoff with sgRNA 14


title: 293AAV cells, sgRNA g6 7

description: Library name: G621

value: CRISPRoff with sgRNA 12


title: C21, tumor

description: Library name: C21


title: C09, tumor

description: Library name: C09


title: C06, tumor

description: Library name: C06


title: 293AAV cells, UG control 8

description: Library name: UG22

value: Unguided CRISPRoff


title: 293AAV cells, sgRNA g6 2

description: Library name: G612

value: CRISPRoff with sgRNA 7


title: 293AAV cells, UG control 7

description: Library name: UG21


title: 293AAV cells, UG control 2

description: Library name: UG12


title: 293AAV cells, UG control 1

description: Library name: UG11


title: 293AAV cells, sgRNA g6 1

description: Library name: G611

value: CRISPRoff with sgRNA 6


title: TFAP2C-HNRNPK knockout biol rep3

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital of Zurich

data_processing:
Transcript alignment was carried out using the STAR package. After normalizing the  library data (Transcripts Per Million, TPM), we conducted differential gene expression analysis using the DESeq2 package. We identified upregulated and downregulated genes considering the log2 fold change and Bonferroni-corrected p-value.
Assembly: Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30
Supplementary files format and content: Microsoft Excel Spreadsheet files include FPKM (Fragments Per Kilobase Million) for each sample

extract_protocol:
RNeasy mini kit
Illumina Truseq Total RNA (ribosomal depletion)


title: 293AAV cells, UG control 3

description: Library name: UG13


title: 293AAV cells, UG control 9

description: Library name: UG23


title: CAMD_multi_CTR_rep1_rep2_ACA_rep4_rep5

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

description:
Library name: Sample 1_2_4_5
10X Genomics

data_processing:
Demultiplexing: The project was for 10X FRP therefore the fastq.gz files requires running "cellranger multi" using the 4 different barcodes (BC001 to BC004) to further demultiplex into 4 different samples using the following barcodes:  Control samples [Sample 1: 1030,BC001,1030; Sample 2: 1071,BC002,1071]; ACA samples [Sample 4: 1075,BC003,1075; Sample 5: 1081,BC004,1081].
Data processing: Human scRNA-seq data were processed with CellRanger (7.1.0) multi pipeline based on human reference genome GRCh38. Individual feature-barcode matrices were read into R and downstream analysis was performed using the Seurat package. The four Seurat objects corresponding to the four samples were merged into a single object. Cells with at least 500 genes, less than 6,000 genes and <5% mitochondrial counts were considered for analysis, resulting in a total of 17,667 genes and 33,965 cells. Counts were normalized and log-transformed using SCTransform, while regressing out UMI counts and the percentage of mitochondrial counts. Principal Component Analysis (PCA) was performed to reduce dimensionality. Principal components (PCs) were fed to Harmony for batch correction using the donor as batch. Dimensionality reduction via UMAP and graph-based clustering were performed using the FindNeighbors and FindClusters functions, resulting in 18 clusters. Cell type assignment was manually performed based on established cell markers and signatures published in Pique-Regi et al. and Kim et al. Note that there were no neutrophils in the human data due to technical limitation of the technique where scRNA-seq data was prepared from paraffin embedded tissue. We first re-clustered the human dNK cells to exclude potential contaminants. The subclustering revealed the presence of cells expressing non-NK markers (e.g collagen genes COL1A1, COL1A2, myeloid genes CD74, SPP1, cell cycle genes MKI67, TOP2A). These cells were removed from further analysis and excluded from the UMAPs in Figure 1 and Supplementary Figure 1.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Each sample has a barcodes file, a features file and matrix file that contains the raw counts for that sample. MEX file format is used to represent the gene-barcode matrix output by CellRanger (10x Genomics). It contains: (1) matrix.mtx file: count matrix in sparse matrix format; (2) barcodes.tsv: list of barcodes for each sample; (3) features.tsv : list of genes detected in samples.
Supplementary files format and content: Samples associated with each processed data file: Sample numbers correspond to the processed data files as follows: Sample 1: End in _1; Sample 2: End in _2; Sample 4: End in _3; Sample 5: End in _4

source_name: chorioamniondecidua

extract_protocol:
Human and Rhesus extra-placental chorioamnion-decidua (CAMD) fetal membranes were collected within 30 minutes of delivery, dissected away from the placenta, and embedded in paraffin. Human CAMD cells were isolated from FFPE tissue sections for use with Chromium Fixed RNA Profiling kit (10X Genomics), according to manufacturer’s instructions. Briefly, four human FFPE CAMD blocks (Healthy, n=2 and ACA n=2) were sectioned at 25 𝜇M. 2 sections/subject were transferred to gentleMACS C tube (Miltenyi Biotech) keeping the scroll intact. Sections were deparaffinized with xylene/ethanol and then transferred to gentleMACS Octo (program 37C_FFPE_1) in dissociation enzyme mix (Liberase TH – Millipore Sigma). Pellet was filtered through a 30 𝜇M strainer (Miltenyi Biotech), washed in PBS, and cells were stained with Ethidium Homodimer-1 and counted with a Countess II FL Automated Cell Counter (ThermoFisher Scientific).
A multiplexed library was constructed using the 4BC Human Transcriptome Chromium Fixed RNA Profiling Kit (PN-1000475; 10X Genomics) according to the manufacturer’s protocol, according to the following specifications: Probes were incubated with single cell suspensions for 20 hrs at 42C. 11 cycles were used for the sample index PCR. The multiplexed library was sequenced on the NovaSeq6000 using the NovaSeq S1 100 cycle flowcell.

treatment_protocol: n/a; observational preterm birth samples later characterized as with or without histologic acute chorioamnionitis

value: chorioamniondecidua

value: chorioamniondecidua cells


title: Clpxfl/fl; Zp3-Cre  ovulated oocyte-CKO3

city: Shenzhen

first: Renwu

last: Hua

address: Haiyuan 1st Road

institute: HKU-SZH

description:
Library name: SAMPLE 14
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: CLPX_CKO3 Read Count/CLPX_CKO3 FRKM

data_processing:
Related bioinformatic analyses were carried out on the Dr.Tom system (https://biosys.bgi.com).
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FRKM for each Sample

source_name: Ovulated oocyte

extract_protocol:
Delivered single-cell samples, which are stored in cell lysis buffer, are processed to cell lysis by PCR instrument.
The reaction system is configured for reverse transcription. First-strand cDNA is synthesized with SMART-SeqII. The reaction system is configured for PCR amplification to process preamplification of cDNAs.

value: Ovulated oocyte

value: Clpxfl/fl; Zp3-Cre

value: CLPX conditional knockout


title: TFAP2C-HNRNPK knockout biol rep2


title: TFAP2C-HNRNPK knockout biol rep1


title: Clpxfl/fl; Zp3-Cre  ovulated oocyte-CKO2

description:
Library name: SAMPLE 13
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: CLPX_CKO2 Read Count/CLPX_CKO2 FRKM


title: Clpxfl/fl; Zp3-Cre  ovulated oocyte-CKO1

description:
Library name: SAMPLE 12
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: CLPX_CKO1 Read Count/CLPX_CKO1 FRKM


title: NT-TFAP2C knockout biol rep1


title: NT-TFAP2C knockout biol rep3


title: 293AAV cells, sgRNA g6 8

description: Library name: G622

value: CRISPRoff with sgRNA 13


title: Clpxfl/f  ovulated oocyte- WT3

description:
Library name: SAMPLE 11
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: CLPX_WT3 Read Count/CLPX_WT3 FRKM

value: Clpxfl/fl


title: Clpxfl/f  ovulated oocyte- WT2

description:
Library name: SAMPLE 10
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: CLPX_WT2 Read Count/CLPX_WT2 FRKM


title: Clpxfl/fl; Zp3-Cre  GV oocyte-CKO4

description:
Library name: SAMPLE 8
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_CKO4 Read Count/CLPX_CKO4 FRKM

source_name: GV oocyte

value: GV oocyte


title: NT3-HNRNPK knockout biol rep1


title: 293AAV cells, sgRNA g6 3

description: Library name: G613

value: CRISPRoff with sgRNA 8


title: NT3-HNRNPK knockout biol rep3


title: Clpxfl/fl; Zp3-Cre  GV oocyte-CKO3

description:
Library name: SAMPLE 7
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_CKO3 Read Count/CLPX_CKO3 FRKM


title: NT3-NT double non-targeting CTRL biol rep3


title: Clpxfl/fl; Zp3-Cre  GV oocyte-CKO2

description:
Library name: SAMPLE 6
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_CKO2 Read Count/CLPX_CKO2 FRKM


title: SVS_DAY14_hnRNPK__biol rep2

data_processing:
For all samples, quality of reads was checked with FastQC. Reads were aligned to the Human Brunello CRISPR ablation pooled library with targeted gene symbols. Reads were counted with the featureCounts function from the R package Rsubread. Differential expression analysis was performed with the R package EdgeR, using a generalized linear model with Trimmed Means of M-values (TMM) normalization. For the clustering analysis, the hclust function from the stats package was used.
Assembly: Human Brunello CRISPR ablation pooled library
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Library strategy: CRISPR screen

extract_protocol:
The extraction of the genomic DNA (gDNA). Briefly, the gDNA was harvested from each of the collected sample using the Zymo Research Quick-gDNA MidiPrep (Zymo Research) according to the manufacture’s protocol.
To amplify the sgRNAs for NGS, a PCR reaction was set up for 23 cycles in 96  PCR plates (Sarstedt). Each gDNA sample was processed by using a mix of 8 P5 primers in combination with 1 unique P7 primer. For the purification of the amplified product, the PCR reaction was mixed with 5 volumes of DNA Binding Buffer (Zymo Research), transferred in the Zymo-Spin V column with Reservoir (Zymo Research) and centrifuged at 500 RCF for 5 minutes at room temperature. The column was washed twice with 2 ml DNA Wash Buffer (Zymo Research) by a second step of centrifugation. The column was transferred to a 2 ml collection tube at spined again at maximum speed for 1 minutes to remove residual wash buffer and finally the purified PCR reaction was eluted with Nuclease-Free Water (Invitrogen). The PCR product was quantified from agarose gel.


title: Clpxfl/fl; Zp3-Cre  GV oocyte-CKO1

description:
Library name: SAMPLE 5
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_CKO1 Read Count/CLPX_CKO1 FRKM


title: SVS_DAY1_biol rep2


title: SVS_DAY14_NT__biol rep2


title: NT3-NT double non-targeting CTRL biol rep1


title: Clpxfl/fl GV oocyte-WT3

description:
Library name: SAMPLE 3
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_WT3 Read Count/CLPX_WT3 FRKM


title: SVS_DAY14_NT__biol rep1


title: Clpxfl/fl GV oocyte-WT2

description:
Library name: SAMPLE 2
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_WT2 Read Count/CLPX_WT2 FRKM


title: SVS_DAY14_hnRNPK__biol rep1


title: SVS_DAY1_biol rep1


title: Clpxfl/fl GV oocyte-WT4

description:
Library name: SAMPLE 4
Column name in  GV oocyte RNA read count.txt/GV oocyte RNA FRKM.txt : CLPX_WT4 Read Count/CLPX_WT4 FRKM


title: Clpxfl/fl GV oocyte-WT1

description:
Library name: SAMPLE 1
Column name in  GV oocyte RNA read count.txt GV oocyte RNA FRKM.txt : CLPX_WT1 Read Count/CLPX_WT1 FRKM


title: THP-1, M0+LPS+IFN-γ+iMSCs, rep4

first: Liang

last: Chen

address: No.22, Zhongguancun South Avenue, Haidian District

department: Department of Periodontology

institute: Peking University School and Hospital of Stomatology

description:
Library name: Sample 16
M1-CM-4

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to human genome (GRCh38) using the Hisat2. HTseq was used to get gene counts and FPKM method was used to determine the gene expression.
Assembly: GRCh38
Supplementary files format and content: xlsx files for all samples

growth_protocol: THP-1 was maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 0.05 nM 2-mercaptoethanol at 37°C in a 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent.
The cDNA libraries for each RNA sample were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, China) following the manufacturer’s instructions

treatment_protocol: To induce differentiation into M0 macrophages, THP-1 cells were exposed to 100 ng/mL Phorbol 12-Myristate 13-Acetate (PMA) for 48 hours. Subsequently, PMA was removed by medium exchange, and M0 macrophages were polarized into the M1 phenotype by incubation with 20 ng/mL IFN-γ and 100 ng/mL LPS from P. gingivalis for an additional 48 hours. For the co-culture of macrophages with iMSCs, THP-1 cells were seeded at a density of 1 × 106 cells per well in six-well plates and differentiated into M0 macrophages using PMA. iMSCs were then plated in the upper chamber of Transwell inserts to establish a co-culture system. LPS and IFN-γ were added to the system to sustain the macrophage activation process for 48 hours.

value: Peripheral blood

value: monocyte

value: M0 macrophages co-cultured with iMSCs under LPS+IFN-γ stimulation for 48 hours


title: THP-1, M0+LPS+IFN-γ+iMSCs, rep2

description:
Library name: Sample 14
M1-CM-2

value: WT


title: P2_UNTR-D

city: Kansas City

first: Kalyani

last: Pyaram

state: KS

address: 2060 W 39th Ave

institute: University of Kansas Medical Center

data_processing:
After concatenation, fastq files were checked for QC using fastqc. Reads were aligned using hg38 and Bowtie2.
Assembly: hg38
Supplementary files format and content: Raw counts after alignment to hg38 using Bowtie2

source_name: T-cells

extract_protocol:
RNA was harvested at 72 hrs of activation of T-cells (Untreated and 100pM RTA-408 treated). Total RNA was extracted using RNeasy Plus Micro kit (Qiagen). 1.5ug of RNA was used for construction of sequencing libraries.
100ng of the RNA was used to perform Agilent TapeStation QC analysis to verify RNA integrity and generate RNA Integrity number (RIN). Using Nova-Seq 6000 S1 200 cycle reagent kit, 25 million pair-ended reads were recorded for construction of mRNA libraries.

value: T-cells

value: Untreated


title: Clpxfl/f  ovulated oocyte- WT1

description:
Library name: SAMPLE 9
Column name in  ovulated oocyte RNA read count.txt/ovulated oocyte RNA read count.txt: CLPX_WT1 Read Count/CLPX_WT1 FRKM


title: P3_UNTR-D


title: THP-1, M0+LPS+IFN-γ+iMSCs, rep1

description:
Library name: Sample 13
M1-CM-1


title: THP-1, M0+LPS+IFN-γ, rep4

description:
Library name: Sample 12
M1-2-4

value: M0 macrophages stimulated with LPS and IFN-γ for 48 hours


title: P2_100pM


title: THP-1, M0+LPS+IFN-γ, rep3

description:
Library name: Sample 11
M1-2-3


title: THP-1, M0+LPS+IFN-γ, rep2

description:
Library name: Sample 10
M1-2-2


title: Healthy control 4

city: Paris

first: Thomas

last: Poisot

address: 1 Avenue Claude Vellefaux

country: France

institute: INSERM

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed from raw FASTQ files to count matrices using Cytonaut v1.4 (https://cytonaut-scipio.bio) with Cytonaut's pre-processing module v6.12.6.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools double-checked by manual inspection.
The provided processed data is composed of one count matrix per sample at full sequencing depth.
Data post-processing (filtering, normalization, HVG, batch correction, PCA, 2D embedding, clustering, DGE) was performed using Seurat v4.3.0.1
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38). Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A; Species: Homo_sapiens; Genome Source: ensembl; Genome Version: GRCh38; Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/; Annotation Source: ensembl; Annotation Version: 99; Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Comma Separated Values (CSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: skin

extract_protocol:
Patients included were adults and had a diagnosis of histologically proven lGVHD from the dermatology and hematology departments of Saint Louis Hospital, Paris, France. Skin biopsies were obtained using 4 mm punch and normal skin were obtained from healthy donors undergoing breast plastic surgery. Skin biopsies were transferred in NaCl 9‰ and immediately digested for 4h30 at 37°C using whole skin dissociation kit (Miltenyi) according to the manufacturer protocol. Single cell suspension obtained was then processed with Asteria kit (Scipio Bioscience) with 30,000 cells input in 2 kits for each sample to generate 3' enriched cDNA with corresponding cell barcode.
The cell barcoded cDNA was fragmented, end-repaired then adapter was ligated to the extremities using NEBNext Ultra II FS DNA libary kit for illumina. Selective amplification of cDNA fragment containing the cell barcode was done with custum P5-R1 library primer from Asteria kit and indexed P7-R2 primier from NEBNext Mulitplex Oligos kit. Libraries were sequenced on the illumina NovaSeq 6000 sequencer to generate paired-end read. 25 bases for read1 and 70 bases for read2. read1 contains cell barcode and read2 contains 3' sequence of cDNA.

value: skin

tag: disease

value: Healthy


title: Healthy control 3


title: THP-1, M0+LPS+IFN-γ, rep1

description:
Library name: Sample 9
M1-2-1


title: Healthy control 1.2

description:
HC1 was sequenced in two stages
count_matrix_HC1.csv


title: Healthy control 2


title: THP-1, M0+iMSCs, rep2

description:
Library name: Sample 6
M0-CM-2

value: M0 macrophages co-cultured with iMSCs for 48 hours


title: THP-1, M0 macrophages, rep4

description:
Library name: Sample 4
M0-4

value: Stimulated with PMA for 48 hours to differentiate into M0 macrophages


title: Lichenoid graft-versus-host-disease 3

value: Lichenoid graft-versus-host-disease


title: THP-1, M0 macrophages, rep3

description:
Library name: Sample 3
M0-3


title: Lichenoid graft-versus-host-disease 2


title: Lichenoid graft-versus-host-disease 1


title: THP-1, M0+iMSCs, rep1

description:
Library name: Sample 5
M0-CM-1


title: P1_UNTR-D