title: BIHi005-A_iPSC_derived_Ectoderm_3

value: Neural Stem Cells Ectoderm Day 7

value: iPSCs were seeded on Geltrex in Essential 8 with 10 µM Y-27632, then switched after 2 days to neural induction medium (DMEM/F12, B27, N2, L-glutamine, HEPES, 10 µM dorsomorphin, 10 µM SB431542) for 7 days with daily medium changes. Differentiation efficiency was assessed by FACS for PAX6, Nestin, SOX1, and SOX2, and samples with >85% expression were stored at -80 °C. Neural stem cells were subsequently derived from ectoderm by maintaining in the induction medium for 18 days with daily medium changes, and harvested at -80 °C.


title: Normal_1_4_6_2

status: Public on Oct 01 2025

type: SRA

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: Sample 437

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

molecule: genomic DNA

organism: Homo sapiens

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: male

tag: age

tag: condition

value: Normal

tag: testis

value: testis


title: HepAD38 shControl-1

city: Wuhan

first: jie

last: yang

address: No. 888 Gaoxin Avenue, Wuhan

institute: Wuhan IGENEBOOK Biotechnology Co.,Ltd

data_processing:
Trimmomatic (version 0.38) was used to filter out low-quality reads. Clean reads were mapped to the genome by Bwa (version 0.7.15), allowing up to two mismatches. Samtools (version 1.3.1) was used to remove potential PCR duplicates, and MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters (bandwidth,300 bp; model fold, 5, 50;q value, 0.05). Wig files produced by MACS software were used for data visualization by IGV (version 2.3.91).
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&TAG

source_name: Cell line

extract_protocol:
50000 cell was harvested and incubated with concanavalin A coated magnetic beads for 15 min at RT. Then, bead-bound cells was resuspended and incubated with the appropriate primary antibody (H3K27ac) overnight at 4℃. Afterwards,  secondary antibody was added to this mixture for 30 min at RT. The magnet stand was used to remove unbound antibodies.pA-Tn5 adapter complex was added at this step at RT for 1 h,then,remove unbound pA-Tn5 protein.Next,cells were resuspended in tagmentation buffer at 37℃ for 1 h. After that, immunoprecipitated DNA was saved.
Library was sequenced on Illumina novaseq 6000 with PE 150 method

tag: tissue

value: Cell line

tag: cell line

tag: cell type

value: HBV hepatoma cells


title: S18_U-87MG-ECFP-AQP4 E5415A+AC biol rep 3

city: Innsbruck

first: Markus

last: Reindl

address: Innrain 66/2

department: Clinical Department of Neurology

country: Austria

institute: Maedical University of Innsbruck

description:
Library name: S18
Column name in gene_count_preprocessed_mev_data_reindl.gct: S18

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software by Novogene. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. Hisat2 was used by Novogene as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. The program featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: The .gct file contains the raw gene counts for each sample (one matrix table for all samples). All genes with <20 counts in all samples were removed.
Supplementary files format and content: all gene counts

molecule: total RNA

growth_protocol: Human primary astrocytes (HA), isolated from human cerebral cortex, were purchased by ScienCell (Lot. No. 33619, Sciencell Research Laboratories, San Diego, CA). For experiments, solely passages 3 to 5 were used. HA were cultured in 2 µg/cm2 poly-L-lysine coated flasks (Sciencell Research Laboratories, San Diego, CA) in astrocyte medium AM (Innoprot, Derio, Spain), containing 2% FCS, 1% P/S and 1% astrocyte growth supplement. Medium was exchanged every other day and cells were passaged when 90% dense. The glioblastoma cell line U-87 MG (ATCC; LGC Standards GmbH, Wesel, Germany) was genetically modified for a stable protein overexpression. Thereby, an overexpression of enhanced cyan fluorescent protein (ECFP) with (U-87MG-AQP4-ECFP) or without (U-87MG-ECFP) AQP4M23 in U-87 MG cells was obtained via lentiviral infection. The vectors were pLIB-MCS-ECFP-iresNeo and pLIB-MCS-AQP4m23-ECFP-iresNeo.  Cells were selected using 10 µg/mL neomycine for 72 hours. HEK293A and U-87 MG cell lines were cultured in DMEM high glucose, 10% FCS and 1% non-essential amino acids and passaged twice a week.

extract_protocol:
Isolation of total RNA was done according to the protocol of the RNeasy Mini Kit (QIAGEN, Hilden, Germany). After quantity and quality determination by a NanoDrop™ System (Thermo Fisher Scientific, Waltham, MA, USA), total RNA samples were sent for sequencing by the Illumina PE150 technology to Novogene (Martinsried, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: U-87MG-ECFP, U-87MG-AQP4-ECFP, HEK293-AQP4 -EmGFP cells or HA were grown in a 12- or 96-well plate until confluent. Then, they were treated with 40% active or heat-inactivated (45 min. at 56 °C) human complement (Cedarline) in X-VIVO 15 medium (Lonza, Basel, Switzerland) and with or without the mouse monoclonal antibody E5415A (in-house production from E5415A-1H6-68 hybridoma cells, #RCB4883, Riken, Tsukubashi, Ibaraki, Japan) (10 µg/mL), followed by an incubation for 90 min. at 37 °C. Afterwards, the cell supernatant was taken to assess cytotoxicity and cells were harvested for RNA isolation, or immunofluorescence staining of the TCC was performed.

value: glioblastoma cell line

tag: genotype

tag: treatment

value: anti-AQP4 antibody E5415A + active human complement


title: BIHi005-A_iPSC_derived_Ectoderm_2

type: genomic

city: Berlin

first: Eilis

last: Perez

address: Charitéplatz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

hyb_protocol: standard Illumina Protocols

scan_protocol: standard Illumina Protocols

data_processing: Raw DNA methylation data were pre-processed using R (v 4.3.3). Signal intensities were obtained from IDAT files using the Bioconductor package minfi (v 1.40.0) (Aryee et al., 2014). Dye bias correction was performed using the Noob (normal-exponential out-of-band) method with the preprocessNoob function without “between-array normalisation” (Triche et al., 2013). Data filtering steps included the removal of probes with detection p-values greater than 0.05 in more than 10% of samples, probes containing single nucleotide polymorphisms (SNPs) at the CpG site, probes located on sex chromosomes, and cross-reactive probes as previously described (Capper et al., 2018; Chen et al., 2013).  Beta values for DNA methylation were calculated from normalised data using the minfi getBeta function.

label: Cy3 and Cy5

label_protocol: standard Illumina Protocols

extract_protocol: DNA extraction was performed on harvested cell pellets using the Maxwell® RSC Instrument (Promega) with either the Maxwell® RSC Cultured Cells DNA Kit (Cat# AS1620) or the  Maxwell® RSC Blood DNA Kit (Cat# AS1400) for fresh and frozen cell samples, and the Maxwell® RSC FFPE Plus DNA Purification Kit (Cat# AS1720) for paraformaldehyde (PFA)-fixed cell samples, with no difference in DNA methylation analysis quality observed. Extracted DNA quantities were measured using the Quantus system together with the “QuantiFluor® ONE dsDNA” kit (Promega).

value: Neural Stem Cells Ectoderm Day 5

tag: Sex

value: Male

tag: cohort

value: Surplus


title: Normal_1_4_5_8

description: Sample 436


title: S22_U-87MG-ECFP-AQP4 AC biol rep 1

description:
Library name: S22
Column name in gene_count_preprocessed_mev_data_reindl.gct: S22

value: active human complement


title: BIHi001-B_iPSC_derived_Ectoderm_6


title: OVCAR8, leptin, RNA-seq, repeat3

first: jingtao

last: wang

address: No. 299, Bayi Road, Wuchang District, Wuhan City, Hubei Province

institute: Wuhan University

data_processing:
For the data analysis, index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Differential expression analysis of two groups was performed using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: featurecounts output files

source_name: Ovary

growth_protocol: OVCAR8 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was havested using RNAiso Plus (TaKaRa, 9108). 1.3 ug of tota RNA was used for the construction of sequencing libraries
Library preparation was conducted with the NEBNext Ultra II Directional RNA Library Prep Kit, followed by sequencing on the Illumina NovaSeq 6000 platform with 150-base pair (bp) paired-end reads

treatment_protocol: OVCAR8 cells were serum starved overnight and then treated with leptin.

value: Ovary

value: Ovarian cancer cells

value: WT

value: Leptin


title: BIHi287-A_iPSC_derived_Ectoderm_1

value: Trilineage Ectoderm

value: 70-80% confluent iPSCs were seeded and differentiated into Ectoderm, Endoderm and Mesoderm using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec), following manufacturer´s instructions. At day 7 of differentiation cells were harvested using Accutase or TrypLE (both Gibco). FACS analysis was performed to characterise ectodermal (SOX2, PAX6), endodermal (CXCR4, SOX17) and mesodermal (CD144, CD140b -Miltenyi Biotec, 130-121-052-) cells. The remaining cells were collected as pellet and stored at -80°C.

value: Validation


title: Normal_1_4_5_7

description: Sample 435

value: male

value: Normal


title: S17_U-87MG-ECFP-AQP4 E5415A+AC biol rep 2

description:
Library name: S17
Column name in gene_count_preprocessed_mev_data_reindl.gct: S17


title: OVCAR8, leptin, RNA-seq, repeat2


title: BIHi001-B_iPSC_derived_Astrocyte_3

value: Astrocyte day 37 (MACS sorted)

value: iPSCs were differentiated into ectoderm for 7 days, dissociated, and seeded (15,000 cells/cm²) onto Geltrex/Matrigel or vitronectin in neural induction medium with 10 µM Y-27632. After 48 h, cells were cultured in Astrocyte Medium (ScienCell) with medium changes every 48 h and passaged at ~90% confluency. After 30 days, GLAST-positive cells were isolated using the Anti-GLAST MicroBead Kit (Miltenyi Biotec) and stored at -80 °C.

value: Training


title: Normal_1_4_5_6

description: Sample 434

value: testis


title: Normal_1_4_5_5

description: Sample 433


title: OVCAR8, leptin, RNA-seq, repeat1


title: S16_U-87MG-ECFP-AQP4 E5415A+AC biol rep 1

description:
Library name: S16
Column name in gene_count_preprocessed_mev_data_reindl.gct: S16

value: glioblastoma cell line

value: anti-AQP4 antibody E5415A + active human complement


title: OVCAR8, Control, RNA-seq, repeat3

value: PBS


title: S14_U-87MG-ECFP biol rep 2

description:
Library name: S14
Column name in gene_count_preprocessed_mev_data_reindl.gct: S14

value: ECFP


title: Normal_1_4_5_3

description: Sample 432


title: OVCAR8, Control, RNA-seq, repeat2

value: Ovary


title: BIHi250-A_iPSC_derived_Astrocyte_10

value: Female


title: BIHi250-A_iPSC_derived_Astrocyte_8


title: BIHi250-A_iPSC_derived_Astrocyte_9


title: S13_U-87MG-ECFP biol rep 1

description:
Library name: S13
Column name in gene_count_preprocessed_mev_data_reindl.gct: S13


title: Normal_1_4_5_2

description: Sample 431


title: S12_U-87MG-ECFP IC biol rep 3

description:
Library name: S12
Column name in gene_count_preprocessed_mev_data_reindl.gct: S12

value: inactive human complement


title: Normal_1_4_5_1

description: Sample 430


title: OVCAR8, Control, RNA-seq, repeat1

value: Ovarian cancer cells

value: WT


title: S11_U-87MG-ECFP IC biol rep 2

description:
Library name: S11
Column name in gene_count_preprocessed_mev_data_reindl.gct: S11


title: OVCAR8, leptin, H3K27ac, ChIP

data_processing:
Basecalls were performed using fastq Novaseq output.
ChIP-seq reads were trimmed with fastp.
ChIP-seq reads were aligned to the hg38 and mm10 genome using Bowtie2 (v2.4.2).
Peaks were called uing MACS v2.2.7.1 (q-value takes default setting).
BigWig files were obtained by deepTools (v3.5.1).
Heatmap and metaplot files were made by plotHeatmap and plotProfile of deepTools (v3.5.1).
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: RPMI 1640, 10% fetal bovine serum (FBS). Cells were cultured in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
To extract chromatin, cells were cross-linked with 1% paraformaldehyde for 10 min and then quenched with 0.125 M glycine for 5 min at room temperature with rotation.
ChIP-seq libraries were prepared using the NEBNext ultra II DNA library prep kit for Illumina.

value: Leptin

tag: chip antibody

value: H3K27ac (ABclonal, A2363)


title: S10_U-87MG-ECFP IC biol rep 1

description:
Library name: S10
Column name in gene_count_preprocessed_mev_data_reindl.gct: S10


title: S15_U-87MG-ECFP biol rep 3

description:
Library name: S15
Column name in gene_count_preprocessed_mev_data_reindl.gct: S15


title: BIHi250-A_iPSC_derived_Astrocyte_7


title: Normal_1_4_4_7

description: Sample 429

value: male


title: BIHi250-A_iPSC_derived_Astrocyte_6


title: OVCAR8, control, H3K27ac, ChIP


title: BIHi250-A_iPSC_derived_Astrocyte_5


title: Normal_1_4_4_6

description: Sample 428

value: Normal


title: OVCAR8, leptin, INPUT


title: Normal_1_4_4_4

description: Sample 426


title: S8_U-87MG-ECFP AC biol rep 2

description:
Library name: S8
Column name in gene_count_preprocessed_mev_data_reindl.gct: S8

value: active human complement


title: BIHi250-A_iPSC_derived_Astrocyte_4

value: Astrocyte day 37 (MACS sorted)

value: iPSCs were differentiated into ectoderm for 7 days, dissociated, and seeded (15,000 cells/cm²) onto Geltrex/Matrigel or vitronectin in neural induction medium with 10 µM Y-27632. After 48 h, cells were cultured in Astrocyte Medium (ScienCell) with medium changes every 48 h and passaged at ~90% confluency. After 30 days, GLAST-positive cells were isolated using the Anti-GLAST MicroBead Kit (Miltenyi Biotec) and stored at -80 °C.


title: OVCAR8, leptin,IgG, ChIP

value: IgG (ABclonal, AC042)


title: BIHi250-A_iPSC_derived_Astrocyte_3

value: Validation


title: S7_U-87MG-ECFP AC biol rep 1

description:
Library name: S7
Column name in gene_count_preprocessed_mev_data_reindl.gct: S7

value: glioblastoma cell line


title: Normal_1_4_4_1

description: Sample 425

value: testis


title: OVCAR8, control, IgG, ChIP

value: PBS


title: OVCAR8, leptin, cJun, ChIP

value: Ovary

value: cJun (CST, 9165)


title: S5_U-87MG-ECFP E5415A+IC biol rep 2

description:
Library name: S5
Column name in gene_count_preprocessed_mev_data_reindl.gct: S5

value: ECFP

value: anti-AQP4 antibody E5415A + inactive human complement


title: BIHi001-B_iPSC_derived_Astrocyte_2

value: Male

value: Training


title: Normal_1_4_3_7

description: Sample 423


title: BIHi001-B_Not_Classifiable_7


title: OVCAR8, control, cJun, ChIP

value: Ovarian cancer cells

value: WT


title: Normal_1_4_3_8

description: Sample 424

value: male

value: Normal


title: BIHi001-B_iPSC_derived_Astrocyte_1

value: Astrocyte day 37 (MACS sorted)


title: S9_U-87MG-ECFP AC biol rep 3

description:
Library name: S9
Column name in gene_count_preprocessed_mev_data_reindl.gct: S9

value: active human complement


title: S4_U-87MG-ECFP E5415A+IC biol rep 1

description:
Library name: S4
Column name in gene_count_preprocessed_mev_data_reindl.gct: S4


title: Normal_1_4_4_5

description: Sample 427


title: OVCAR8, control, INPUT


title: Normal_1_4_3_6

description: Sample 422


title: S3_U-87MG-ECFP E5415A+AC biol rep 3

description:
Library name: S3
Column name in gene_count_preprocessed_mev_data_reindl.gct: S3

value: anti-AQP4 antibody E5415A + active human complement


title: icam1 kd ilf3r1

city: Nanjing

first: siyuan

last: jiang

state: Jiangsu

address: sipailou NO2

department: Zhongda Hospital

institute: Southeast University

description: RNA-seq of CALU-1 cells

data_processing:
Assess the quality of raw reads.
Remove low-quality bases and adapter sequences.
Align trimmed reads to the reference genome.
Identify regions of significant protein-DNA interactions.
Create BigWig files for visualization.
Assembly: hg38
Supplementary files format and content: Coverage of aligned reads across the genome.
Library strategy: CUT&Tag

source_name: Lung

growth_protocol: CALU-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer's protocol. For CUT&Tag, nuclei were isolated and tagmented according to the CUT&Tag protocol.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit. CUT&Tag libraries were prepared using the Illumina

treatment_protocol: For knockdown experiments, cells were transfected with siRNA targeting ICAM1 using Lipofectamine RNAiMAX. For knockout experiments, CRISPR-Cas9 was used to generate ICAM1 knockout cell lines.

value: Lung

value: Lung adenocarcinoma cells

value: ICAM1 KD/KO

value: shNC lentivius


title: S2_U-87MG-ECFP E5415A+AC biol rep 2

description:
Library name: S2
Column name in gene_count_preprocessed_mev_data_reindl.gct: S2

value: glioblastoma cell line


title: BIHi250-A_iPSC_derived_Astrocyte_2

value: Female

value: iPSCs were differentiated into ectoderm for 7 days, dissociated, and seeded (15,000 cells/cm²) onto Geltrex/Matrigel or vitronectin in neural induction medium with 10 µM Y-27632. After 48 h, cells were cultured in Astrocyte Medium (ScienCell) with medium changes every 48 h and passaged at ~90% confluency. After 30 days, GLAST-positive cells were isolated using the Anti-GLAST MicroBead Kit (Miltenyi Biotec) and stored at -80 °C.


title: icam1 kd ilf3r2

description: RNA-seq of CALU-1 cells


title: Normal_1_4_3_4

description: Sample 421

value: testis


title: Normal_1_4_3_3

description: Sample 420


title: BIHi250-A_iPSC_derived_Astrocyte_1


title: BIHi001-B_Not_Classifiable_5

value: Astrocyte Day 14

value: Male

value: Surplus


title: icam1 kd ilf2r2

description: RNA-seq of CALU-1 cells

value: ICAM1 KO

value: shICAM1 lentivius


title: S1_U-87MG-ECFP E5415A+AC biol rep 1

description:
Library name: S1
Column name in gene_count_preprocessed_mev_data_reindl.gct: S1

value: ECFP


title: sample.MM.1S_E9_GFP_3

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

country: USA

institute: Washington University in St. Louis

description: Library name: sample.MM.1S_E9_GFP_3

data_processing:
RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a
Aligned reads were imported to Partek Flow software for downstream analysis
Genes were filtered based on: maximum reads across all samples < 30
DEGs were identified with DESeq2 package implemented in Partek Flow
Assembly: Ensembl release 101
Supplementary files format and content: tab-delimited tsv file includes raw gene counts for each sample

growth_protocol: Both cell lines were maintained in culture for no longer than 6 months after initial thawing. Cells were cultured in Gibco Roswell Park Memorial Institute (RPMI)-1640 medium (Thermo Fisher) supplemented with 10% Gibco heat-inactivated fetal bovine serum (Thermo Fisher), 1% L-glutamate, 1% MEM nonessential amino acids (Corning), 1% amphotericin-B, 1% sodium pyruvate, and 1% Gibco penicillin-streptomycin (Thermo Fisher) to provide optimal cellular growth conditions. Cultures were routinely monitored for pH changes, indicated by the phenol red dye in the media, and for contamination, assessed using brightfield microscopy. Trypan blue exclusion assays were performed weekly14, and cells were passaged based on media pH and growth rates to ensure optimal conditions for proliferation. All cultures were incubated at 37°C in a humidified atmosphere with 5% CO₂ and handled using aseptic techniques in cell culture flasks.

extract_protocol:
From the sorted populations, three biological replicates were prepared for each cell line, MM.1S WT and KO respectively, snap frozen in liquid nitrogen, and stored at –80°C. RNA extraction was carried out at the Tissue Procurement Core of Washington University using the QIAamp RNA Mini Kit (Qiagen). Total RNA integrity number (RIN) was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.

treatment_protocol: Fluorescence-activated cell sorting (FACS) was performed to confirm the complete knockout of CD38 expression in the MM.1S-CBR-GFP-KO cell line, ensuring the accuracy of the genetically modified KO. Sorting was conducted at the Siteman Cancer Center Flow Cytometry Core using a MoFlo Astrios EQ cell sorter (Beckman Coulter). Both cell lines were stained with 7-AAD (Thermo Fisher Scientific) to assess cell viability, and anti-human CD38 conjugated to a phycoerythrin (PE) fluorophore (3:100, mouse monoclonal, BD Pharmingen, catalog #555460) for detection of CD38 protein surface expression. Conventional gating techniques were employed to exclude 7-AAD+ cells, thereby removing cellular debris and dead cells from the sorted populations. For the MM.1S WT cells, gating was adjusted to conservatively collect only CD38+ cells, while for the MM.1S CD38 KO cells, gating ensured that only CD38-negative cells were collected. No detectable CD38-positive cell populations were identified in the KO cell line during FACS analysis, with carefully defined gating parameters confirming that all collected KO cells showed an absence of CD38 expression. Recovered cell populations were subsequently subjected to RNA sequencing to analyze gene expression profiles.

value: B lymphoblast

value: CD38 KO


title: icam1 kd ilf2r1

description: RNA-seq of CALU-1 cells


title: Normal_1_4_3_2

description: Sample 419

value: male

value: Normal


title: S6_U-87MG-ECFP E5415A+IC biol rep 3

description:
Library name: S6
Column name in gene_count_preprocessed_mev_data_reindl.gct: S6

value: anti-AQP4 antibody E5415A + inactive human complement


title: Normal_1_4_3_1

description: Sample 418


title: puro ilf3r2

description: RNA-seq of CALU-1 cells

value: Lung

value: Lung adenocarcinoma cells

value: ICAM1 KD/KO


title: BIHi001-B_Not_Classifiable_4

value: Astrocyte Day 27


title: sample.MM.1S_E9_GFP_2

description: Library name: sample.MM.1S_E9_GFP_2


title: Normal_1_4_2_8

description: Sample 417


title: sample.MM.1S_E9_GFP_1

description: Library name: sample.MM.1S_E9_GFP_1


title: puro ilf3r1

description: RNA-seq of CALU-1 cells

value: shNC lentivius


title: sample.MM.1S_WT_GFP_3

description: Library name: sample.MM.1S_WT_GFP_3

value: WT


title: Normal_1_4_2_6

description: Sample 416

value: testis


title: puro ilf2r2

description: RNA-seq of CALU-1 cells


title: BIHi005-A_iPSC_6

value: iPSC

value: Male

value: iPSCs) were cultured on growth factor–reduced Geltrex (Gibco) in E8 or mTeSR (Stem Cell Technologies) medium with daily exchange. Cells were passaged as clumps with 0.5 mM EDTA (Thermo Fisher) every 2–4 days once >70% confluent. All lines were obtained from the BIH Core Unit Pluripotent Stem Cells and Organoids (BIH-CUSCO) with ethical approval. Full protocols are available at https://www.protocols.io/view/good-practices-in-hpsc-handling-gdqmbs5u7.


title: BIHi001-B_iPSC_6

value: Surplus


title: Normal_1_4_2_5

description: Sample 415


title: sample.MM.1S_WT_GFP_2

description: Library name: sample.MM.1S_WT_GFP_2


title: sample.MM.1S_WT_GFP_1

description: Library name: sample.MM.1S_WT_GFP_1


title: untreated, SARS-CoV-2(B1.1.7)-infected primary bronchial epithelial cells of bALI9

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to process raw sequencing data with the GRCh38 reference augmented by the SARS-CoV-2 (NC_045512.2) genome. Viral transcripts including 3'UTR sequences were extracted from the Genbank records and added to the Gencode v33 reference.
We used CellBender (doi:10.1101/791699) to remove background RNA
ScRNA-seq data analysis was performed in R (version 4.0.3) with Seurat (version 4.3.0) (doi:10.1016/j.cell.2021.04.048). Cells with at least 500 and less than 8000 detected genes, less than 100000 UMIs and less than 10% mitochondrial content were combined from each library. We further constructed a score for nuclear-localized genes using Seurat's AddModuleScore and the top 50 genes enriched in single-nuc vs. single-cell libraries from Table S2 of Bakken et al. (doi: 10.1371/journal.pone.0209648) and removed cells with abnormal content of nuclear genes (score larger than a threshold of 0.267 obtained using k-means clustering of one-dimensional data with the Binarize R package (v1.3))
We then used SCTransform (doi:10.1186/s13059-021-02584-9), regressing out cell cycle scores and ignoring viral genes during PCA with 20 components. Finally, we used Seurat's IntegrateData workflow to remove batch effects between different samples and annotated clusters using a combination of marker genes from the literature together with label transfer from reference datasets for lung and other ALI models. We finally removed doublets using DoubletFinder (v2.0.3; doi:10.1016/j.cels.2019.03.003)
Assembly: GRCh38 + NC_045512.2
Supplementary files format and content: cellranger raw feature bc matrix files (h5)
Supplementary files format and content: seurat object (rds)

molecule: polyA RNA

source_name: primary bronchial epithelial cells

growth_protocol: Primary airway epithelial cells cultured under ALI conditions were generated by the conditionally reprogrammed cell culture method as previously described. Briefly, primary nasal and bronchial epithelial cells were expanded in a co-culture with irradiated 3T3 mouse fibroblasts in presence of Rho-kinase inhibitor Y-27632, then seeded at passage 2 or 3 on Snapwell cell culture inserts (Corning) in an in-house differentiation medium termed UNC-ALI. Cultures were differentiated at ALI for 30 days prior to infection studies.

extract_protocol:
For single-cell isolation the cell culture inserts were transferred into a fresh 6-well plate, the cell culture inserts were washed with D-PBS and enzymatically digested using 200 µl TrypLETM Express Enzyme (GibcoTM) + 50 µg/ml DNAse at 37 °C for 10 min. After 10 min, TrypLETM Express Enzyme + 50 µg/ml DNAse was added again, pipetted up and down, and medium was added (1:1 (v/v)). Afterwards, the cell suspension was gently pulled three times through a 23G needle, washed with D-PBS, and passed through a 40 µm cell strainer. Cells were counted using trypan blue and checked for cell viability above 90% before starting the GEM generation.
The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 3′ V3.1 library preparation kit according to the manufacturer’s protocol (10x Genomics). The adequate quality of the obtained cDNA and library was ensured using a 2100 Bioanalyzer (Agilent).

treatment_protocol: Approximately 200,000 human nasal airway epithelial cells (hNAECs) or human bronchial airway epithelial cells (hBAEC) were infected with SARS-CoV-2 wildtype (BetaCoV/Munich/ChVir984/2020) or SARS-CoV-2 variant Alpha (B1.1.7, BetaCoV/Baden-Wuerttemberg/ChVir21528/2021) at a MOI of 0.1 in 150 µl D-PBS containing 0.3% BSA for 1 h at 37 °C in a 5% CO2 atmosphere with 95% humidity. Afterwards, cells were washed apically with D-PBS and fresh medium with and without CM (100 µM) was added basolaterally directly after virus incubation. Samples were taken at the indicated time points from the apical surface by applying 200 μl D-PBS to the cells. To ensure that virus particles diffuse into the solution, D-PBS was incubated on the cells for 30 min at 37 °C before samples were collected from the supernatant.

value: primary bronchial epithelial cells

tag: donor

tag: infection

value: untreated


title: puro ilf2r1

description: RNA-seq of CALU-1 cells

value: ICAM1 KO


title: Testis, D180-2 (miRNA-seq)

city: Nanning

first: Zhiqiang

last: Wang

address: No. 6 TaoYuan Rd.

institute: Guangxi Academy of Medical Sciences and the People’s Hospital of Guangxi Zhuang Autonomous Region

data_processing:
Bowtie V1.1.2 for alignment
miRDeep2 V2.0.0.8 and miRBase V21 for Identification of miRNA and expression
Assembly: GCF_001704415.2
Supplementary files format and content: csv files with fpkm value

organism: Capra hircus

source_name: Testis

extract_protocol:
The total RNA was extracted from the testes using TRIzol reagent (Invitrogen Life Technologies Inc., Carlsbad, CA, USA), 1 μg of total RNA was used for the construction of sequencing libraries.
RNA  libraries for  RNA-seq were prepared using tthe Small RNA Sample Preparation Kit (Illumina, RS-200-0048) according to the manufacturer’s instructions.

value: Testis


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary bronchial epithelial cells of bALI9

value: male

value: Camostattreated


title: Normal_1_4_2_3

description: Sample 414

value: Normal


title: Normal_1_4_2_1

description: Sample 413


title: Testis, D180-3 (miRNA-seq)


title: Testis, D90-3 (miRNA-seq)


title: untreated, SARS-CoV-2-infected primary bronchial epithelial cells of bALI9


title: BIHi005-A_Not_Classifiable_1

value: iPSCs were differentiated into ectoderm for 7 days, dissociated, and seeded (15,000 cells/cm²) onto Geltrex/Matrigel or vitronectin in neural induction medium with 10 µM Y-27632. After 48 h, cells were cultured in Astrocyte Medium (ScienCell) with medium changes every 48 h and passaged at ~90% confluency. After 30 days, GLAST-positive cells were isolated using the Anti-GLAST MicroBead Kit (Miltenyi Biotec) and stored at -80 °C.


title: neuron_WT_control_rep3_2

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads were mapped to Mus musculus genome build mm10 with Bowtie2 (v2.4.5).
Six million reads from each biological replicate were subset and each condition was then merged across biological replicates (SAMtools v1.15).
Metaplots were generated using ngs.plot (v2.63).
Peaks were called using MACS3 (v3.0.0b1) and annotated using Homer (v4.10).
Assembly: mm10
Supplementary files format and content: bigwig files generated from subsetted bam files aligned to bowtie2
Library strategy: CUT&Tag

organism: Mus musculus

source_name: primary cortical neurons

extract_protocol:
At 12DIV, ~500K primary cortical neurons were collected in wash buffer (Kaya-Okur et al. 2019) and CUT&Tag was performed with anti-H2BE antibody (Millipore ABE1384)
CUT&Tag was performed according to published protocols (Kaya-Okur et al. 2019) with the following adaptation: DNA was isolated using Zymo DNA Clean & Concentrator Kit (D4013).

value: primary cortical neurons

value: control


title: Normal_1_4_12_5

description: Sample 411


title: Normal_1_4_12_8

description: Sample 412


title: Normal_1_4_12_3

description: Sample 410


title: neuron_WT_control_rep3_1


title: Testis, D90-2 (miRNA-seq)


title: Camostattreated, mock-infected primary bronchial epithelial cells of bALI9

value: mock


title: neuron_WT_BDNF24h_rep2

value: WT


title: Normal_1_4_12_2

description: Sample 409

value: testis


title: untreated, mock-infected primary bronchial epithelial cells of bALI9


title: Testis, D30-3 (miRNA-seq)


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary bronchial epithelial cells of bALI8

value: female


title: Normal_1_4_11_8

description: Sample 408


title: Testis, D90-1 (miRNA-seq)


title: Testis, D180-1 (miRNA-seq)


title: neuron_WT_control_rep2_2


title: Testis, D30-2 (miRNA-seq)


title: neuron_WT_BDNF24h_rep1


title: Testis, D30-1 (miRNA-seq)


title: untreated, SARS-CoV-2(B1.1.7)-infected primary bronchial epithelial cells of bALI8


title: Camostattreated, SARS-CoV-2-infected primary bronchial epithelial cells of bALI9


title: Normal_1_4_11_6

description: Sample 406


title: neuron_WT_control_rep1_2


title: neuron_WT_BDNF24h_rep3


title: Normal_1_4_11_5

description: Sample 405


title: Camostattreated, SARS-CoV-2-infected primary bronchial epithelial cells of bALI8


title: Testis, D3-3 (miRNA-seq)


title: untreated, SARS-CoV-2-infected primary bronchial epithelial cells of bALI8


title: Testis, D3-2 (miRNA-seq)


title: neuron_WT_control_rep1_1


title: Camostattreated, mock-infected primary bronchial epithelial cells of bALI8


title: Normal_1_4_11_4

description: Sample 404


title: Normal_1_4_10_8

description: Sample 403


title: neuron_KO_BDNF24h_RNA-seq_rep4

data_processing:
Reads were mapped to Mus musculus genome build mm10 with Star (v2.7.9a)
The R packages DESeq2 (v1.38.3) and limma (v3.54.2) via edgeR (v3.40.2) were used to perform differential gene expression analysis
Assembly: mm10
Supplementary files format and content: csv of raw counts

extract_protocol:
RNA was isolated from primary cortical neurons using Zymo Quick-RNA Miniprep Plus Kit (R1057).
Sequencing libraries were prepared using the TruSeq Stranded mRNA kit (Illumina 20020595).


title: neuron_WT_control_rep2_1


title: neuron_KO_BDNF30m_RNA-seq_rep4


title: T_BWI-30_5

first: Meixian

last: Yin

address: No. 58 Zhongshan Er Road

department: Organ Transplant Centre

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Gene expression levels were quantified using established bioinformatics pipelines (featureCounts Version 2.0.1). Differential gene expression analysis was performed to identify genes exhibiting significant changes in expression between the experimental conditions, using a threshold of log2(fold change) >1 and a P value <0.05. GO Processes analysis was analyzed using MetaCore.
Assembly: RNA-seq reads were mapped to the reference genome (susScr11) using alignment algorithms (STAR version 2.7.3a).
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 RPKM values for each sample.

organism: Sus scrofa

source_name: temporal cortex

extract_protocol:
RNA was harvested using Trizol method.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy mRNA-Seq Library Prep Kit V3.0（96 RXN） following manufacturer's protocols.

treatment_protocol: In vivo brains were performed 30-minutes global cerebral ischemia with simultaneous hepatic ischemia (BLWI-30) or without hepatic ischemia (BWI-30).

value: temporal cortex

value: global cerebral ischemia


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary bronchial epithelial cells of bALI7


title: Normal_1_4_10_7

description: Sample 402


title: neuron_KO_control_RNA-seq_rep4


title: Normal_1_4_11_7

description: Sample 407


title: T_BWI-30_4


title: Normal_1_4_10_5

description: Sample 401


title: untreated, SARS-CoV-2(B1.1.7)-infected primary bronchial epithelial cells of bALI7


title: neuron_KO_BDNF24h_RNA-seq_rep3


title: Normal_1_4_10_4

description: Sample 400


title: Camostattreated, SARS-CoV-2-infected primary bronchial epithelial cells of bALI7


title: neuron_KO_BDNF30m_RNA-seq_rep3


title: T_BWI-30_2


title: Normal_1_4_10_3

description: Sample 399


title: T_BWI-30_3


title: untreated, SARS-CoV-2-infected primary bronchial epithelial cells of bALI7


title: T_BWI-30_1


title: Normal_1_4_10_2

description: Sample 398


title: Camostattreated, mock-infected primary bronchial epithelial cells of bALI7


title: neuron_KO_control_RNA-seq_rep3


title: Testis, D3-1 (miRNA-seq)


title: T_BLWI-30_4

value: global cerebral ischemia with simultaneous hepatic ischemia


title: untreated, mock-infected primary bronchial epithelial cells of bALI8

value: primary bronchial epithelial cells


title: untreated, mock-infected primary bronchial epithelial cells of bALI7

value: untreated


title: neuron_KO_BDNF24h_RNA-seq_rep2


title: neuron_KO_BDNF30m_RNA-seq_rep2


title: Normal_1_4_10_1

description: Sample 397


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI6

source_name: primary nasal epithelial cells

value: primary nasal epithelial cells


title: Normal_1_4_1_8

description: Sample 396


title: neuron_KO_control_RNA-seq_rep2


title: untreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI6


title: T_BLWI-30_2


title: Normal_1_4_1_7

description: Sample 395


title: neuron_KO_BDNF24h_RNA-seq_rep1


title: Camostattreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI6


title: Normal_1_4_1_5

description: Sample 394


title: T_BLWI-30_1


title: Camostattreated, mock-infected primary nasal epithelial cells of nALI6


title: untreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI6


title: F_BWI-30_6

source_name: frontal cortex

value: frontal cortex


title: neuron_KO_control_RNA-seq_rep1


title: Normal_1_4_1_4

description: Sample 393

value: male


title: neuron_KO_BDNF30m_RNA-seq_rep1


title: F_BWI-30_5


title: F_BWI-30_4


title: T_BLWI-30_3


title: neuron_WT_BDNF30m_RNA-seq_rep4


title: neuron_WT_BDNF24h_RNA-seq_rep4


title: F_BWI-30_3


title: untreated, mock-infected primary nasal epithelial cells of nALI6


title: neuron_WT_control_RNA-seq_rep4


title: Normal_1_4_1_1

description: Sample 391


title: Normal_1_3_9_8

description: Sample 390


title: F_BWI-30_2


title: Normal_1_3_9_7

description: Sample 389


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI5

value: Camostattreated


title: untreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI5


title: neuron_WT_BDNF24h_RNA-seq_rep3


title: F_BWI-30_1


title: neuron_WT_BDNF30m_RNA-seq_rep3


title: Normal_1_3_9_6

description: Sample 388

value: Normal


title: untreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI5


title: F_BLWI-30_4


title: neuron_WT_control_RNA-seq_rep3


title: Normal_1_3_9_5

description: Sample 387


title: Normal_1_4_1_2

description: Sample 392


title: Camostattreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI5


title: untreated, mock-infected primary nasal epithelial cells of nALI5


title: F_BLWI-30_2


title: Normal_1_3_9_1

description: Sample 385


title: F_BLWI-30_3


title: neuron_WT_BDNF24h_RNA-seq_rep2


title: F_BLWI-30_1


title: untreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI4


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI4


title: Normal_1_3_8_6

description: Sample 383


title: neuron_WT_BDNF24h_RNA-seq_rep1


title: Normal_1_3_8_8

description: Sample 384


title: neuron_WT_control_RNA-seq_rep2


first: Binfeng

last: Chen

address: 58 Zhongshan Second Road

institute: Department of Rheumatology, The First Affiliated Hospital, Sun Yat-sen University

data_processing:
HISAT2 were used for reads alignment.
Gene expression was quantified using featurecounts (version 2.0.1).
Assembly: mm10
Supplementary files format and content: The matrix named expr_matrix_Vista_KO_WT.csv consisted of the counts of gene expression

source_name: Colon

extract_protocol:
Subsequently colons were collected  in TRIzol reagent for RNA sequencing.
Libraries were sequenced on a BGIseq500 platform (BGI-Shenzhen, China) to generate single end 50 bases reads.

treatment_protocol: Mice were exposed to 2% DSS in drinking water for 7 days.

value: Colon

value: Oral DSS administration


title: Camostattreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI4


value: Vista-/-


title: neuron_WT_BDNF30m_RNA-seq_rep1

value: primary cortical neurons


title: Normal_1_3_8_3

description: Sample 381


title: untreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI4


title: Normal_1_3_8_1

description: Sample 380


title: Normal_1_3_9_3

description: Sample 386


title: neuron_WT_control_RNA-seq_rep1

value: WT

value: control


title: Camostattreated, mock-infected primary nasal epithelial cells of nALI5

value: female

value: mock


title: Camostattreated, mock-infected primary nasal epithelial cells of nALI4


title: Mouse_DSS_vista_WT_VS_KO_colon_3.WT.69A

description: Mouse_DSS_vista_WT_VS_KO_colon_3.bam.WT.69A.bam

data_processing:
Libraries were sequenced on a BGIseq500 platform (BGI-Shenzhen, China) to generate single end 50 bases reads.
HISAT2 (version 2.2.1) and Human reference genome (GRCh38) were used for reads alignment.
Gene expression was quantified using featurecounts (version 2.0.1).
Assembly: GRCh38
Supplementary files format and content: featurecounts

source_name: colon

extract_protocol: BGIseq500 platform

treatment_protocol: Mice were exposed to 2% DSS in drinking water for 7 days and subsequently colons were collected  in TRIzol reagent for RNA sequencing.

value: colon

value: dextran sulfate sodium


title: GT8-IL-21-NIC

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: 10x Genomics

data_processing:
CellRanger suite (pipeline v7.0.0 https://support.10xgenomics.com) was used with refdata-gex-mm10-2020-A transcriptome as a reference to map reads on the mouse genome.
Assembly: mm10
Supplementary files format and content: 10x Cellranger output with barcodes, features, and matrix

source_name: Lymph node

extract_protocol:
Antigen-specific germinal center B cells were sorted and subsequently uniquely barcoded using the 10× Genomics Chromium single-cell platform, and complementary DNA (cDNA) libraries were prepared for Next Generation Sequencing according to the manufacturer’s protocol (Chromium NextGem Single Cell 3' V2 Library and Gel Bead Kit, 10× Genomics, USA). Cell suspensions of each sample, reverse transcription master mix, and partitioning oil were loaded on a single-cell “G” chip with a targeted cell output of 10,000 cells per library and then run on the Chromium Controller. A total of 4 lanes were used on the G chip, 1 lane/sample. Reverse transcription was performed within the droplets at 53°C for 45 min and newly synthesized cDNA was amplified for 11 cycles on a Veriti Thermal Cycler (Thermofisher, USA). cDNA size selection was performed using SPRIselect beads (Beckman Coulter, USA) following manufacturer’s protocol. cDNA was analyzed on an Agilent Tapestation High Sensitivity D5000 (Agilent, USA) for qualitative and quantitative control purposes.
cDNA was then used to make libraries according to manufacturer’s protocol (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1). cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32°C, followed by end-repair and A-tailing at 65°C for 30 min. cDNA was double-sided size selected using SPRIselect beads. Sequencing adaptors were ligated to the cDNA at 20°C for 15 min. and after a round of post-ligation SPRIselect bead clean-up, cDNA was amplified for 14 cycles using a sample-specific index oligo as a primer. A final round of double-sided size selection using SPRIselect beads followed. Final library size and quantity was determined using an Agilent Tapestation High Sensitivity D5000 (Agilent, USA) and a Qubit dsDNA High Sensitivity Assay kit (Thermofisher, USA), respectively. Additional library quantification was done using the Kapa Library Quantification kit for Illumina Libraries (Roche, USA).

value: Lymph node

value: Germinal center B cell


title: Normal_1_3_7_8

description: Sample 379

value: testis


title: untreated, mock-infected primary nasal epithelial cells of nALI4

value: primary nasal epithelial cells

value: untreated


title: Normal_1_3_7_6

description: Sample 378

value: male


title: neuron_WT_BDNF30m_RNA-seq_rep2


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI3

value: Camostattreated


title: GT8-60mer

description: 10x Genomics


title: Mouse_DSS_vista_WT_VS_KO_colon_3.WT.67A

description: Mouse_DSS_vista_WT_VS_KO_colon_3.bam.WT.67A.bam


title: Normal_1_3_8_5

description: Sample 382

value: Normal


title: Mouse_DSS_vista_WT_VS_KO_colon_3.KO.94A

description: Mouse_DSS_vista_WT_VS_KO_colon_3.bam.KO.94A.bam

value: VISTA knockdown


title: MDA-MB-468 Radioresistant cells, shHNRNPL knockdown Replicate1

city: Worcester

first: Kensei

last: Kishimoto

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description: Library name: sh45_Replicate_1

data_processing:
High-accuracy basecalling was done on MinION or using dorado version 0.8.0 for ShCtrl Replicate 2. Passed reads or all reads for ShCtrl Replicate 2 were used as an input for CIRI-long using human genome assembly GRCh38.p14 and GENCODE comprehensive gene annotations to identify circRNAs. CircRNA isoforms identified from all replicates were collapsed and counted using CIRI-long collapse program. circRNA isoforms with an average CPM of less than 3 in either condition were filtered out and summed at the gene-level. Gene-level circRNA counts were used for DESeq2 with a default parameter to identify differentially expressed circRNAs.
Assembly: GRCh38.p14
Supplementary files format and content: isoform level raw counts or counts per million (CPM) of circular RNA and with annotations from CIRI-long collapse output.

growth_protocol: Cells were grown in DMEM/F12 medium supplemented with 10% FBS, 1% Pen/Strep

extract_protocol:
Total RNA from the cell lines (MDA-MB-468-RR shctrl and shHNRNPL-1) were extracted using a NucleoSpin RNA kit (740955.50 Macherey-Nagel).
IMCR-seq libraries are prepared as follows: A total of 4 tubes were taken and each tube contained: 500ng of total RNA (max 6uL), 2 uL 100 uM random N6 (NEB #S1230S), and 2 uL ddH2O. The tubes were incubated at 72°C for 5 minutes then cooled down to 4°C with 0.1°C/s ramp. Each tube was then taken and the following were added to reach a total volume of 40 uL: 8 ul 5X Induro Buffer, 4.8 ul MgCl2 (NEB B9021S: 25 mM), 2 ul 10 mM dNTPs, 2 ul Induro RT (NEB M0681: 200 units/ul), and 13.2 ul ddH2O. The tubes were incubated at: 23°C for 10 minutes, 30°C for 5 minutes, warmed up to 55°C with 0.1°C/sec ramp, 55°C for 1 hour, and 95°C for 1 minute to heat inactivate the RT. All four tubes were collected for a total volume of 160 uL and then mixed with 40 uL water and 200 uL AMPure beads (A63880, Beckman Coulter). The tubes were put on a rotator for 10 minutes. The tubes were placed on a magnetic rack to remove the liquid on the magnet and then resuspended in 300 uL 10mM Tris-HCl pH:8.0, with 72 uL Mg500PEG5 solution (500mM MgCl and 5% PEG8000 in 10mM Tris-HCl pH:8.0). The tubes were on the rotator for 30 minutes, placed on magnetic rack to remove the liquid, washed with fresh 80% EtOH and eluted the cDNA in 33 uL water. A 5uL aliquot of the cDNA was taken and mixed with 5 ul 10X Phi29 Buffer, 5 ul 10mM dNTPs, 2.5 ul 1mM Exo-resistant N6 primers (SO181 Thermo Scientific), 2 ul phi29 (M0269 NEB), and 30.5 ul ddH2O. This was done for a total of 6 tubes and all of them were incubated at 30°C for 6 hours. All tubes were combined together along with 15 ul NEBuffer 2 (B7002S NEB), 100 uL ddH2O, and 75 uL T7 Endonuclease I (M0302S NEB). The tube is incubated at 37°C for 1 hour. 500 uL of AMPure beads will be added to the mixture and incubated on the rotator for 10 minutes. The liquid is removed by placing the tube on the magnetic stand and the beads are mixed with 300 ul 10mM Tris-HCl pH:8.0 and 72 ul Mg500PEG5 solution (500mM MgCl and 5% PEG8000 in 10mM Tris-HCl pH:8.0). The tube is placed on the rotator for 30 minutes. Lastly the liquid is removed with the magnetic stand, beads are washed with fresh 80% EtOH twice, and finally eluted in 60ul water. 1.5ug of DNA from IMCR-seq was used for library preparation using Nanopore ligation sequencing kit (SQK-LSK114) according to the manufacturer's protocol, with the following specific alterations.. During library preparation, pipetting of DNA samples was avoided to minimize shearing of long DNA. Incubation time for all steps was extended by 5-10 minutes. For last Ampure clean-up set, 100uL was used. Long Fragment Buffer was used twice to wash. And all elutions were done at 55C. All libraries were sequenced on R10 flow cell on MinION for 24 hours with a minimum read cutoff of 1 kilobase.

treatment_protocol: Treatment regimen for developing radioresistant cells was giving a total of 50 Gy over the course of 6-8 weeks using the following treatment schedule: 2Gyx5, 4Gyx3, 6Gyx3, and 10Gyx1.

value: Breast Cancer

value: HNRNPL knockdown


title: untreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI3


title: MDA-MB-468 Radioresistant cells, shHNRNPL knockdown Replicate2

description: Library name: sh45_Replicate_2


title: MDA-MB-468 Radioresistant cells, ShCtrl Replicate 2

description: Library name: RR_Replicate_2

value: WT


title: Mouse_DSS_vista_WT_VS_KO_colon_3.WT.61A

description: Mouse_DSS_vista_WT_VS_KO_colon_3.bam.WT.61A.bam


title: Mouse_DSS_vista_WT_VS_KO_colon_3.KO.93A

description: Mouse_DSS_vista_WT_VS_KO_colon_3.bam.KO.93A.bam


title: MDA-MB-468 Radioresistant cells, shCtrl Replicate 1

description: Library name: RR_Replicate_1


title: Normal_1_3_7_2

description: Sample 375

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.


title: Camostattreated, mock-infected primary nasal epithelial cells of nALI3


title: Mouse_DSS_vista_WT_VS_KO_colon_3.KO.52A

description: Mouse_DSS_vista_WT_VS_KO_colon_3.bam.KO.52A.bam


title: SU-DHL-6 Rep2 cfChromatin, cfMNase-Seq, 30 min MNase digestion

city: Toronto

first: Scott

middle: Victor

last: Bratman

state: ON

address: 101 College Ave.

department: Medical Biophysics

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: SUDHL6_cfMNase_Rep2

library_source: other

data_processing:
UMIs were extracted using UMI-tools (v1.1.1) with a regular expression pattern to identify and append UMIs to the read headers.
Processed reads were aligned to the hg38 human genome using Bowtie2 (v2.4.1).
Duplicates were removed based on UMIs and alignment coordinates using UMI-tools. Low-quality mapped reads were filtered with Samtools view (v1.9) using a mapping quality threshold of 30. Quality metrics, including alignment statistics, were assessed at each step using Samtools flagstat.
Counts per 10,000 bp bin were calculated from BAM files (in bigWig format), using DeepTools. bigWig files were generated with Reads Per Kilobase per Million mapped reads (RPKM) normalization, centered and extended read options.
Assembly: hg38
Supplementary files format and content: bigWig, for all samples
Library strategy: cfMNase-Seq

molecule: other

source_name: Lymph node; B cell

growth_protocol: All cell lines were grown in their respective media (CAMA-1, MCF7, and A549 in Dulbecco's Modified Eagle Medium; HCT116 and SUD-HL-6 in Roswell Park Memorial Institute 1640) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution (Wisent Bioproducts). Cell lines were grown in adherent/suspension dishes and in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Conditioned media was collected in exponential growth phase. The media was spun at 2500g for 10 min at 4 °C, transferred to a new tube, and spun again at 16100g for 10 min at 4 °C. The supernatant was transferred to a new tube and kept at 4 °C until MNase digestion.
MNase master mix was prepared at 20,000 Units/mL (U/mL) by combining 440 μL of ddH20, 50 μL of MNase buffer, 5 μL of BSA, and 5 μL of 2,000,000 U/mL MNase (New England Biolabs, CAT #M0247S). MNase was added to cell line conditioned media supernatant at a final concentration of 133 U/mL and incubated in a 37 ºC water bath for 30 min. The reaction was stopped by adding 5 mM EDTA (Invitrogen, CAT #15575020).
After MNase digestion, purification of DNA from cell-free chromatin was performed using the Qiagen Circulating Nucleic Acid kit (CAT #55114). The DNA was quantified using the Qubit High Sensitivity dsDNA kit (Life Technologies, CAT #Q33231) and analyzed with a Agilent 2100 Bioanalyzer using the High Sensitivity DNA kit (CAT #5067-4626).
Libraries were prepared from 20 ng of purified DNA using the KAPA Hyperprep Kit with Library Amplification Primer Mix (Roche, CAT #07962363001) and adapters containing unique molecular identifiers from Integrated DNA Technologies. The libraries were cleaned-up using Beckman Coulter AMPure XP beads (CAT #A63882) with a 0.8× cleanup before library amplification and a 0.9X cleanup afterward. The libraries were amplified with six PCR cycles. Quality control was performed with a Qubit High Sensitivity dsDNA kit and  Agilent 2100 Bioanalyzer.

value: Lymph node; B cell

value: Hematopoietic


title: Normal_1_3_7_1

description: Sample 374


title: untreated, mock-infected primary nasal epithelial cells of nALI3

value: mock


title: Normal_1_3_6_8

description: Sample 373


title: Kdm5b 2C, three blastomeres from different embryos, biol rep 6

city: Oslo

first: Gareth

last: Greggains

address: Boks 1072 Blindern

country: Norway

institute: University of Oslo (UiO)

description:
Library name: Sample 35
k5b_3xS2c_U88

data_processing:
Initial quality control using the tool FastQC (Andrews, 2010), and absence of contaminating sequences was verified with FastQ Screen (Wingett and Andrews, 2018). The reads were trimmed by means of the FASTQ pre-processor fastp (Chen et al., 2018) v0.21.0 with default settings, except for the following: --detect_adapter_for_pe --correction --trim_poly_g --trim_poly_x --cut_tail --trim_front1 8  --trim_front2 8 --trim_tail1 1 --trim_tail2 1.
The trimmed reads were mapped to the Mus musculus GRCm38 genome assembly (Genome Reference Consortium, 2012) using the alignment tool STAR (Dobin et al., 2013) v2.7.3a. The alignment was performed in two-pass mode and was guided by a RefSeq gene annotation (NCBI Mus musculus Updated Annotation Release 108.20200622) using the following settings: --sjdbGTFfile <refseq.gtf> --sjdbOverhang 88  --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 25 --outFilterMismatchNmax 5 --peOverlapNbasesMin 20.
After mapping, additional quality assessment was performed by various functions in SAMtools (Danecek et al., 2021) v1.10 (stats, flagstats, idxstats) and in RSeQC (Wang et al., 2012) v2.6.4 (geneBody_coverage, tin, read_distribution, inner_distance, junction_annotation, junction_saturation, read_duplication, read_hexamer, infer_experiment).
Then the reads were assigned to RefSeq genes, using the same gene annotation as previously (NCBI Mus musculus Updated Annotation Release 108.20200622), with featureCounts (Liao et al., 2014) v1.5.1 and the following settings: -p -B -C -s 2. A gene-by-sample read count table was generated, and the total number of fragments per sample that was assigned to genes was in the range 8.7–17.8 M.
In order to compare Kdm5b-yfp mRNA-injected versus water-injected control samples and look for differentially expressed genes, statistical analysis of the count data was run using the package DESeq2 (Love et al., 2014) v1.30.1 in the software environment R (R Core Team, 2021) v4.0.3. The injected Kdm5b mRNA artificially affected the counts and could potentially skew the data normalisation (Kdm5b-mapped counts constituted 2.3–15.8% of all counts in Kdm5b samples; 0–1% in control samples). We therefore removed the Kdm5b-assigned reads prior to normalisation and statistical analysis. The zygotes and the 2C embryos were first analysed separately. Then the control zygotes and the control 2C embryos were compared.
To quantify transposable elements (TEs) in our sequence reads, we used SalmonTE (Jeong et al., 2018). The default behaviour of SalmonTE is to assign reads to consensus sequences of repetitive elements from the Repbase database. To achieve finer resolution, however, we decided to map against all repeat instances in the RepeatMasker v4.0.5 database (Smit et al., 2014). For each repeat (n = 18 538), all chromosomal instance sequences were extracted, including 25bp flanks, and concatenated using a string of 200 N's as spacer sequence (as in the RepEnrich method). A salmon index was created on the concatenated instance sequences ('salmon index') and the reads were aligned to the repeat index ('salmon quant --exprtype=count'). Finally, we tested for differential expression ('SalmonTE.py test --tabletype=csv --figtype=png --analysis_type=DE --conditions=<Group1>,<Group2>'). As Kdm5b mRNA was injected in the test group, any repeats overlapping with Kdm5b would get artificially high counts and skew the results. We therefore removed two repeats ('(AGCTGCC)n' and '(T)n') that mapped to Kdm5b exons after the quantification, but before the statistical tests.
Assembly: GRCm38
Supplementary files format and content: feaureCounts_ncbiRefSeqCurated_mm10.tsv tab-delimited text file contains raw gene counts for each sample
Supplementary files format and content: salmonTE_rm405_allSamples_noKdm5b_EXPR.csv comma-delimited text file contains raw TE counts for each sample

source_name: 2-cell embryo

growth_protocol: In vivo fertilised zygotes were cultured in pre-equilibrated micro-droplet dishes (Vitrolife), with 25 µl G-1 PLUS medium (Vitrolife) per well, overlaid with OVOIL-100 paraffin oil (Vitrolife). Approximately 10 zygotes were added per well and maintained at 37 °C in 6% CO₂, both before and after microinjection. For 2C embryos, we used thawed zygotes to precisely manage developmental timing. Zygotes were previously isolated and cryopreserved immediately using the Embryo Freezing Pack (Origio, CooperSurgical) following the manufacturer’s protocol. They were loaded into CBS High Security embryo straws (Cryo Bio System, NordicCell; 20–30 per straw), and slow-frozen using an Asymptote EF600M controlled rate freezer (Grant Instruments) before being stored in LN2. On the morning of the experiment, straws were thawed with the Embryo Thawing Pack (Origio, CooperSurgical), and the zygotes were cultured as described above. Embryos were monitored hourly for cleavage, and resulting 2C embryos were microinjected 1–2 h post-division.

extract_protocol:
Individual zygotes and 2C embryos were transferred to a drop of M2 medium (Sigma-Aldrich, Merck), then briefly (~10–30 sec) held in a drop of Tyrode’s Solution, Acidic (Sigma-Aldrich, Merck) to remove the zona pellucida. Next, the zygote/2C embryo was swiftly washed through three drops of DPBS (without calcium and magnesium chloride). In an RNase-free environment, the zygote/embryo was carefully pipetted together with 1 µl DPBS into an 8-tube 0.2 ml PCR strip (Axygen) containing 6 µl DPBS supplemented with RiboLock RNase inhibitor (1:200; Thermo Fisher Scientific) in each tube. Once the strip was filled, samples were flash frozen by submerging the bottom part of the tubes in LN2 and then transferred to -80 °C for storage until library preparation.
Library preparation was performed with SMART-Seq Stranded Kit (634443, Takara Bio) for full transcriptome analysis. Libraries of zygotes and 2C embryos were prepared on two separate days following the kit’s user manual starting from intact cells (option 1, with fragmentation). For PCR1, we used indexes from a SMARTer RNA Unique Dual Index Kit – 96U Set A (634452, Takara Bio) to avoid index hopping, and we used 10 cycles (ultra-low input workflow). We did not pool the samples after PCR1. For PCR2, we used 13 cycles, based on a prior pilot experiment. Final RNA-seq libraries were purified using AMPure beads (Agencourt AMPure XP, Beckman Coulter) with a single round of clean-up to minimise sample loss. Successful removal of adapter dimers and appropriate library size distribution were confirmed using an 2100 Bioanalyzer (Agilent). Libraries were quantified with Qubit dsDNA HS kit (Thermo Fisher Scientific), pooled in equimolar ratios, and subjected to a final 1.2x AMPure bead purification. The pooled library was eluted in EB buffer (10 mM Tris-HCl, pH 8.5) and submitted for sequencing. Sequencing was performed at the Norwegian Sequencing Centre (Department of Medical Genetics Ullevål, Oslo University Hospital) on an Illumina NovaSeq 6000 using an SP flow cell with 200 cycles, generating 100 bp paired-end reads.

treatment_protocol: Zygotes or 2C embryos were microinjected with either in vitro transcribed Kdm5b-yfp mRNA (~1150 ng/µl) or nuclease-free water as a control (the same water used to elute the mRNA during cleanup with the RNeasy MinElute Cleanup Kit; Qiagen, 74204). Controlled cytoplasmic injections were carried out with a FemtoJet microinjector (Eppendorf), and a Piezo PMM4G (Prime Tech) for easier penetration of the membrane. Injections were performed in a consistent manner such that the disturbance seen in the cytoplasm upon injection was about the size of a (pro)nucleus.

tag: strain

tag: developmental stage

value: Theiler stage 2

value: 2-cell embryo

value: Kdm5b-yfp mRNA-injected


title: Kdm5b 2C, biol rep 5

description:
Library name: Sample 34
k5b_1x2c_U92


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI2

value: female


title: SU-DHL-6 Rep1 cfChromatin, cfMNase-Seq, 30 min MNase digestion

description: Library name: SUDHL6_cfMNase_Rep1


title: Normal_1_3_6_7

description: Sample 372

value: testis


title: Normal_1_3_7_5

description: Sample 377


title: Kdm5b 2C, biol rep 4

description:
Library name: Sample 33
k5b_1x2c_U84


title: A549 Rep2 cfChromatin, cfMNase-Seq, 30 min MNase digestion

description: Library name: A549_cfMNase_Rep2

source_name: Lung; Alveolar epithelium

value: Lung; Alveolar epithelium

value: Epithelial


title: A549 Rep1 cfChromatin, cfMNase-Seq, 30 min MNase digestion

description: Library name: A549_cfMNase_Rep1


title: Camostattreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI3

value: primary nasal epithelial cells

value: male


title: untreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI2

value: untreated


title: Normal_1_3_7_4

description: Sample 376

value: Normal


title: Kdm5b 2C, biol rep 3

description:
Library name: Sample 32
k5b_1x2c_U83


title: Camostattreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI2

value: Camostattreated


title: Normal_1_3_6_5

description: Sample 370


title: untreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI2


title: untreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI3


title: Kdm5b 2C, biol rep 2

description:
Library name: Sample 31
k5b_1x2c_U82


title: 4C

city: Montreal

first: Philippe

last: Roux

state: QC

address: 2950 Polytechnic Rd

institute: Université de Montréal

description: Library name: 4C

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 40 (based on Ensembl 106)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 40
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: melanoma

value: BRAF-mutated

tag: batch


title: Camostattreated, mock-infected primary nasal epithelial cells of nALI2


title: Normal_1_3_6_3

first: Lin

last: Li

address: Shatai South Road

institute: Southern Medical University

description: Sample 368

tag: gender


title: 4A

description: Library name: 4A


title: Ctrl water 2C, three blastomeres from different embryos, biol rep 9

description:
Library name: Sample 29
ctrl_3xS2c_U91

value: WT

value: Water-injected


title: Normal_1_3_6_1

description: Sample 367

tag: age


title: Normal_1_3_6_6

description: Sample 371

tag: condition


title: 3C

description: Library name: 3C


title: Ctrl water 2C, three blastomeres from different embryos, biol rep 8

description:
Library name: Sample 28
ctrl_3xS2c_U89


title: Normal_1_3_5_8

description: Sample 366

tag: testis


title: 3B

description: Library name: 3B


title: untreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI1

tag: tissue


title: Normal_1_3_5_5

description: Sample 365


title: 3A

description: Library name: 3A

tag: cell line


title: Ctrl water 2C, two blastomeres from different embryos, biol rep 7

description:
Library name: Sample 27
ctrl_2xS2c_U90

tag: cell type


title: Ctrl water 2C, biol rep 6

description:
Library name: Sample 26
ctrl_1x2c_U95

tag: genotype


title: 2C

description: Library name: 2C

tag: treatment


title: Camostattreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI1

tag: Sex


title: Normal_1_3_6_4

description: Sample 369


title: Normal_1_3_5_3

description: Sample 363


title: Normal_1_3_5_4

description: Sample 364


title: Ctrl water 2C, biol rep 5

description:
Library name: Sample 25
ctrl_1x2c_U94


title: untreated, SARS-CoV-2-infected primary nasal epithelial cells of nALI1


title: Camostattreated, mock-infected primary nasal epithelial cells of nALI1

description: ALI-Camo

value: mock


title: 4B

description: Library name: 4B


title: Ctrl water 2C, biol rep 4

description:
Library name: Sample 24
ctrl_1x2c_U93

value: Theiler stage 2


title: Normal_1_3_5_2

description: Sample 362


title: 2B

description: Library name: 2B


title: Ctrl water 2C, biol rep 3

description:
Library name: Sample 23
ctrl_1x2c_U87

value: 2-cell embryo


title: 2A

description: Library name: 2A


title: Kdm5b 2C, biol rep 1

description:
Library name: Sample 30
k5b_1x2c_U81

value: Kdm5b-yfp mRNA-injected


title: untreated, mock-infected primary nasal epithelial cells of nALI1

description: ALI-Ctrl


title: untreated, mock-infected primary nasal epithelial cells of nALI2

value: female


title: Camostattreated, SARS-CoV-2(B1.1.7)-infected primary nasal epithelial cells of nALI1


title: Ctrl water 2C, biol rep 2

description:
Library name: Sample 22
ctrl_1x2c_U86


title: 1C

description: Library name: 1C

value: DMSO


title: Normal_1_3_4_7

description: Sample 360

value: testis


title: KO_2H10_rep3

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.11b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.1.3).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.44.0) to determine differential expression between groups, within the R statistical computing environment (v4.4.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

source_name: iPSC-derived microglia

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: iPSC-derived microglia


title: Ctrl water 2C, biol rep 1

description:
Library name: Sample 21
ctrl_1x2c_U85


title: 1B

description: Library name: 1B


title: KO_1F37_rep3


title: Kdm5b zygote, biol rep 10

description:
Library name: Sample 20
k5b_1zyg_U76

source_name: 1-cell embryo

value: Theiler stage 1

value: 1-cell embryo


title: Normal_1_3_4_4

description: Sample 358

source_name: testis

value: male


title: Normal_1_3_4_5

description: Sample 359

value: Normal


title: 1A

description: Library name: 1A


title: KO_2H10_rep2


title: Kdm5b zygote, biol rep 9

description:
Library name: Sample 19
k5b_1zyg_U75


title: Normal_1_3_4_3

description: Sample 357


title: Normal_1_3_4_2

description: Sample 356


title: KO_2H10_rep1


title: Normal endometrium-on-a-chip 1

city: Seongnam-si

first: Yu-Gyeong

last: Lee

state: Gyeonggi-do

address: 335 Pangyo-ro

department: Life Science

country: South Korea

institute: CHA University

description: Library name: 24_6_c.fq.gz

data_processing:
Raw sequencing reads were preprocessed using fastp v0.23.1 to remove adapter sequences and low-quality reads.
Filtered reads were aligned to the human reference genome (GRCh38) using STAR v2.7.10b with default parameters.
Gene-level read counts were quantified using featureCounts v2.0.6.
Differential expression analysis was performed using the edgeR v3.42.4 (Bioconductor) package, with normalization by TMM-based log2(CPM+1) transformation.
Assembly: GRCh38
Supplementary files format and content: R25GdP2652_Single_Report.xlsx

source_name: Endometrium (chip-derived)

growth_protocol: Cells cultured in the EoC device were maintained in the upper media channel supplied with EGM-2 medium supplemented with sphingosine-1-phosphate (1 nM), VEGF-A (100 ng/mL), VEGF-C (50 ng/mL), and basic fibroblast growth factor (bFGF, 50 ng/mL), and incubated for a total of 7 days.

extract_protocol:
Total RNA from samples was extracted using Labozol reagent per sample. After adding chloroform and thorough mixing, the tubes were centrifuged at 13,000 rpm for 20 min at 4 °C. The aqueous phase was transferred to new tubes, and an equal volume of isopropanol was added, followed by centrifugation at 13,000 rpm for 30 min at 4 °C. Pellets were washed with 70% ethanol. RNA pellets were dissolved in 20 μL of nuclease-free water. RNA quality was evaluated using a NanoDrop spectrophotometer, and only samples with 260/280 and 260/230 absorbance ratios between 1.9 and 2.2 were used for RNA-seq analysis.
For control and test RNAs, the construction of library was performed using QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD (Lexogen) according to the manufacturer’s instructions. In brief, each total RNA were prepared and an oligo-dT primer containing an Illumina compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina compatible linker sequence at its 5’ end. The double stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. High-throughput sequencing was performed as single-end 100bp sequencing using NextSeq 2000 (Illumina Inc.).

treatment_protocol: No additional treatment was applied prior to RNA extraction.

value: Endometrium (chip-derived)

value: HUVEC

value: primary endometrial stromal cells; primary endometrial epithelial cells

tag: disease state

value: batch #1


title: Normal_1_3_4_1

description: Sample 355


title: Kdm5b zygote, biol rep 8

description:
Library name: Sample 18
k5b_1zyg_U72

value: WT


title: KO_1G4_rep1


title: Normal_1_3_5_1

description: Sample 361


title: Kdm5b zygote, biol rep 6

description:
Library name: Sample 16
k5b_1zyg_U70


title: KO_1G4_rep2


title: Kdm5b zygote, biol rep 7

description:
Library name: Sample 17
k5b_1zyg_U71


title: Normal endometrium tissue 2

description: Library name: 24_8.fq.gz

source_name: Endometrium

value: Endometrium


title: KO_1F37_rep2


title: Normal_1_3_3_5

description: Sample 354


title: Normal endometrium tissue 1

description: Library name: 24_6.fq.gz


title: Kdm5b zygote, biol rep 5

description:
Library name: Sample 15
k5b_1zyg_U69


title: RIF endometrium-on-a-chip 3

description: Library name: 24_5_2_c.fq.gz

value: recurrent implantation failure


title: Normal_1_3_3_2

description: Sample 353


title: Kdm5b zygote, biol rep 4

description:
Library name: Sample 14
k5b_1zyg_U64


title: RIF endometrium tissue 3

description: Library name: 24_5_2.fq.gz


title: Normal_1_3_3_1

description: Sample 352


title: KO_1F37_rep1


title: MHS_237_rep2


title: Normal endometrium-on-a-chip 2

description: Library name: 24_8_c.fq.gz


title: RIF endometrium-on-a-chip 2

description: Library name: 24_4_c.fq.gz


title: Normal_1_3_2_7

description: Sample 351


title: MHS_2H9_rep2


title: Kdm5b zygote, biol rep 2

description:
Library name: Sample 12
k5b_1zyg_U62


title: RIF endometrium tissue 2

description: Library name: 24_4.fq.gz


title: Kdm5b zygote, biol rep 1

description:
Library name: Sample 11
k5b_1zyg_U61


title: Normal_1_3_2_6

description: Sample 350


title: RIF endometrium-on-a-chip 1

description: Library name: 24_1_2_c.fq.gz


title: MHS_2H9_rep1


title: Normal_1_3_2_2

description: Sample 348


title: MHS_2H11_rep3


title: hSI82,seqRun0

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

description:
Library name: hSI82
gene_counts_IBD_orgs.txt.gz

data_processing:
Reads were de-multiplexed using SABRE version 663365f.
Reads were mapped to the human genome reference, GRCh38.p12, using STAR v2.7.2b, and aliments sorted using SAMtools v1.9.
Positional puplicate alignments were marked using Picard MarkDuplicates v2.18.9. UMIs of positional duplicates were analysed with Je markdupes version 2.0RC and true duplicates were flagged.
Non-duplicate alignments within gene features were counted using FeatureCounts in Rsubread version 1.6.1 resulting in a gene-count matrix.
Assembly: GRCh38.p12
Supplementary files format and content: tab-separated values. Table of unique read counts per gene, columns as samples, genes as rows.

growth_protocol: Biopsy samples were collected for organoid and bacterial culturing from control patients and patients newly diagnosed with IBD. Organoids were grown as described in: Engel RM, Jardé T, Oliva K, Kerr G, Chan WH, Hlavca S, et al. Modeling colorectal cancer: A bio-resource of 50 patient-derived organoid lines. J Gastroenterol Hepatol. 2022;37(5):898-907.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen, #74004) and assessed for quality using the Bioanalyzer (Agilent) and Qubit (Invitrogen).
Novel MHTP pooled RNA-Seq pipeline (Version 03/04/2018) for generating Illumina-compatible libraries. All samples were processed starting with 20 ng of total RNA respectively, quantitated by Qubit. Libraries were made by individual first strand synthesis with an indexed pA primer to add the index sequence, then cDNA of all samples in a sequencing run were pooled for subsequent processing. Pooled samples were amplified using a template switching oligo. P5 is added by PCR and P7 by Nextera transposase. I7 indexes were added to the final libraries to enable parsing of sample sets. Library is designed so custom R1 primer reads directly into index followed by 10bp UMI. R2 primer reads into RNA in the sense direction.

treatment_protocol: For microinjections, glass capillaries were pulled to a fine point with a 5 - 10 μm opening and loaded with 4 kDa fluorescein isothiocyanate (FITC)- dextran, with or without bacterial sample, or 40 kda FITC-dextran in 1X PBS for microinjection into cystic organoids. All microinjections were carried out under a Zeiss SteREO Discovery V8 microscope using the Injectman 4 Micromanipulator coupled with FemtoJet 4i system (Eppendorf). Injection parameters were set at 120 hPa (injection pressure), 0.25 seconds (injection time) and 0 hPa (compensation pressure). Microinjected bacterial strains included the two closely related Bacteroidaceae isolates E4 (CC01454; from a healthy patient) and E2 (CC01453; from a Crohn's patient with inflammation). They also included the two closely related Enterobacteriaceae isolates B2 (CC00517; from healthy patient) and G11 (CC00518; from an ulcerative colitis patient with inflammation).

value: organoids

tag: patient id

value: none,Non Inflammed


title: RIF endometrium tissue 1

description: Library name: 24_1_2.fq.gz

value: female


title: MHS_2H11_rep2


title: Ctrl water zygote, biol rep 10

description:
Library name: Sample 10
ctrl_1zyg_U74

value: Water-injected


title: Normal_1_3_2_3

description: Sample 349

value: testis


title: Ctrl water zygote, biol rep 9

description:
Library name: Sample 9
ctrl_1zyg_U73


title: Ctrl water zygote, biol rep 8

description:
Library name: Sample 8
ctrl_1zyg_U68


title: hSI81,seqRun0

description:
Library name: hSI81
gene_counts_IBD_orgs.txt.gz

source_name: Duodenum

value: Duodenum


title: Normal_1_3_12_8

description: Sample 346


title: MHS_2H11_rep1

value: iPSC-derived microglia


title: Normal_1_3_2_1

description: Sample 347


title: MHS_237_rep1


title: hSI68,seqRun0

description:
Library name: hSI68
gene_counts_IBD_orgs.txt.gz

value: Crohns,Inflammed


title: Kdm5b zygote, biol rep 3

description:
Library name: Sample 13
k5b_1zyg_U63

value: Theiler stage 1

value: 1-cell embryo

value: Kdm5b-yfp mRNA-injected


title: hSI67,seqRun0

description:
Library name: hSI67
gene_counts_IBD_orgs.txt.gz


title: Ctl_D4N_rep2


title: Ctl_D4N_rep1


title: Ctrl water zygote, biol rep 6

description:
Library name: Sample 6
ctrl_1zyg_U66


title: hSI66,seqRun0

description:
Library name: hSI66
gene_counts_IBD_orgs.txt.gz


title: Ctrl water zygote, biol rep 5

description:
Library name: Sample 5
ctrl_1zyg_U65


title: Ctl_71N_rep2


title: Ctrl water zygote, biol rep 4

description:
Library name: Sample 4
ctrl_1zyg_U60


title: Normal_1_3_12_5

description: Sample 343

value: male

value: Normal


title: hSI65,seqRun0

description:
Library name: hSI65
gene_counts_IBD_orgs.txt.gz


title: Normal_1_3_12_3

description: Sample 341


title: Ctl_71N_rep1


title: Ctrl water zygote, biol rep 7

description:
Library name: Sample 7
ctrl_1zyg_U67


title: hSI62,seqRun0

description:
Library name: hSI62
gene_counts_IBD_orgs.txt.gz


title: Ctrl water zygote, biol rep 3

description:
Library name: Sample 3
ctrl_1zyg_U59


title: Normal_1_3_12_1

description: Sample 340


title: Ctl_42N_rep2


title: Normal_1_3_11_8

description: Sample 339


title: Normal_1_3_12_7

description: Sample 345


title: Ctrl water zygote, biol rep 2

description:
Library name: Sample 2
ctrl_1zyg_U58


title: hSI61,seqRun0

description:
Library name: hSI61
gene_counts_IBD_orgs.txt.gz


title: Ctl_42N_rep1


title: Ctrl water zygote, biol rep 1

description:
Library name: Sample 1
ctrl_1zyg_U57


title: D4_double-KO_rep3

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: Sample 24

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools (v1.13)
Reads were trimmed Trim Galore 3.4
Reads were mapped to the mouse  reference assembly (mm10) using STAR 2.7.10a
Reads were quantiﬁed using RSEM 1.3.1
Read count means, fold-change (FC) and p-adj were calculated with DEseq2 v1.34.0
Assembly: mm10
Supplementary files format and content: Tab-delimited .tsv matrix: rows contain gene symbols, columns contain all samples. The values are DESeq2 size-factor normalized counts (no log transform). The header is included.

source_name: Double-KO differentiated cells

growth_protocol: mESC were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM (Thermo Fisher Scientific, 10829018) supplemented with 15% fetal bovine serum (FBS; Thermo Fisher Scientific, A5256801), 1x antibiotic and antimycotic solution (Sigma-Aldrich, A5955), 1x glutaMAX (Thermo Fisher Scientific, 35050038), 1x non-essential amino acids (NEAA; Thermo Fisher Scientific, 11140035), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, 21985023) and leukemia inhibitory factor (LIF; made in-house). Cells were maintained at 37 °C with 5% CO2. For the multilineage differentiation, cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days.

extract_protocol:
Total RNA was extracted using the NZY Total RNA Isolation Kit (NZYTech, MB13402), according to the protocol provided by the manufacturer. Libraries were prepared with the RNA sample preparation kit (Truseq stranded mRNA Library).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Starting from a previously described Cre-inducible Mll2-KO mESC line, Mll1-KO mESC were generated via CRISPR editing. Two sg-RNAs were designed flanking the region to-be deleted for each line, using Benchling’s CRISPR tool (https://www.benchling.com/crispr). For each sgRNA, two oligonucleotides were synthesized , annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p, provided by Leo Kurian’s lab). mESC were transfected with CRISPR-Cas9 constructs using LipofectamineTM 3000 (Thermo Fisher Scientific, L3000001).  For the generation of Mll2-KO and double-KO mESC lines, cells were treated with (Z)-4-Hydroxytamoxifen (4-OHT; Sigma-Aldrich, H7904) at a final concentration of 800 nM for 48 hours.

value: Double-KO differentiated cells

value: Differentiated cells

value: Double-KO

value: 4-OHT treated


title: BNP_PEDOT_PSF_AG_3

city: Chengdu

first: Xinyi

last: Fang

address: Guoxue alley

institute: Lab for Aging Research and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University

data_processing:
OmicStudio tools
Assembly: HISAT2
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 RPKM values for each Sample

source_name: PDLSC

extract_protocol:
RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.
At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: PDLSCs cultured on the various hydrogels under high glucose and inflammatory conditions (33mM glucose, 100ug/L LPS) with 600mV electrical stimulation  for 3 days.

value: PDLSC

value: mesenchymal stem cells

value: PDLSC cultured on the BNP-PEDOT- PSF-AG hydrogel under high glucose and inflammatory conditions (LPS stimulation) with 600mV ES potentials.


title: hSI60,seqRun0

description:
Library name: hSI60
gene_counts_IBD_orgs.txt.gz

value: organoids

value: none,Non Inflammed


title: hSI59,seqRun0

description:
Library name: hSI59
gene_counts_IBD_orgs.txt.gz

value: Duodenum


title: Normal_1_3_11_6

city: Guangzhou

description: Sample 338

value: testis


title: Normal_1_3_12_6

description: Sample 344


title: hSI57,seqRun0

description:
Library name: hSI57
gene_counts_IBD_orgs.txt.gz

value: Crohns,Inflammed


title: BNP_PEDOT_PSF_AG_1


title: BNP_PEDOT_PSF_AG_2


title: hSI56,seqRun0

description:
Library name: hSI56
gene_counts_IBD_orgs.txt.gz

value: Crohns,Non Inflammed


title: D4_double-KO_rep2

description: Library name: Sample 23


title: Normal_1_3_11_5

description: Sample 337


title: Normal_1_3_12_4

description: Sample 342


title: PEDOT_PSF_AG_3

value: PDLSC cultured on the PEDOT- PSF-AG hydrogel under high glucose and inflammatory conditions (LPS stimulation) with 600mV ES potentials.


title: Normal_1_3_11_3

description: Sample 336


title: hSI55,seqRun0

description:
Library name: hSI55
gene_counts_IBD_orgs.txt.gz

value: UC,Inflammed


title: D4_double-KO_rep1

description: Library name: Sample 22


title: hSI54,seqRun0

description:
Library name: hSI54
gene_counts_IBD_orgs.txt.gz

value: UC,Non Inflammed


title: Normal_1_3_11_2

description: Sample 335

value: male

value: Normal


title: D4_Mll2-KO_rep3

description: Library name: Sample 21

source_name: Mll2-KO differentiated cells

value: Mll2-KO differentiated cells

value: Differentiated cells


title: D4_Mll2-KO_rep2

description: Library name: Sample 20

value: 4-OHT treated


title: Normal_1_3_11_1

description: Sample 334


title: hSI52,seqRun0

description:
Library name: hSI52
gene_counts_IBD_orgs.txt.gz


title: D4_Mll2-KO_rep1

description: Library name: Sample 19


title: PEDOT_PSF_AG_2

value: PDLSC


title: PEDOT_PSF_AG_1

value: mesenchymal stem cells


title: PSF_AG_3

value: PDLSC cultured on the PSF-AG hydrogel under high glucose and inflammatory conditions (LPS stimulation) with 600mV ES potentials.


title: Normal_1_3_10_4

description: Sample 332


title: D4_Mll1-KO_rep2

description: Library name: Sample 17

source_name: Mll1-KO differentiated cells

value: Mll1-KO differentiated cells

value: Untreated


title: hSI50,seqRun0

description:
Library name: hSI50
gene_counts_IBD_orgs.txt.gz

value: organoids


title: Normal_1_3_10_3

description: Sample 331

value: testis


title: D4_Mll1-KO_rep3

description: Library name: Sample 18


title: hSI49,seqRun0

description:
Library name: hSI49
gene_counts_IBD_orgs.txt.gz

value: Duodenum


title: PSF_AG_2


title: PSF_AG_1


title: hSI43,seqRun0

description:
Library name: hSI43
gene_counts_IBD_orgs.txt.gz

value: Crohns,Non Inflammed


title: BNP_PEDOT_PSF_AG_3

treatment_protocol: THP-1 cultured on the various hydrogels under high glucose and inflammatory conditions (33mM glucose, 100ug/L LPS)  for 3 days.

value: macrophage

value: THP-1 cultured on the BNP-PEDOT-PSF-AG hydrogel under high glucose and inflammatory conditions (LPS stimulation)


title: D4_WT_rep3

description: Library name: Sample 15

source_name: WT differentiated cells

value: WT differentiated cells

value: WT


title: Normal_1_3_10_2

description: Sample 330

value: male

value: Normal


title: hSI42,seqRun0

description:
Library name: hSI42
gene_counts_IBD_orgs.txt.gz

value: Crohns,Inflammed


title: BNP_PEDOT_PSF_AG_2


title: Normal_1_3_10_1

description: Sample 329


title: hSI53,seqRun0

description:
Library name: hSI53
gene_counts_IBD_orgs.txt.gz

value: UC,Non Inflammed


title: hSI40,seqRun0

description:
Library name: hSI40
gene_counts_IBD_orgs.txt.gz


title: Normal_1_3_1_8

description: Sample 328


title: BNP_PEDOT_PSF_AG_1


title: Normal_1_3_10_7

description: Sample 333


title: Normal_1_3_1_7

description: Sample 327


title: D4_WT_rep2

description: Library name: Sample 14

value: Differentiated cells


title: PEDOT_PSF_AG_3

value: THP-1 cultured on the PEDOT-PSF-AG hydrogel under high glucose and inflammatory conditions (LPS stimulation)


title: D0_double-KO_rep3

description: Library name: Sample 12

source_name: Double-KO mESC

value: Double-KO mESC

value: mESC

value: Double-KO

value: 4-OHT treated


title: hSI39,seqRun0

description:
Library name: hSI39
gene_counts_IBD_orgs.txt.gz

value: organoids


title: Normal_1_3_1_6

description: Sample 326

value: testis


title: PEDOT_PSF_AG_2


title: hSI33,seqRun0

description:
Library name: hSI33
gene_counts_IBD_orgs.txt.gz

value: none,Non Inflammed


title: D4_Mll1-KO_rep1

description: Library name: Sample 16

value: Mll1-KO differentiated cells

value: Untreated


title: hSI32,seqRun0

description:
Library name: hSI32
gene_counts_IBD_orgs.txt.gz

value: Duodenum


title: Normal_1_3_1_4

description: Sample 324


title: D0_double-KO_rep1

description: Library name: Sample 10


title: D0_double-KO_rep2

description: Library name: Sample 11


title: hSI31,seqRun0

description:
Library name: hSI31
gene_counts_IBD_orgs.txt.gz


title: AG_3

value: macrophage

value: THP-1 cultured on the AG hydrogel under high glucose and inflammatory conditions (LPS stimulation)


title: AG_2


title: hSI30,seqRun0

description:
Library name: hSI30
gene_counts_IBD_orgs.txt.gz


title: D0_Mll2-KO_rep3

description: Library name: Sample 9

source_name: Mll2-KO mESC

value: Mll2-KO mESC


title: Normal_1_3_1_2

description: Sample 322

value: male

value: Normal


title: D4_WT_rep1

description: Library name: Sample 13

value: WT differentiated cells

value: Differentiated cells

value: WT


title: hSI29,seqRun0

description:
Library name: hSI29
gene_counts_IBD_orgs.txt.gz

value: Crohns,Non Inflammed


title: hSI28,seqRun0

description:
Library name: hSI28
gene_counts_IBD_orgs.txt.gz


title: AG_1


title: D0_Mll2-KO_rep2

description: Library name: Sample 8

value: mESC


title: D0_Mll1-KO_rep3

description: Library name: Sample 6

source_name: Mll1-KO mESC

value: Mll1-KO mESC


title: D0_Mll1-KO_rep2

description: Library name: Sample 5


title: Normal_1_3_1_5

description: Sample 325


title: Normal_1_2_9_5

description: Sample 319


title: PEDOT_PSF_AG_1

value: THP-1 cultured on the PEDOT-PSF-AG hydrogel under high glucose and inflammatory conditions (LPS stimulation)