title: ZNF729-FH_24h_REP4

city: Stanford

first: Raquel

last: Fueyo

address: 265 Campus Drive

institute: Stanford University

description: Library name: ZNF729-FH_24h_REP4

data_processing:
Illumina adapters were trimmed from reads using Skewer. Transcript alignment and quantification was performed using Salmon. For differential gene expression analysis we used DESeq2 after excluding transcripts with less than 10 reads across the tested samples. DESeq2 compared the effect of nontarg-CARGO or LTR5Hs-CARGO in the hnPSCs and the biological replicates were used as covariates.
Assembly: gencode v47
Supplementary files format and content: txt, TPM

source_name: hnPSCs

growth_protocol: hnPSCs were grown in PXGL

extract_protocol:
RNA was extracted with Trizol and purified with Direct-zol columns
Messenger RNA was purified 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. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification and they were checked with Qubit and qPCR for quantification and Bioanalyzer for size distribution detection.

value: hnPSCs

value: human naive pluripotent stem cells


title: zebrafish embryo, 22C 40A total validation set 13h 1

status: Public on Jul 13 2025

type: SRA

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: 22C_40A_total_v_13h_1

library_source: other

data_processing:
constant sequences were trimmed
reporter 3'UTR sequences were aligned against the full set of 90,000 reporter sequences
number of unique molecular identifiers (UMIs) that match each reporter sequence were counted
Assembly: the full set of 90,000 reporter sequences
Supplementary files format and content: tab-delimited text files include readcount for each reporter in each sample

molecule: other

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA was isolated using tri-reagent (Sigma T9424) and quantified using nanodrop
We used a two-step RNA-Seq library construction approach that specifically targeted the variable 3′UTR region of reporters. In the first step, total-RNA was reverse-transcribed with Maxima RT (Thermo Fisher) and a gene-specific primer that matched the 20nt downstream 3′UTR universal adaptor. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step, resulting cDNA was amplified by 18 cycles of PCR with primers that matched the 20nt upstream 3′UTR universal adaptor and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing adaptors,  resulting in the final RNA-Seq library.

treatment_protocol: 1 pg mRNA from reporters injection at 1-cell stage

tag: tissue

value: whole embryo


title: END-seq_G292_E2

city: BETHESDA

first: Benura

last: Azeroglu

state: Maryland

address: National Cancer Institute, NIH, Building 37, Room 1108 37 Convent Drive

country: USA

institute: NIH

description: Library name: Library 11

library_source: genomic

data_processing:
We developed a Python script, "getTelomereENDseq," to analyze gzipped FASTQ files for the presence of telomeric motifs in DNA sequences on a command-line environment using a Linux-based operating system and the statistical environment RStudio. The script identifies sequences containing G-rich and C-rich telomeric repeats, quantifies their occurrences, and calculates their relative frequencies. It takes a gzipped FASTQ file as input, and the minimum number of telomeric repeats is required. It generates two output files: one with sequences containing G-rich motifs and another with sequences containing C-rich motifs. For this study, we used a minimum of 4 consecutive TTAGGG repeats for G-rich reads and a minimum of 4 consecutive CCCTAA repeats for C-rich reads.
Assembly: hg19, mm10
Supplementary files format and content: The .txt files contain reads corresponding to the G- and C-strands.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human, mouse, and dog cell lines were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 0.5 mg/ml penicillin, streptomycin and L-glutamine (Gibco) and cultured at 37°C and 5%CO2. HeLa cells used in this study were HeLa1.2.11. G292 cells were grown in McCoy medium supplement with 15% FBS and 0.5 mg/ml penicillin, streptomycin and L-glutamine (Gibco). Cell lines were tested for mycoplasma contamination.

extract_protocol:
Cells were washed with PBS, treated with Trypsin/EDTA, and neutralized with growth media. After pelleting and resuspending in neutralization buffer, cells were processed for END-seq or S1-END-seq. For S1-END-seq, cells were embedded in agarose plugs, lysed with Proteinase K, treated with RNase A, and equilibrated in S1 nuclease buffer. S1 nuclease was added to the plugs, incubated on ice for 15 minutes, then at 37°C for 20 minutes before terminating the reaction with EDTA.
For S1/END-seq, plugs were processed through the standard END-seq protocol.

tag: cell line

tag: genotype

value: wild-type


title: ZNF729-FH_3h_REP4

state: CA

description: Library name: ZNF729-FH_3h_REP4

library_source: transcriptomic

molecule: polyA RNA

tag: cell type

tag: treatment


title: ZNF729-FH_DMSO_REP4

description: Library name: ZNF729-FH_DMSO_REP4

value: DMSO


title: zebrafish embryo, 22C 40A total validation set 11h 2

description: Library name: 22C_40A_total_v_11h_2


title: zebrafish embryo, 22C 40A total validation set 11h 1

description: Library name: 22C_40A_total_v_11h_1


title: zebrafish embryo, 22C 40A polyA 9hr 2

description: Library name: 22C_40A_polyA_9hr_2


title: ZNF729-FH_3h_REP3

description: Library name: ZNF729-FH_3h_REP3


title: ZNF729-FH_24h_REP3

description: Library name: ZNF729-FH_24h_REP3


title: zebrafish embryo, 22C 40A polyA 9hr 1

description: Library name: 22C_40A_polyA_9hr_1


title: ZNF729-FH_DMSO_REP3

description: Library name: ZNF729-FH_DMSO_REP3


title: zebrafish embryo, 22C 40A polyA 7hr 1

description: Library name: 22C_40A_polyA_7hr_1


title: zebrafish embryo, 22C 40A polyA 7hr 2

description: Library name: 22C_40A_polyA_7hr_2


title: ZNF729-FH_3h_REP2

description: Library name: ZNF729-FH_3h_REP2


title: ZNF729-FH_24h_REP2

description: Library name: ZNF729-FH_24h_REP2


title: ZNF729-FH_DMSO_REP2

description: Library name: ZNF729-FH_DMSO_REP2


title: zebrafish embryo, 22C 40A polyA 5hr 1

description: Library name: 22C_40A_polyA_5hr_1


title: zebrafish embryo, 22C 40A polyA 3hr 2

description: Library name: 22C_40A_polyA_3hr_2


title: zebrafish embryo, 22C 40A polyA 5hr 2

description: Library name: 22C_40A_polyA_5hr_2


title: zebrafish embryo, 22C 40A polyA 3hr 1

description: Library name: 22C_40A_polyA_3hr_1


title: ZNF729-FH_3h_REP1

description: Library name: ZNF729-FH_3h_REP1


title: zebrafish embryo, 22C 40A polyA 1hr 2

description: Library name: 22C_40A_polyA_1hr_2


title: zebrafish embryo, 22C 40A polyA 1hr 1

description: Library name: 22C_40A_polyA_1hr_1


title: zebrafish embryo, 22C 40A polyA 15hr 2

description: Library name: 22C_40A_polyA_15hr_2


title: ZNF729-FH_24h_REP1

description: Library name: ZNF729-FH_24h_REP1


title: ZNF729-FH hnPSCs treated with DMSO, replicate 1, H3K27ac ChIP

description: Library name: H3K27ac_REP1

data_processing:
Standard Illumina adapters were cut from the Illumina reads using using Cutadapt. Reads were aligned to the Homo sapiens (hg38) genome using Bowtie in its default behavior. PCR duplicates were removed from the analysis using Samtools. Coverage bigwig files were generated with Deeptools bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig, ChIP-seq signal

growth_protocol: hnPSCs are grown in PXGL

extract_protocol:
Chromatin was sonicated and after the IPand reverse crosslinking the DNA was recovered using a Qiagen kit
NEBNext Ultra II Library Prep kit (New England Biolabs, E7645S)

treatment_protocol: DMSO or dTAGv-1 500 nM for 24 hours, fix in 10 min with 1% methanol free formaldehyde

value: naive embryonic stem cells


title: ZNF729-FH hnPSCs treated with DMSO, replicate 1, H3K4me3 ChIP

description: Library name: H3K4me3_REP1


title: ZNF729-FH hnPSCs treated with dTAG, replicate 2, TRIM28 ChIP

description: Library name: TRIM28_dTAG_ZNF729FH_REP2

value: dTAG


title: zebrafish embryo, 22C 40A polyA 13hr 2

description: Library name: 22C_40A_polyA_13hr_2


title: ZNF729-FH hnPSCs treated with DMSO, replicate 2, H3K4me3 ChIP

description: Library name: H3K4me3_REP2


title: ZNF729-FH hnPSCs treated with DMSO, replicate 2, H3K27ac ChIP

description: Library name: H3K27ac_REP2


title: zebrafish embryo, 22C 40A polyA 13hr 1

description: Library name: 22C_40A_polyA_13hr_1


title: zebrafish embryo, 22C 40A polyA 15hr 1

description: Library name: 22C_40A_polyA_15hr_1


title: ZNF729-FH hnPSCs treated with dTAG, replicate 2, input, corresponding to the TRIM28 ChIP

description: Library name: INPUT_dTAG_ZNF729FH_REP2


title: zebrafish embryo, 22C 40A polyA 11hr 2

description: Library name: 22C_40A_polyA_11hr_2


title: ZNF729-FH hnPSCs treated with DMSO, replicate 2, TRIM28 ChIP

description: Library name: TRIM28_DMSO_ZNF729FH_REP2


title: zebrafish embryo, 22C 40A polyA 11hr 1

description: Library name: 22C_40A_polyA_11hr_1


title: zebrafish embryo, 22C 0A total validation set source

description: Library name: 22C_0A_total_v_source


title: ZNF729-FH_DMSO_REP1

description: Library name: ZNF729-FH_DMSO_REP1


title: zebrafish embryo, 22C 0A total validation set 9h 2

description: Library name: 22C_0A_total_v_9h_2


title: ZNF729-FH hnPSCs treated with dTAG, replicate 1, input, corresponding to the TRIM28 ChIP

description: Library name: INPUT_dTAG_ZNF729FH_REP1


title: ZNF729-FH hnPSCs treated with dTAG, replicate 1, TRIM28 ChIP

description: Library name: TRIM28_dTAG_ZNF729FH_REP1


title: zebrafish embryo, 22C 0A total validation set 7h 2

description: Library name: 22C_0A_total_v_7h_2


title: ZNF729-FH hnPSCs treated with DMSO, replicate 1, TRIM28 ChIP

description: Library name: TRIM28_DMSO_ZNF729FH_REP1


title: zebrafish embryo, 22C 0A total validation set 7h 1

description: Library name: 22C_0A_total_v_7h_1


title: KIRI-2

city: wenzhou

first: Longwei

last: Zhao

address: University-Town, Wenzhou, Zhejiang, P.R.China

country: China

institute: Wenzhou Medical university

description:
Library name: sample2
KIRI-2-FPKM

data_processing:
After library construction, initial quantification was performed using Qubit 2.0 Fluorometer. Libraries were diluted to 1.5 ng/μl, followed by insert size analysis on Agilent 2100 Bioanalyzer. Upon confirming expected insert sizes, qRT-PCR was used for accurate quantification of effective library concentration (>2 nM) to ensure quality.
Upon passing QC, qualified libraries were pooled based on effective concentration and desired sequencing depth for Illumina sequencing. The process utilizes Sequencing by Synthesis (SBS) technology. During sequencing, four fluorescently-labeled dNTPs, DNA polymerase, and adapter primers are added to the flow cell for amplification. As each sequencing cluster extends the complementary strand, incorporation of a fluorescent dNTP releases a corresponding signal. The sequencer captures these fluorescence signals, which are then converted into sequencing peaks through software analysis to determine the sequence.
Eukaryotic mRNA sequencing was performed on the HiSeq platform to analyze the complete transcriptome of specific tissues/cells. Library preparation followed the Illumina TruSeq™ RNA Sample Prep Kit protocol.
Assembly: GRCm39
Supplementary files format and content: The text file contains count values, FPKM values, and gene names for each sample.

molecule: total RNA

organism: Mus musculus

source_name: nephridial tissue

extract_protocol:
Kidney tissues were homogenized in TRIzol, chloroform-separated, and RNA was precipitated (isopropanol), ethanol-washed, and resuspended. Alternatively, the RNeasy Mini Kit (Qiagen) was used with on-column DNase digestion to ensure genomic DNA removal.
RNA libraries were prepared for sequencing using standard illumina protocols

value: nephridial tissue

value: Mouse whole kidney cells

value: all cells

value: WT

tag: batch

value: single batch


title: zebrafish embryo, 22C 0A total validation set 5h 2

description: Library name: 22C_0A_total_v_5h_2


title: KIRI-1

description:
Library name: sample1
KIRI-1-FPKM


title: ZNF729-FH hnPSCs treated with DMSO, replicate 1, input, corresponding to the TRIM28 ChIP

description: Library name: INPUT_DMSO_ZNF729FH_REP1


title: ZNF729-FH hnPSCs treated with dTAG, replicate 2, ZNF729-HA ChIP

description: Library name: ZNF729-HA_dTAG_REP2


title: ZFK-1

description:
Library name: sample3
ZFK-1-FPKM

value: Zafirlukast


title: total RNA from HepG2 rep2

type: RNA

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

hyb_protocol: The BeadChips were incubated in an Ilumina Hybridization oven at 58C for 14 to 20 hours at a rocking speed of 5.

scan_protocol: Beadchips were washed also according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide and scanned on an Illumina iScan Reader.

data_processing: Data analysis was performed with the Expression module (Illumina HumanHT-12 V4.0) of the GenomeStudio software (Illumina; version 2011.1)

label: biotin

label_protocol: The labeled cRNA was then normalized at (250ng) and hybridized on (Human HT-12_v4 arrays) according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide.

growth_protocol: HepG2, SKHep1 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies), supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco). NorHep were maintained in human hepatocyte cell culture complete medium (Celprogen)

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Life Technologies) according to the manufacturer's protocol.

tag: source gender

value: male

value: cancer HCC cells line


title: total RNA from SKHep1 rep1


title: ZNF729-FH hnPSCs treated with DMSO, replicate 2, input, corresponding to the TRIM28 ChIP

description: Library name: INPUT_DMSO_ZNF729FH_REP2


title: total RNA from NorHep rep2

source_name: NorHep

value: primary liver cells (NorHep)


title: zebrafish embryo, 22C 0A total validation set 5h 1

description: Library name: 22C_0A_total_v_5h_1


title: total RNA from NorHep rep3


title: total RNA from SKHep1 rep3


title: ZNF729-FH hnPSCs treated with dTAG, replicate 2, input

description: Library name: INPUT_dTAG_REP2


title: ND567 with APC feeder cells

city: Philadelphia

first: Gregory

middle: M

last: Chen

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: ND567_feeder
Single-cell RNA-Seq performed in gamma-delta CCR5KI-CAR19 T cells manufactured with APC feeder cells

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned and summarized as feature-barcode matrices by cellranger v8.8.0 with the GRCh38-2024-A reference.
Assembly: GRCh38
Supplementary files format and content: .h5 files consisting of the cellranger output filtered_feature_bc_matrix.h5 file

source_name: T cells

growth_protocol: Gamma-delta CCR5KI-CAR19 T cells were grown with our without APC feeder cells as indicated

extract_protocol:
Single-cell RNA-Seq was performed using the Chromium GEM-X Single Cell 3' kit.
Single-cell RNA-Seq was performed using the Chromium GEM-X Single Cell 3' kit. Libraries were constructed with Chromium Connect according to manufacturer's specifications. Sequencing was performed using a NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles)

treatment_protocol: APC feeder cells vs No APC feeder cells

value: T cells

value: Gamma-delta CCR5KI-CAR19

value: APC feeder cells


title: ND570 with APC feeder cells

description:
Library name: ND570_feeder
Single-cell RNA-Seq performed in gamma-delta CCR5KI-CAR19 T cells manufactured with APC feeder cells


title: total RNA from NorHep rep1


title: zebrafish embryo, 22C 0A total validation set 3h 2

description: Library name: 22C_0A_total_v_3h_2

value: whole embryo


title: ZNF729-FH hnPSCs treated with DMSO, replicate 2, ZNF729-HA ChIP

description: Library name: ZNF729-HA_DMSO_REP2

value: hnPSCs


title: ND567 with no APC feeder cells

description:
Library name: ND567_nofeeder
Single-cell RNA-Seq performed in gamma-delta CCR5KI-CAR19 T cells manufactured with no APC feeder cells

value: No APC feeder cells


title: ND570 with no APC feeder cells

description:
Library name: ND570_nofeeder
Single-cell RNA-Seq performed in gamma-delta CCR5KI-CAR19 T cells manufactured with no APC feeder cells


title: ND624 with APC feeder cells

description:
Library name: ND624_feeder
Single-cell RNA-Seq performed in gamma-delta CCR5KI-CAR19 T cells manufactured with APC feeder cells


title: ZFK-2

description:
Library name: sample4
ZFK-2-FPKM


title: zebrafish embryo, 22C 0A total validation set 3h 1

description: Library name: 22C_0A_total_v_3h_1


title: total RNA from SKHep1 rep2


title: total RNA from HepG2 rep3


title: total RNA from HepG2 rep1


title: IC-LOC, H1N1, MOI=10, 48hpi

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

description: Library name: H1N1_48hr

data_processing:
Using Cellranger 7.1 version with introns
Assembly: GRCh38
Supplementary files format and content: .tsv, .mtx

source_name: organ on chip

extract_protocol:
Cells were harvested from organ-on-chip devices using 0.25% trypsin and were resuspended in a single-cell suspension
scRNAseq gene expression using 10x genomics chroumium platform 3' mRNA

value: organ on chip

value: HUVEC, NHLF, SAEC, macrophage, dendritic cell, RBC-depleted whole blood

value: endothelial cell, fibroblast, small airway epithelial cell, immune cells


title: ZNF729-FH hnPSCs treated with DMSO, replicate 2, input

description: Library name: INPUT_DMSO_REP2

value: naive embryonic stem cells

value: DMSO


title: zebrafish embryo, 22C 0A total validation set 1h 2

description: Library name: 22C_0A_total_v_1h_2


title: ZNF729-FH hnPSCs treated with dTAG, replicate 1, ZNF729-HA ChIP

description: Library name: ZNF729-HA_dTAG_REP1

value: dTAG


title: zebrafish embryo, 22C 0A total validation set 1h 1

description: Library name: 22C_0A_total_v_1h_1


title: IC-LOC, H1N1, MOI=10, 24hpi

description: Library name: H1N1_24hr

value: WT


title: IC-LOC, uninfected control

description: Library name: Control


title: IC-LOC, H1N1, MOI=10, 8hpi

description: Library name: H1N1_08hr


title: LU99 cells, MRTX1719+Adagrasib, rep 3

city: Washington D.C.

first: Kathleen

last: Mulvaney

address: 7144 13th PL NW

department: Fralin Biomedical Research Institute

institute: Virginia Tech Cancer Research Center DC

description:
Library name: Sample 18
Combo_U_3

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides.
Reads were aligned to the human genome (GRCh38) with STAR (v2.5.2b)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

growth_protocol: Cells were grown at 37°C in 5% CO2 in a humidied incubator, cultured in RPMI media with 10% FBS and 1% pen-strep

extract_protocol:
Total RNA was extracted from frozen cell samples using the Qiagen RNeasy Plus Universal Mini Kit according to the manufacturer's instructions.
The RNA sequencing libraries were prepared using the ABclonal mRNA-seq Lib Prep Kit for Illumina (poly A selection)

treatment_protocol: 5 days with DMSO control, 20nM MRTX1719, 300nM Adagrasib, or 1uM Belvarafenib

value: non-small cell lung cancer cell line


title: zebrafish embryo, 22C 0A total validation set 15h 2

description: Library name: 22C_0A_total_v_15h_2


title: ZNF729-FH hnPSCs treated with dTAG, replicate 1, input

description: Library name: INPUT_dTAG_REP1


title: LU99 cells, MRTX1719+Belvarafenib, rep 1

description:
Library name: Sample 13
Combo_B_1


title: LU99 cells, MRTX1719+Adagrasib rep 2

description:
Library name: Sample 17
Combo_U_2


title: zebrafish embryo, 22C 0A total validation set 15h 1

description: Library name: 22C_0A_total_v_15h_1


title: LU99 cells, MRTX1719+Adagrasib, rep 1

description:
Library name: Sample 16
Combo_U_1


title: LU99 cells, MRTX1719+Belvarafenib, rep 2

description:
Library name: Sample 14
Combo_B_2


title: LU99 cells, MRTX1719+Belvarafenib, rep 3

description:
Library name: Sample 15
Combo_B_3


title: LU99 cells, DMSO, rep 3

description:
Library name: Sample 12
DMSO_3


title: ZNF729-FH hnPSCs treated with DMSO, replicate 1, input

description: Library name: INPUT_DMSO_REP1


title: zebrafish embryo, 22C 0A total validation set 13h 2

description: Library name: 22C_0A_total_v_13h_2


title: blastoids_R4

description:
Library name: blastoids_R4
dark_spheres_blastoids_TPMs.txt

source_name: blastoids

value: blastoids

value: multi-lineage


title: blastoids_R3

description:
Library name: blastoids_R3
dark_spheres_blastoids_TPMs.txt


title: zebrafish embryo, 22C 0A total validation set 13h 1

description: Library name: 22C_0A_total_v_13h_1


title: blastoids_R2

description:
Library name: blastoids_R2
dark_spheres_blastoids_TPMs.txt


title: LU99 cells, MRTX1719, rep 1

description:
Library name: Sample 7
MRTX_1


title: LU99 cells, DMSO, rep 2

description:
Library name: Sample 11
DMSO_2


title: zebrafish embryo, 22C 0A total validation set 11h 2

description: Library name: 22C_0A_total_v_11h_2


title: LU99 cells, DMSO, rep 1

description:
Library name: Sample 10
DMSO_1


title: zebrafish embryo, 22C 0A total validation set 11h 1

description: Library name: 22C_0A_total_v_11h_1


title: LU99 cells, MRTX1719, rep 3

description:
Library name: Sample 9
MRTX_3


title: LU99 cells, MRTX1719, rep 2

description:
Library name: Sample 8
MRTX_2


title: LU99 cells, Adagrasib, rep 3

description:
Library name: Sample 6
Ulix_3

value: Adagrasib


title: zebrafish embryo, 22C 0A total 9h 2

description: Library name: 22C_0A_total_9h_2


title: LU99 cells, Adagrasib, rep 2

description:
Library name: Sample 5
Ulix_2


title: LU99 cells, Adagrasib, rep 1

description:
Library name: Sample 4
Ulix_1


title: ZNF729-FH hnPSCs treated with DMSO, replicate 1, ZNF729-HA ChIP

description: Library name: ZNF729-HA_DMSO_REP1


title: dark_spheres_R4

description:
Library name: dark_spheres_R4
dark_spheres_blastoids_TPMs.txt

source_name: dark spheres

value: dark spheres


title: LU99 cells, Belvarafenib, rep 3

description:
Library name: Sample 3
Belv_3

value: Belvarafenib


title: zebrafish embryo, 22C 0A total 9h 1

description: Library name: 22C_0A_total_9h_1


title: LU99 cells, Belvarafenib, rep 2

description:
Library name: Sample 2
Belv_2


title: dark_spheres_R3

description:
Library name: dark_spheres_R3
dark_spheres_blastoids_TPMs.txt


title: LU99 cells, Belvarafenib, rep 1

description:
Library name: Sample 1
Belv_1


title: zebrafish embryo, 22C 0A total 7h 2

description: Library name: 22C_0A_total_7h_2


title: dark_spheres_R2

description:
Library name: dark_spheres_R2
dark_spheres_blastoids_TPMs.txt


title: A172 cells, PRMT5i, rep 3

description:
Library name: Sample 6
MRTX_3

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides.
Reads were aligned to the human genome (hg38) using HISAT2 and quantified using featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

growth_protocol: Cells were grown at 37°C in 5% CO2 in a humidied incubator, cultured in DMEM media with 10% FBS and 1% pen-strep

treatment_protocol: 5 days with DMSO control or 20nM MRTX1719

value: glioblastoma cell line

value: PRMT5i (MRTX1719 20nM)


title: A172 cells, PRMT5i, rep 2

description:
Library name: Sample 5
MRTX_2


title: zebrafish embryo, 22C 0A total 7h 1

description: Library name: 22C_0A_total_7h_1

value: whole embryo


title: A172 cells, PRMT5i, rep 1

description:
Library name: Sample 4
MRTX_1


title: zebrafish embryo, 22C 0A total 5h 2

description: Library name: 22C_0A_total_5h_2


title: nontarg_CARGO_R3

description:
Library name: nontarg_CARGO_R3
high_medium_non_TPMs.txt

value: hnPSCs


title: zebrafish embryo, 22C 0A total 5h 1

description: Library name: 22C_0A_total_5h_1


title: A172 cells, DMSO, rep 1

description:
Library name: Sample 1
DMSO_1


title: blastoids_R1

description:
Library name: blastoids_R1
dark_spheres_blastoids_TPMs.txt


title: zebrafish embryo, 22C 0A total 3h 2

description: Library name: 22C_0A_total_3h_2


title: A172 cells, DMSO, rep 2

description:
Library name: Sample 2
DMSO_2


title: AxD, day 9, replicate 3

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

description:
UNC-R16-d9 (column name in processed data file)
counts_normalized_D9.txt

data_processing:
UMIs and TATA spacers were removed using umi_tools (1.0.1). Quality of the data was checked using FastQC (0.11.9) and FastQ Screen (0.11.1). TrimmomaticSE (0.36) was used for trimming the sequences.
Ribosomal and mitochondrial reads were removed using SortMeRNA (2.1b).
Data were aligned to human genome with STAR (2.7.0f).
Count matrices were generated by htseq-count (0.11.4). ENSEMBL-IDs were used to identify the transcripts.
Data were further analyzed with R programming language (4.2.2), using DESeq2 (1.36) package, processing samples from each time point separately.
Assembly: Homo sapiens GRCh38.87
Supplementary files format and content: counts_normalized .txt files contain normalized counts extracted from the DESeq object. Each time point has its own count file. Genes in rows, samples in columns, comma separated.

growth_protocol: Embryoid bodies were grown in AggrewellTM800 24-wells plates: seeded 3.5 million cells per well to generate roughly 300 embryoid bodies with approximately 11.500 cells. At day 2, embryoid bodies were transfered to ultra-low attachment round-bottom shaped 96-well plates. Neural induction medium was added since day 6.

extract_protocol:
Total RNA was extracted using Qiazol, chloroform, isopropanol method. Five or more organoids were pooled in each sample.
QuantSeq 3‘ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) with dual i5 and i7 indexing, equimolar pool 22nM

tag: time point

tag: replicate


title: nontarg_CARGO_R1

description:
Library name: nontarg_CARGO_R1
high_medium_non_TPMs.txt


title: AxD, day 9, replicate 2

description:
UNC-R15-d9 (column name in processed data file)
counts_normalized_D9.txt


title: dark_spheres_R1

description:
Library name: dark_spheres_R1
dark_spheres_blastoids_TPMs.txt


title: control, day 9, replicate 4

description:
UNC-CR-R17-d9 (column name in processed data file)
counts_normalized_D9.txt

value: GFAP corrected


title: AxD, day 9, replicate 4

description:
UNC-R17-d9 (column name in processed data file)
counts_normalized_D9.txt


title: zebrafish embryo, 22C 0A total 3h 1

description: Library name: 22C_0A_total_3h_1


title: AxD, day 9, replicate 1

description:
UNC-R9-d9 (column name in processed data file)
counts_normalized_D9.txt


title: control, day 9, replicate 3

description:
UNC-CR-R16-d9 (column name in processed data file)
counts_normalized_D9.txt


title: LTR5Hs_CARGO_medium_c5_R3

description:
Library name: LTR5Hs_CARGO_medium_c5_R3
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A total 1h 2

description: Library name: 22C_0A_total_1h_2


title: control, day 9, replicate 2

description:
UNC-CR-R15-d9 (column name in processed data file)
counts_normalized_D9.txt


title: LTR5Hs_CARGO_medium_c5_R2

description:
Library name: LTR5Hs_CARGO_medium_c5_R2
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A total 1h 1

description: Library name: 22C_0A_total_1h_1


title: A172 cells, DMSO, rep 3

description:
Library name: Sample 3
DMSO_3


title: AxD, day 7, replicate 4

description:
UNC-R17-d7 (column name in processed data file)
counts_normalized_D7.txt


title: control, day 9, replicate 1

description:
UNC-CR-R9-d9 (column name in processed data file)
counts_normalized_D9.txt


title: nontarg_CARGO_R2

description:
Library name: nontarg_CARGO_R2
high_medium_non_TPMs.txt


title: AxD, day 7, replicate 3

description:
UNC-R16-d7 (column name in processed data file)
counts_normalized_D7.txt


title: LTR5Hs_CARGO_medium_c4_R3

description:
Library name: LTR5Hs_CARGO_medium_c4_R3
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A total 15h 2

description: Library name: 22C_0A_total_15h_2


title: control, day 7, replicate 4

description:
UNC-CR-R17-d7 (column name in processed data file)
counts_normalized_D7.txt


title: AxD, day 7, replicate 2

description:
UNC-R15-d7 (column name in processed data file)
counts_normalized_D7.txt


title: zebrafish embryo, 22C 0A total 13h 2

description: Library name: 22C_0A_total_13h_2


title: control, day 7, replicate 3

description:
UNC-CR-R16-d7 (column name in processed data file)
counts_normalized_D7.txt


title: zebrafish embryo, 22C 0A total 13h 1

description: Library name: 22C_0A_total_13h_1


title: AxD, day 7, replicate 1

description:
UNC-R9-d7 (column name in processed data file)
counts_normalized_D7.txt


title: control, day 7, replicate 1

description:
UNC-CR-R9-d7 (column name in processed data file)
counts_normalized_D7.txt


title: zebrafish embryo, 22C 0A total 15h 1

description: Library name: 22C_0A_total_15h_1


title: AxD, day 5, replicate 3

description:
UNC-R16-d5 (column name in processed data file)
counts_normalized_D5.txt


title: LTR5Hs_CARGO_medium_c4_R2

description:
Library name: LTR5Hs_CARGO_medium_c4_R2
high_medium_non_TPMs.txt


title: LTR5Hs_CARGO_medium_c4_R1

description:
Library name: LTR5Hs_CARGO_medium_c4_R1
high_medium_non_TPMs.txt


title: AxD, day 5, replicate 4

description:
UNC-R17-d5 (column name in processed data file)
counts_normalized_D5.txt


title: LTR5Hs_CARGO_medium_c3_R2

description:
Library name: LTR5Hs_CARGO_medium_c3_R2
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A total 11h 2

description: Library name: 22C_0A_total_11h_2


title: control, day 7, replicate 2

description:
UNC-CR-R15-d7 (column name in processed data file)
counts_normalized_D7.txt


title: LTR5Hs_CARGO_medium_c3_R3

description:
Library name: LTR5Hs_CARGO_medium_c3_R3
high_medium_non_TPMs.txt


title: AxD, day 5, replicate 2

description:
UNC-R15-d5 (column name in processed data file)
counts_normalized_D5.txt


title: LTR5Hs_CARGO_medium_c5_R1

description:
Library name: LTR5Hs_CARGO_medium_c5_R1
high_medium_non_TPMs.txt


title: control, day 5, replicate 4

description:
UNC-CR-R17-d5 (column name in processed data file)
counts_normalized_D5.txt


title: AxD, day 5, replicate 1

description:
UNC-R9-d5 (column name in processed data file)
counts_normalized_D5.txt


title: zebrafish embryo, 22C 0A total 11h 1

description: Library name: 22C_0A_total_11h_1


title: zebrafish embryo, 22C 0A polyA 9h 2

description: Library name: 22C_0A_polyA_9h_2


title: control, day 5, replicate 2

description:
UNC-CR-R15-d5 (column name in processed data file)
counts_normalized_D5.txt


title: control, day 5, replicate 3

description:
UNC-CR-R16-d5 (column name in processed data file)
counts_normalized_D5.txt


title: LTR5Hs_CARGO_medium_c2_R3

description:
Library name: LTR5Hs_CARGO_medium_c2_R3
high_medium_non_TPMs.txt


title: control, day 5, replicate 1

description:
UNC-CR-R9-d5 (column name in processed data file)
counts_normalized_D5.txt


title: zebrafish embryo, 22C 0A polyA 9h 1

description: Library name: 22C_0A_polyA_9h_1


title: zebrafish embryo, 22C 0A polyA 7h 2

description: Library name: 22C_0A_polyA_7h_2


title: LTR5Hs_CARGO_medium_c2_R2

description:
Library name: LTR5Hs_CARGO_medium_c2_R2
high_medium_non_TPMs.txt


title: AxD, day 3, replicate 4

description:
UNC-R17-d3 (column name in processed data file)
counts_normalized_D3.txt


title: LTR5Hs_CARGO_medium_c2_R1

description:
Library name: LTR5Hs_CARGO_medium_c2_R1
high_medium_non_TPMs.txt


title: LTR5Hs_CARGO_medium_c1_R2

description:
Library name: LTR5Hs_CARGO_medium_c1_R2
high_medium_non_TPMs.txt


title: AxD, day 3, replicate 3

description:
UNC-R16-d3 (column name in processed data file)
counts_normalized_D3.txt


title: AxD, day 3, replicate 1

description:
UNC-R9-d3 (column name in processed data file)
counts_normalized_D3.txt


title: AxD, day 3, replicate 2

description:
UNC-R15-d3 (column name in processed data file)
counts_normalized_D3.txt


title: zebrafish embryo, 22C 0A polyA 7h 1

description: Library name: 22C_0A_polyA_7h_1


title: control, day 3, replicate 4

description:
UNC-CR-R17-d3 (column name in processed data file)
counts_normalized_D3.txt


title: LTR5Hs_CARGO_medium_c1_R1

description:
Library name: LTR5Hs_CARGO_medium_c1_R1
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A polyA 3h 2

description: Library name: 22C_0A_polyA_3h_2


title: zebrafish embryo, 22C 0A polyA 5h 1

description: Library name: 22C_0A_polyA_5h_1


title: LTR5Hs_CARGO_medium_c3_R1

description:
Library name: LTR5Hs_CARGO_medium_c3_R1
high_medium_non_TPMs.txt


title: HEK293_SeV_0hr_rep1

city: beijing

first: ao

last: zhang

address: Peking University, No.5 Yiheyuan Road Haidina District, Beijing, P.R.China 10087

institute: peking university

description: circRNA expression in HEK293 infected without sendai virus

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 ℃ for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65℃ in an Agilent Hybridization Oven

scan_protocol: The Agilent Scanner G2505C was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, circRNAs that at least 6 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: HEK293, Sendai virus, 0hr, replicate 1

label_protocol: Rnase R (Epicentre, Madison, WI) was used to remove linear RNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA by using a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The concentration and specific activity of the labeled cRNAs (pmol Cy3/渭g cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The HEK293 cells were cultured in Dulbecco modified Eagle medium (DMEM, Thermo Fisher Scientific), which contained 10% heat-inactivated fetal bovine serum (FBS, CellMax), 100 U/mL penicillin, and 100 ng/mL streptomycin (Thermo-Fisher Scientific).

extract_protocol: Total RNA was extracted from HEK293 cells by using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacture’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: The HEK293 cells were subject to Sendai virus (SeV) infection for 0h or 12h

value: control


title: HEK293_SeV_0hr_rep2

source_name: HEK293, Sendai virus, 0hr, replicate 2


title: HEK293_SeV_12hr_rep3

description: circRNA expression in HEK293 infected with sendai virus

source_name: HEK293, Sendai virus, 12hr, replicate 3

value: Sendai virus, 12hr


title: HEK293_SeV_0hr_rep3

source_name: HEK293, Sendai virus, 0hr, replicate 3


title: HEK293_SeV_12hr_rep2

source_name: HEK293, Sendai virus, 12hr, replicate 2


title: zebrafish embryo, 22C 0A polyA 3h 1

description: Library name: 22C_0A_polyA_3h_1


title: control, day 3, replicate 3

description:
UNC-CR-R16-d3 (column name in processed data file)
counts_normalized_D3.txt


title: zebrafish embryo, 22C 0A polyA 1h 2

description: Library name: 22C_0A_polyA_1h_2


title: LTR5Hs_CARGO_high_c3_R2

description:
Library name: LTR5Hs_CARGO_high_c3_R2
high_medium_non_TPMs.txt

value: naive embryonic stem cells


title: IgGs hnPSCs

data_processing:
Standard Illumina adapters were cut from the Illumina reads using Skewer and then aligned to a combined hg38 and E. coli genome version using Bowtie2 with the -dovetail parameter on. PCR duplicates were removed from the analysis. Coverage bigwig files were generated with Deeptools bamCoverage and the –scaleFactor was set to the number obtained from the normalization of fragments mapped to the human genome (hg38) and the mapped fragments to the E. coli k12 MG1655 genome.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
CUT&RUN protocol (Meers et al.) was followed with minor modifications. 500 K nontarg-CARGO or LTR5Hs-CARGO hnPSCs per condition were permeabilized using 0.005% of digitonin and 0.5 ug of H3K9me3 or IgG primary antibodies were used.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit

value: human naive pluripotent stem cells

value: wild type


title: LTR5Hs_CARGO_high_c4_R2

description:
Library name: LTR5Hs_CARGO_high_c4_R2
high_medium_non_TPMs.txt


title: ΔEx15_rep3

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
The adapter sequence and low-quality reads were removed using trimmomatic (v0.38).
Trimmed reads were mapped to reference genome hg38 using Kallisto (v0.46.2).
The count matrix data from Kallisto was loaded into R software (v4.2.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq RNA Library Prep Kit following manufacturer's protocols.

value: iPSC derived NS/PCs


title: ΔEx15_rep2

value: non


title: zebrafish embryo, 22C 0A polyA 15h 2

description: Library name: 22C_0A_polyA_15h_2


title: WT_rep3


title: LTR5Hs_CARGO_high_c4_R1

description:
Library name: LTR5Hs_CARGO_high_c4_R1
high_medium_non_TPMs.txt


title: control, day 3, replicate 2

description:
UNC-CR-R15-d3 (column name in processed data file)
counts_normalized_D3.txt


title: zebrafish embryo, 22C 0A polyA 5h 2

description: Library name: 22C_0A_polyA_5h_2


title: LTR5Hs_CARGO_high_c3_R3

description:
Library name: LTR5Hs_CARGO_high_c3_R3
high_medium_non_TPMs.txt


title: WT_rep2


title: LTR5Hs_CARGO_high_c4_R3

description:
Library name: LTR5Hs_CARGO_high_c4_R3
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A polyA 15h 1

description: Library name: 22C_0A_polyA_15h_1


title: LTR5Hs_CARGO_high_c2_R3

description:
Library name: LTR5Hs_CARGO_high_c2_R3
high_medium_non_TPMs.txt


title: ND624 with no APC feeder cells

description:
Library name: ND624_nofeeder
Single-cell RNA-Seq performed in gamma-delta CCR5KI-CAR19 T cells manufactured with no APC feeder cells

value: T cells

value: Gamma-delta CCR5KI-CAR19

value: No APC feeder cells


title: LTR5Hs_CARGO_high_c3_R1

description:
Library name: LTR5Hs_CARGO_high_c3_R1
high_medium_non_TPMs.txt


title: H3K9me3 nontarg-CARGO hnPSCs

value: nontarg-CARGO


title: zebrafish embryo, 22C 0A polyA 1h 1

description: Library name: 22C_0A_polyA_1h_1


title: ΔEx15_rep1


title: control, day 3, replicate 1

description:
UNC-CR-R9-d3 (column name in processed data file)
counts_normalized_D3.txt


title: zebrafish embryo, 22C 0A polyA 13h 2

description: Library name: 22C_0A_polyA_13h_2


title: H3K9me3 LTR5Hs-CARGO hnPSCs


title: WT_rep1


title: LTR5Hs_CARGO_high_c2_R2

description:
Library name: LTR5Hs_CARGO_high_c2_R2
high_medium_non_TPMs.txt


title: CD,ileum,SARS-CoV-2,patient9_2

city: Graz

first: Barbara

last: Jelusic

address: Auenbruggerpl. 2

country: Austria

institute: Med Uni Graz

data_processing:
Following base calling adaptor clipping was performed using cutadapt 2.4 (http://journal.embnet.org/index.php/embnetjournal/article/view/200). Data was mapped against the GRCh38 genome and SARS COV2  using STAR v 2.7.5a  (STAR: ultrafast universal RNA-seq aligner.: Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR). Read counts per gene (Gencode Ensembl v 94) were used for further analyses.
Differences in gene expression were analysed using the R package DESeq2 (Love 2014). Two monolayer replicates from a certain patient and treatment were pooled during the analysis after confirming a high correlation (Suppl.Fig.1). The effects of SARS-CoV-2 infection were determined for each group separately and by pairing the infected with the control sample originating from the same patient. If control or infected sample was missing due to low sequencing quality, this patient was removed from the analysis. When assessing the differences in gene expression due to IBD itself, control samples from an IBD group were compared to control samples from the corresponding healthy organ.
Assembly: GRCh98
Supplementary files format and content: Table of genes and read counts per sample and gene.

source_name: ileum organoid

growth_protocol: Intestinal organoids were cultured from intestinal epithelial cell isolates of biopsy specimens retrieved from endoscopy of IBD patients and healthy controls at University Hospital Innsbruck using IntestiCult Organoid Growth Medium (STEMCELL Technologies Inc., Vancouver, Canada) and a protocol adapted from the manufacturer’s instructions. Starting number of patients and their characteristics can be found in Table 1. Briefly, two to three ileal or colonic biopsies, taken from an inflamed site in case of IBD patients, were flushed with ice cold PBS and minced into small pieces. Tissue was then transferred to Gentle Cell Dissociation Reagent (GCDR, STEMCELL Technologies) and incubated at 4°C on a rocking platform for 30 min. After centrifugation, tissue suspension was transferred to 1 ml of ice cold 1% BSA/DMEM. Tissue was dissolved by gentle mixing and passed through a 70 μm cell strainer. The suspension containing whole intestinal crypts was seeded in 50 μl Matrigel Matrix, Growth Factor Reduced (Corning Inc., Corning, New York, US) on a pre-warmed 24-well plate and allowed to solidify for 10 min at 37 °C, after which 500 μl IntestiCult Growth Medium supplemented with 100 U/ml penicillin and 100 μg/ml streptomycin (Biochrom, Berlin, Germany) was added. Medium was exchanged three times per week and organoids passaged every 5–10 days depending on their growth, with a maximum of 12 passages. During passaging, ileal organoids could be disrupted by pipetting only, as opposed to colonic organoids that needed chemical disruption with GCDR as per manufacturer’s protocol. To create monolayers, organoids (24 well plate) were harvested, disrupted, trypsinized, washed and seeded in a 96 well plate pre-coated with 5% Matrigel. Four monolayers were created for each patient in order to have two replicates for infection and two for control. Remaining 3D organoids were passaged further and split into two wells, one for each treatment.

extract_protocol:
After centrifugation at 2 000 g for 5 minutes, the supernatant was split into two tubes and frozen at -80 °C. 200 µl of TRIzol (Thermo Fisher Scientific) was added to each monolayer well and replicates were collected separately. Cell lysates in TRIzol were vortexed and frozen at -20 °C. Total RNA was isolated according to manufacturer’s protocol. Aliquots were taken from samples originating from different monolayer plates to test for the presence of SARS-CoV-2 RNA.
After initial quality control using Agilent’s Bioanalyzer sequencing libraries were prepared from 25-250ng of total RNA per sample following Roche’s strand specific “KAPA RNA Hyper Prep Kit + RiboErase (HMR)” library preparation protocol for double indexed Illumina libraries:   First, the rRNA fraction was depleted using complementary DNA oligonucleotides. rRNA-DNA hybrids and DNA baits were removed by treatment with RNase H and DNase.  RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A-tailing Illumina sequencing compatible adapters carrying unique dual indices were ligated (NEXTFLEX® Unique Dual Index Barcodes).  Following bead-based clean-up steps the libraries were amplified using 13 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out on an Illumina NovaSeq6000 system in PE100bp mode yielding between 20-40 million fragments per sample.

treatment_protocol: 3D organoids and monolayers were infected on day 13 after seeding the monolayers. Protocol was developed based on M. M. Lamers et al., Science 2020 and K. Ettayebi et al., Science 2016. Inoculum was prepared by diluting the virus to 105 PFU in a serum-free medium, AD: Advanced DMEM/F-12 (Thermo Fisher Scientific Inc., Waltham, Massachusetts, US) +HEPES 1M (Merck KGaA, Darmstadt, Germany), +GlutaMAX (Thermo Fisher Scientific), +Pen/Strep(Thermo Fisher Scientific). Conditioned medium from Vero cells was used as control. Monolayers were washed once with 150 µl of AD and then treated with 100 µl of inoculum or control medium. 3D organoids were washed with 500 µl of AD and left for 5 minutes for the washing medium to penetrate the Matrigel. Upon removal of AD, 500 µl of inoculum or control medium was added to the organoids. Monolayers and organoids were incubated for two hours at 37 °C and 5% CO2 to allow for the virus to attach. Treatments were then removed and the monolayers and organoids washed two times with AD, waiting for 5 minutes after each washing step for the organoids. 150 µl and 500 µl of IntestiCult™ was added to monolayers and organoids, respectively, and incubated for 48 hours. Conditioned medium from two monolayer replicates was collected and pooled.

value: ileum organoid

value: CD


title: LTR5Hs_CARGO_high_c2_R1

description:
Library name: LTR5Hs_CARGO_high_c2_R1
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A polyA 13h 1

description: Library name: 22C_0A_polyA_13h_1


title: HEK293_SeV_12hr_rep1

source_name: HEK293, Sendai virus, 12hr, replicate 1


title: CD4+T cells under Th1 condition for 72h with Idelalisib treatment, biol rep 2

city: tianjin

first: hu

last: lu

state: State

address: fu kang lu

institute: TMU

description: Library name: ID2

data_processing:
Raw data quality control and adapter trimming were performed using fastp to remove adapter-containing reads, poly-N reads and low-quality reads. Q20, Q30 and GC content were calculated.
Trimmed clean reads were aligned to the mm10 reference genome using HISAT2 v2.0.5 with splice-aware alignment (genome index built using gene model annotations)
Gene-level read counts were quantified using featureCounts v1.5.0-p3 with mm10 gene annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: CD4+ T cells

extract_protocol:
Total RNA were extracted using Trizol, RNA integrity was verified using the Agilent Bioanalyzer 2100.
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: strain

value: CD4+ T cells


title: CD4+T cells under Th1 condition for 72h with Idelalisib treatment, biol rep 3

description: Library name: ID3


title: LTR5Hs_CARGO_high_c1_R3

description:
Library name: LTR5Hs_CARGO_high_c1_R3
high_medium_non_TPMs.txt


title: CD,ileum,SARS-CoV-2,patient7_2


title: CD,ileum,SARS-CoV-2,patient7_1


title: LTR5Hs_CARGO_high_c1_R2

description:
Library name: LTR5Hs_CARGO_high_c1_R2
high_medium_non_TPMs.txt


title: zebrafish embryo, 22C 0A polyA 11h 1

description: Library name: 22C_0A_polyA_11h_1

value: whole embryo


title: zebrafish embryo,22C,15hpf,2

extract_protocol:
Total RNA was isolated using tri-reagent (Sigma T9424) and quantified using nanodrop
We used a two-step RNA-Seq library construction approach that specifically targeted the variable 3′UTR region of reporters. In the first step, total-RNA was reverse-transcribed with Maxima RT (Thermo Fisher) and a gene-specific primer that matched the 20nt downstream 3′UTR universal adaptor. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step, resulting cDNA was amplified by 18 cycles of Phusion PCR (NEB) with primers that matched the 20nt upstream 3′UTR universal adaptor and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing adaptors,  resulting in the final RNA-Seq library.

tag: Stage

tag: temperature


title: CD4+T cells under Th1 condition for 72h with Idelalisib treatment, biol rep 1

description: Library name: ID1


title: CD4+T cells under Th1 condition for 72h, biol rep 3

description: Library name: T3


title: LTR5Hs_CARGO_high_c1_R1

description:
Library name: LTR5Hs_CARGO_high_c1_R1
high_medium_non_TPMs.txt

value: hnPSCs


title: zebrafish embryo,22C,15hpf,1


title: CD4+T cells under Th1 condition for 72h, biol rep 2

description: Library name: T2


title: CD,ileum,SARS-CoV-2,patient8_1


title: plasmid library nanopore sequencing

city: Boston

first: Gue-ho

last: Hwang

state: MA

address: 300 Longwood Ave

institute: Boston Children's hospital

data_processing:
Nanopore sequencing data was base-called using guppy with high accuracy mode.
Nanopore sequencing reads were aligned to reference that is expected library reference using minimap2 and the combinations of barcode and enhancer sequence were extracted using alignment results.
The reads that do not align to the start and end of reference or the reads that do not clearly align to enhancer sequence were excluded.
The combinations were used to define the barcode in mRNA and gRNA samples.
Assembly: Customized library reference sequence.
Supplementary files format and content: Tab delimited text file includes raw counts for each sample

organism: synthetic construct

source_name: plasmid library

extract_protocol:
The plasmid library was extracted using plasmid prep kit from E.coli that was used for library cloning.
The library prepared using ligation sequencing kit V14 (LSK-114, nanopore oxford).
PCR free Nanopore sequencing. PromethION 2 Solo.

value: plasmid library


title: CD,ileum,SARS-CoV-2,patient22_2


title: CD4+T cells under Th1 condition for 72h, biol rep 1

description: Library name: T1


title: T-3

city: Lanzhou City

first: Lan

middle: Lan

last: Yu

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

institute: Northwest Normal University

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
Afterremoving adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcript by using Trinity (vesion:2.4) in paired-end method.
The longest transcript was choose as a unigene based the similarity and length of a sequence for subsequent analysis.
Assembly: De novo RNA-seq
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Inocutis levis

source_name: fungi

growth_protocol: Different concentrations of Triton X-100 were incubated, Day10

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated NanoDrop 2000 spectrophotometer (Thermo Scientific,USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions. The libraries were finally sequenced using the Illumina Novaseq 6000 platform. 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: fungi

value: WT

value: 15ml Triton X-100,Day10


title: zebrafish embryo,22C,13hpf,2

data_processing:
constant sequences were trimmed
reporter 3'UTR sequences were aligned against the full set of 90,000 reporter sequences
number of unique molecular identifiers (UMIs) that match each reporter sequence were counted
Assembly: the full set of 90,000 reporter sequences
Supplementary files format and content: tab-delimited text files include readcount for each reporter in each sample

source_name: whole embryo


title: CD,ileum,SARS-CoV-2,patient11_2


title: T-2


title: zebrafish embryo, 22C 0A polyA 11h 2

description: Library name: 22C_0A_polyA_11h_2

extract_protocol:
Total RNA was isolated using tri-reagent (Sigma T9424) and quantified using nanodrop
We used a two-step RNA-Seq library construction approach that specifically targeted the variable 3′UTR region of reporters. In the first step, total-RNA was reverse-transcribed with Maxima RT (Thermo Fisher) and a gene-specific primer that matched the 20nt downstream 3′UTR universal adaptor. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step, resulting cDNA was amplified by 18 cycles of PCR with primers that matched the 20nt upstream 3′UTR universal adaptor and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing adaptors,  resulting in the final RNA-Seq library.


title: CD,ileum,SARS-CoV-2,patient9_1


title: CD,ileum,SARS-CoV-2,patient22_1


title: zebrafish embryo,22C,11hpf,2


title: T-1


title: CD,ileum,SARS-CoV-2,patient11_1


title: SLAMF6_ChipSeq_1

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

department: School of Medicine

institute: Guangxi University

description: Library name: sample10

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChlP-seg reads were trimmed from 3' end until the final base had a quality score > 30.using Trimmomatic v0.33, discarding reads left with < 20 bp
ChlP-seg reads were aligned to the Ucsc hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChlP-seg coverage plots, the locations of the mapped ChlP-seg reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million , rpm) and reformatted in the bigWVig file format.
Peaks were called uing MAcS v2.1.0 with the significance cut-off g-value <=0.01
Assembly: mm10
Library strategy: CUT&Tag

source_name: spleen and lymph node

extract_protocol:
Mice were immunized with MOG/CFA to induce EAE. CD4+ YFP+ cells from spleen at the peak of disease were sorted on an AriaIII cell sorter into 15-ml tubes containing complete media, counted, and placed on ice. All samples were spun down at 500g for 10 min. The supernatant was removed, and cells were resuspended in 100 μl of 1 × PBS (Thermo Fisher Scientific).
Cut & Tag libraries were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following manufacturer's protocols.

value: spleen and lymph node

value: primary cell


title: CK-3

value: 0ml Triton X-100,Day10


title: CXCR6_ChipSeq_1

description: Library name: sample8


title: zebrafish embryo,22C,9hpf,1


title: CK-2


title: CD,ileum,SARS-CoV-2,patient10_1


title: zebrafish embryo,22C,13hpf,1


title: AxD, day 9, replicate 3, Aggrewell

description:
R24-d9 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d9.txt

data_processing:
Quality of the data was checked using FastQC (0.11.9) and FastQ Screen (0.11.1). TrimmomaticSE (0.36) was used for trimming the sequences.
Ribosomal and mitochondrial reads were removed using SortMeRNA (2.1b).
Data were aligned to human genome with STAR (2.7.0f).
Count matrices were generated by htseq-count (0.11.4). ENSEMBL-IDs were used to identify the transcripts.
Data were further analyzed with R programming language (4.2.2), using DESeq2 (1.36) package, processing samples from each time point separately.
Assembly: Homo sapiens GRCh38.87
Supplementary files format and content: ds-only processed data files contain normalized counts extracted from the DESeq object, when direct-seeding samples were analyzed alone. In this experiment, Aggrewell samples were not analyzed alone, for that refer to experiment number 1 in this superseries. Each time point has its own count file. ds-AW processed data files contain normalized counts extracted from the DESeq object, when direct-seeding and Aggrewell method was analyzed together to compare between the two protocols. Each time point and condition (control, AxD) have their own count files. Genes in rows, samples in columns, comma separated.

growth_protocol: Aggrewell protocol: embryoid bodies were grown in AggrewellTM800 24-wells plates, seeded 3.5 million cells per well to generate roughly 300 embryoid bodies with approximately 11.500 cells. At day 2, embryoid bodies were transfered to ultra-low attachment round-bottom shaped 96-well plates. Direct-seeding protocol: embryoid bodies were grown in ultra-low attachment round-bottom shaped 96-well plates, each well starting with  ~9000 iPS cells. From day 4 onward, the protocol was the same for both approaches. Neural induction medium was added since day 6.

extract_protocol:
Total RNA was extracted using Qiazol, chloroform, isopropanol method. Five or more organoids were pooled in each sample.
QuantSeq 3‘ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) with single i7 indexing, equimolar pool 60nM

tag: cultivation protocol

value: Aggrewell


title: zebrafish embryo,22C,7hpf,2


title: UC,colon,SARS-CoV-2,patient21_2

source_name: colon organoid

value: colon organoid

value: UC


title: WT_ChipSeq_1

description: Library name: sample6


title: zebrafish embryo,22C,7hpf,1


title: ID2_ChipSeq_2

description: Library name: sample5


title: SLAMF6_ChipSeq_2

description: Library name: sample11


title: AxD, day 9, replicate 2, Aggrewell

description:
R23-d9 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d9.txt


title: zebrafish embryo,22C,5hpf,2


title: UC,colon,SARS-CoV-2,patient20_1


title: UC,colon,SARS-CoV-2,patient20_2


title: zebrafish embryo,22C,11hpf,1


title: CXCR6_ChipSeq_2

description: Library name: sample9


title: UC,colon,SARS-CoV-2,patient21_1


title: zebrafish embryo,22C,5hpf,1


title: ID2_ChipSeq_1

description: Library name: sample4


title: zebrafish embryo,22C,9hpf,2


title: CD,ileum,SARS-CoV-2,patient10_2


title: zebrafish embryo,22C,3hpf,2


title: WT_ChipSeq_2

description: Library name: sample7


title: AxD, day 9, replicate 1, Aggrewell

description:
R22-d9 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d9.txt


title: control, day 9, replicate 3, Aggrewell

description:
R24-CR-d9 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d9.txt

value: GFAP corrected


title: CK-1


title: ID2_old_ChipSeq

description: Library name: sample2


title: UC,colon,SARS-CoV-2,patient19_1


title: UC,colon,SARS-CoV-2,patient19_2


title: zebrafish embryo,22C,3hpf,1


title: UC,colon,SARS-CoV-2,patient18_2


title: DKO_old_ChipSeq

description: Library name: sample1


title: zebrafish embryo, 34C 40A total validation set 8h 1

description: Library name: 34C_40A_total_v_8h_1


title: control, day 9, replicate 1, Aggrewell

description:
R22-CR-d9 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d9.txt


title: AxD, day 7, replicate 3, Aggrewell

description:
R24-d7 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d7.txt


title: zebrafish embryo,22C,1hpf,2


title: zebrafish embryo,22C,1hpf,1


title: zebrafish embryo,34C,8hpf,2


title: UC,colon,SARS-CoV-2,patient17_2


title: UC,colon,SARS-CoV-2,patient17_1


title: AxD, day 7, replicate 1, Aggrewell

description:
R22-d7 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d7.txt


title: zebrafish embryo, 34C 40A total validation set 7h 2

description: Library name: 34C_40A_total_v_7h_2


title: AxD, day 7, replicate 2, Aggrewell

description:
R23-d7 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d7.txt


title: WT_old_ChipSeq

description: Library name: sample3


title: zebrafish embryo, 34C 40A total validation set 7h 1

description: Library name: 34C_40A_total_v_7h_1


title: zebrafish embryo,34C,8hpf,1


title: zebrafish embryo, 34C 40A total validation set 6h 2

description: Library name: 34C_40A_total_v_6h_2


title: zebrafish embryo, 34C 40A total validation set 6h 1

description: Library name: 34C_40A_total_v_6h_1


title: control, day 7, replicate 2, Aggrewell

description:
R23-CR-d7 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d7.txt


title: control, day 7, replicate 3, Aggrewell

description:
R24-CR-d7 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d7.txt


title: zebrafish embryo, 34C 40A total validation set 5h 2

description: Library name: 34C_40A_total_v_5h_2


title: control, day 7, replicate 1, Aggrewell

description:
R22-CR-d7 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d7.txt


title: control, day 9, replicate 2, Aggrewell

description:
R23-CR-d9 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d9.txt


title: healthy,ileum,SARS-CoV-2,patient2_2

value: healthy


title: zebrafish embryo,34C,7hpf,2


title: healthy,ileum,SARS-CoV-2,patient2_1

value: ileum organoid


title: zebrafish embryo,34C,7hpf,1


title: zebrafish embryo, 34C 40A total validation set 4h 2

description: Library name: 34C_40A_total_v_4h_2


title: healthy,ileum,SARS-CoV-2,patient3_2


title: zebrafish embryo,34C,6hpf,1


title: UC,colon,SARS-CoV-2,patient18_1


title: zebrafish embryo,34C,5hpf,2


title: AxD, day 5, replicate 1, Aggrewell

description:
R22-d5 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d5.txt


title: zebrafish embryo,34C,6hpf,2


title: zebrafish embryo, 34C 40A total validation set 5h 1

description: Library name: 34C_40A_total_v_5h_1


title: AxD, day 5, replicate 3, Aggrewell

description:
R24-d5 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d5.txt


title: healthy,ileum,SARS-CoV-2,patient3_1


title: zebrafish embryo,34C,3hpf,2


title: AxD, day 5, replicate 2, Aggrewell

description:
R23-d5 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d5.txt


title: healthy,ileum,SARS-CoV-2,patient5_1


title: healthy,ileum,SARS-CoV-2,patient6_2


title: control, day 5, replicate 1, Aggrewell

description:
R22-CR-d5 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d5.txt


title: zebrafish embryo, 34C 40A total validation set 4h 1

description: Library name: 34C_40A_total_v_4h_1


title: zebrafish embryo,34C,5hpf,1


title: zebrafish embryo, 34C 40A total validation set 3h 2

description: Library name: 34C_40A_total_v_3h_2


title: healthy,ileum,SARS-CoV-2,patient6_1


title: control, day 5, replicate 3, Aggrewell

description:
R24-CR-d5 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d5.txt


title: AxD, day 3, replicate 3, Aggrewell

description:
R26-d3 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d3.txt


title: healthy,ileum,SARS-CoV-2,patient5_2


title: zebrafish embryo, 34C 40A total validation set 1h 2

description: Library name: 34C_40A_total_v_1h_2


title: zebrafish embryo,34C,3hpf,1


title: control, day 5, replicate 2, Aggrewell

description:
R23-CR-d5 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d5.txt


title: zebrafish embryo, 34C 40A total validation set 3h 1

description: Library name: 34C_40A_total_v_3h_1


title: zebrafish embryo, 34C 40A total validation set 2h 2

description: Library name: 34C_40A_total_v_2h_2


title: zebrafish embryo,34C,1hpf,2


title: healthy,ileum,SARS-CoV-2,patient1_2


title: healthy,ileum,SARS-CoV-2,patient4_2


title: healthy,ileum,SARS-CoV-2,patient4_1


title: AxD, day 3, replicate 2, Aggrewell

description:
R25-d3 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d3.txt


title: zebrafish embryo,34C,1hpf,1


title: zebrafish embryo, 34C 40A total validation set 2h 1

description: Library name: 34C_40A_total_v_2h_1


title: control, day 3, replicate 3, Aggrewell

description:
R26-CR-d3 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d3.txt


title: zebrafish embryo,28C,A0,5hpf,polyA


title: zebrafish embryo,28C,A0,8hpf,polyA


title: zebrafish embryo, 34C 40A total validation set 1h 1

description: Library name: 34C_40A_total_v_1h_1


title: healthy,ileum,SARS-CoV-2,patient1_1


title: control, day 3, replicate 2, Aggrewell

description:
R25-CR-d3 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d3.txt


title: zebrafish embryo, 34C 0A total validation set 8h 2

description: Library name: 34C_0A_total_v_8h_2


title: zebrafish embryo,28C,A0,6hpf,polyA


title: zebrafish embryo,28C,A0,4hpf,polyA


title: control, day 3, replicate 1, Aggrewell

description:
R22-CR-d3 (column name in the processed data file)
ds-AW_counts_normalized_CTRL_d3.txt


title: AxD, day 3, replicate 1, Aggrewell

description:
R22-d3 (column name in the processed data file)
ds-AW_counts_normalized_AxD_d3.txt


title: zebrafish embryo,28C,A0,3hpf,polyA


title: zebrafish embryo, 34C 0A total validation set 8h 1

description: Library name: 34C_0A_total_v_8h_1


title: zebrafish embryo, 34C 0A total validation set 7h 1

description: Library name: 34C_0A_total_v_7h_1


title: zebrafish embryo,28C,A0,2hpf,polyA


title: zebrafish embryo, 34C 0A total validation set 7h 2

description: Library name: 34C_0A_total_v_7h_2


title: healthy,colon,SARS-CoV-2,patient16_2


title: zebrafish embryo, 34C 0A total validation set 6h 2

description: Library name: 34C_0A_total_v_6h_2


title: healthy,colon,SARS-CoV-2,patient15_2


title: zebrafish embryo, 34C 0A total validation set 6h 1

description: Library name: 34C_0A_total_v_6h_1


title: AxD, day 9, replicate 2, direct-seeding

description:
R23-LC-d9 (column name in the processed data file)
ds-only_counts_normalized_D9.txt
ds-AW_counts_normalized_AxD_d9.txt

value: direct-seeding


title: healthy,colon,SARS-CoV-2,patient16_1


title: zebrafish embryo,28C,A0,1hpf,polyA


title: healthy,colon,SARS-CoV-2,patient12_2


title: AxD, day 9, replicate 1, direct-seeding

description:
R22-LC-d9 (column name in the processed data file)
ds-only_counts_normalized_D9.txt
ds-AW_counts_normalized_AxD_d9.txt


title: zebrafish embryo,28C,A0,0hpf,polyA


title: zebrafish embryo, 34C 0A total validation set 5h 2

description: Library name: 34C_0A_total_v_5h_2


title: healthy,colon,SARS-CoV-2,patient12_1


title: zebrafish embryo,28C,A40,8hpf,polyA


title: healthy,colon,SARS-CoV-2,patient14_2


title: zebrafish embryo, 34C 0A total validation set 5h 1

description: Library name: 34C_0A_total_v_5h_1


title: control, day 9, replicate 2, direct-seeding

description:
R23-CR-LC-d9 (column name in the processed data file)
ds-only_counts_normalized_D9.txt
ds-AW_counts_normalized_CTRL_d9.txt


title: healthy,colon,SARS-CoV-2,patient14_1


title: zebrafish embryo, 34C 0A total validation set 4h 2

description: Library name: 34C_0A_total_v_4h_2


title: zebrafish embryo,28C,A40,5hpf,polyA


title: zebrafish embryo,28C,A40,6hpf,polyA


title: zebrafish embryo, 34C 0A total validation set 4h 1

description: Library name: 34C_0A_total_v_4h_1


title: healthy,colon,SARS-CoV-2,patient13_1


title: AxD, day 9, replicate 3, direct-seeding

description:
R24-LC-d9 (column name in the processed data file)
ds-only_counts_normalized_D9.txt
ds-AW_counts_normalized_AxD_d9.txt


title: AxD, day 7, replicate 3, direct-seeding

description:
R24-LC-d7 (column name in the processed data file)
ds-only_counts_normalized_D7.txt
ds-AW_counts_normalized_AxD_d7.txt


title: healthy,colon,SARS-CoV-2,patient13_2


title: zebrafish embryo, 34C 0A total validation set 3h 2

description: Library name: 34C_0A_total_v_3h_2


title: zebrafish embryo,28C,A40,4hpf,polyA


title: AxD, day 7, replicate 1, direct-seeding

description:
R22-LC-d7 (column name in the processed data file)
ds-only_counts_normalized_D7.txt
ds-AW_counts_normalized_AxD_d7.txt


title: CD,ileum,control,patient9_2

value: CD

value: control


title: zebrafish embryo,28C,A40,2hpf,polyA

value: whole embryo


title: control, day 9, replicate 3, direct-seeding

description:
R24-CR-LC-d9 (column name in the processed data file)
ds-only_counts_normalized_D9.txt
ds-AW_counts_normalized_CTRL_d9.txt


title: CD,ileum,control,patient9_1


title: zebrafish embryo, 34C 0A total validation set 3h 1

description: Library name: 34C_0A_total_v_3h_1


title: AxD, day 7, replicate 2, direct-seeding

description:
R23-LC-d7 (column name in the processed data file)
ds-only_counts_normalized_D7.txt
ds-AW_counts_normalized_AxD_d7.txt


title: zebrafish embryo,28C,A40,3hpf,polyA


title: zebrafish embryo, 34C 0A total validation set 2h 2

description: Library name: 34C_0A_total_v_2h_2


title: healthy,colon,SARS-CoV-2,patient15_1


title: control, day 7, replicate 3, direct-seeding

description:
R24-CR-LC-d7 (column name in the processed data file)
ds-only_counts_normalized_D7.txt
ds-AW_counts_normalized_CTRL_d7.txt


title: CD,ileum,control,patient7_2


title: zebrafish embryo,28C,A40,1hpf,polyA


title: zebrafish embryo, 34C 0A total validation set 2h 1

description: Library name: 34C_0A_total_v_2h_1


title: control, day 9, replicate 1, direct-seeding

description:
R22-CR-LC-d9 (column name in the processed data file)
ds-only_counts_normalized_D9.txt
ds-AW_counts_normalized_CTRL_d9.txt


title: CD,ileum,control,patient7_1


title: control, day 7, replicate 2, direct-seeding

description:
R23-CR-LC-d7 (column name in the processed data file)
ds-only_counts_normalized_D7.txt
ds-AW_counts_normalized_CTRL_d7.txt


title: zebrafish embryo, 34C 0A total validation set 1h 2

description: Library name: 34C_0A_total_v_1h_2


title: zebrafish embryo,28C,A40,0hpf,polyA


title: zebrafish embryo,28C,A0,8hpf,total


title: CD,ileum,control,patient8_1


title: zebrafish embryo, 34C 0A total validation set 1h 1

description: Library name: 34C_0A_total_v_1h_1


title: zebrafish embryo,28C,A0,6hpf,total


title: CD,ileum,control,patient11_2


title: WT_stationary _rep3

city: Baton Rouge

first: Anne

last: Grove

state: LA

address: 103 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

data_processing:
Quality assessment using FastQC for fastq files
The Trim Galore toolkit  was applied to remove sequencing adapters and unidentified bases (N) and to trim bases of low quality (phred score cutoff = 20)
The genome was indexed using SAMtools
Subsequent alignment of the high-quality reads to this reference genome was performed using the HISAT2 aligner
Post-alignment, SAMtools was utilized to construct SAM and BAM files from the aligned reads that used for further analysis.
Gene expression quantification was conducted using FeatureCounts
The differentially expressed genes between exponential and stationary phases  were identified using DESeq2
Genes were considered significantly differentially expressed if they exhibited a log2-fold change of ≥2 or ≤-2 and if they met the statistical significance threshold with a false discovery rate (FDR) of <0.05.
Assembly: The reference genome of B. thailandensis was retrieved from the Burkholderia Genome Database (https://www.burkholderia.com)
Supplementary files format and content: Excel File include mean normalized counts, fold changes, and log2 fold change values for each gene across exponential and stationary phases. Data includes p-values, adjusted p-values (PAdj), and false discovery rate (FDR) for significance testing. Protein annotations, gene lengths, and genomic coordinates are also provided, along with normalized counts for biological replicates.

organism: Burkholderia thailandensis

growth_protocol: Cells were cultivated in 2xYT medium (16 g/L tryptone, 10 g/L yeast extract, 5 g/L NaCl; adjusted to pH 7.0). Cultures were incubated at 37°C with continuous shaking at 250 rpm. An overnight culture was diluted 1:100 in fresh 2xYT medium. Samples representing exponential phase cells were collected at an OD600 of 0.6 ± 0.05. The stationary phase cells were collected at an OD600 of 2.6 ± 0.05.

extract_protocol:
RNA extraction was conducted using the Monarch Total RNA Miniprep Kit (New England BioLabs), following the manufacturer’s guidelines.
Library preparation was done using the Illumina TruSeq Stranded mRNA Library Prep Kit, adhering to the manufacturer’s instructions.

tag: growth phase

value: stationary

value: wild-type

value: untreated


title: AxD, day 5, replicate 3, direct-seeding

description:
R24-LC-d5 (column name in the processed data file)
ds-only_counts_normalized_D5.txt
ds-AW_counts_normalized_AxD_d5.txt


title: AxD, day 5, replicate 2, direct-seeding

description:
R23-LC-d5 (column name in the processed data file)
ds-only_counts_normalized_D5.txt
ds-AW_counts_normalized_AxD_d5.txt


title: zebrafish embryo,28C,A0,5hpf,total


title: zebrafish embryo,28C,A0,3hpf,total


title: CD,ileum,control,patient10_2


title: CD,ileum,control,patient10_1


title: WT_exponential _rep3

value: exponential


title: control, day 5, replicate 3, direct-seeding

description:
R24-CR-LC-d5 (column name in the processed data file)
ds-only_counts_normalized_D5.txt
ds-AW_counts_normalized_CTRL_d5.txt


title: zebrafish embryo,28C,A0,4hpf,total


title: AxD, day 5, replicate 1, direct-seeding

description:
R22-LC-d5 (column name in the processed data file)
ds-only_counts_normalized_D5.txt
ds-AW_counts_normalized_AxD_d5.txt


title: WT_stationary _rep2


title: WT_stationary_rep1


title: UC,colon,control,patient21_2


title: control, day 7, replicate 1, direct-seeding

description:
R22-CR-LC-d7 (column name in the processed data file)
ds-only_counts_normalized_D7.txt
ds-AW_counts_normalized_CTRL_d7.txt


title: zebrafish embryo,28C,A0,2hpf,total


title: control, day 5, replicate 2, direct-seeding

description:
R23-CR-LC-d5 (column name in the processed data file)
ds-only_counts_normalized_D5.txt
ds-AW_counts_normalized_CTRL_d5.txt


title: UC,colon,control,patient21_1


title: control, day 5, replicate 1, direct-seeding

description:
R22-CR-LC-d5 (column name in the processed data file)
ds-only_counts_normalized_D5.txt
ds-AW_counts_normalized_CTRL_d5.txt


title: AxD, day 3, replicate 3, direct-seeding

description:
R26-LC-d3 (column name in the processed data file)
ds-only_counts_normalized_D3.txt
ds-AW_counts_normalized_AxD_d3.txt


title: zebrafish embryo,28C,A0,1hpf,total


title: UC,colon,control,patient20_1


title: WT_exponential _rep2


title: WT_exponential _rep1


title: 17cre-DKO

description: Library name: Sample9

data_processing:
Use fastqc and multiqc to check the data quality · Use fastp software to perform quality control on the fastq data, filter low-quality reads · Use STAR to align the RNA-Seq reads to the murine genome · Use featureCounts to convert the alignment results to gene expression matrix
Assembly: mm10

extract_protocol:
Mice were immunized with MOG/CFA to induce EAE. CD4+ YFP+ cells from spleen at the peak of disease were sorted on an AriaIII cell sorter into 15-ml tubes containing complete media, counted, and placed on ice. All samples were spun down at 500g for 10 min. The supernatant was removed, and cells were lysed by Trizol.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM II RNA Library Prep Kit for Illumina  following manufacturer's protocols.

value: spleen and lymph node

value: total RNA

value: paired-end

value: Illumina NovaSeq X Plus


title: zebrafish embryo,28C,A0,0hpf,total


title: AxD, day 3, replicate 2, direct-seeding

description:
R25-LC-d3 (column name in the processed data file)
ds-only_counts_normalized_D3.txt
ds-AW_counts_normalized_AxD_d3.txt


title: UC,colon,control,patient19_1

value: colon organoid


title: CD,ileum,control,patient11_1


title: 17cre-wt

description: Library name: Sample8

value: primary cell


title: zebrafish embryo,28C,A40,8hpf,total


title: UC,colon,control,patient18_2

value: UC


title: AxD, day 3, replicate 1, direct-seeding

description:
R22-LC-d3 (column name in the processed data file)
ds-only_counts_normalized_D3.txt
ds-AW_counts_normalized_AxD_d3.txt


title: zebrafish embryo,28C,A40,6hpf,total


title: control, day 3, replicate 3, direct-seeding

description:
R26-CR-LC-d3 (column name in the processed data file)
ds-only_counts_normalized_D3.txt
ds-AW_counts_normalized_CTRL_d3.txt

value: GFAP corrected


title: 17cre-id2

description: Library name: Sample7


title: UC,colon,control,patient18_1


title: CXCR6_2

description: Library name: Sample6


title: control, day 3, replicate 1, direct-seeding

description:
R22-CR-LC-d3 (column name in the processed data file)
ds-only_counts_normalized_D3.txt
ds-AW_counts_normalized_CTRL_d3.txt


title: zebrafish embryo,28C,A40,5hpf,total


title: UC,colon,control,patient17_2


title: CXCR6_1

description: Library name: Sample5


title: healthy,ileum,control,patient2_2

value: ileum organoid

value: healthy


title: No0548_hex50, ATRX_sc

data_processing:
Adaptor was removed and low quality reads were trimmed using Trimmomatic version 0.33.
ChIP-seq and CUT&RUN-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.1.0 with default settings.
Peaks were called using MACS version 3.
Assembly: hg38
Supplementary files format and content: bigwig files were generated using Deeptools (bamCoverage) with the following option --binSize 50 --fragmentLength 200.
Library strategy: CUT&Run

extract_protocol:
Double fixation for ChIP-seq, the cells were first fixed with 2 mM EGS for 30 min followed by with 1% formaldehyde-containing medium for 10min. For CUT&RUN, we used unfixed cells.
Libraries were prepared using KAPA Hyperprep Kit.
ChIP-Seq and CUT&RUN-seq

value: ltNES cells

tag: antibody


title: healthy,ileum,control,patient2_1

value: control


title: No0547_hex50, Input

value: non


title: SLAMF6_2

description: Library name: Sample4


title: zebrafish embryo,28C,A40,3hpf,total

value: whole embryo


title: zebrafish embryo,28C,A40,2hpf,total


title: SLAMF6_1

description: Library name: Sample3


title: zebrafish embryo,28C,A40,1hpf,total


title: KO_Id2

description: Library name: Sample2


title: No0545_hex15, Input


title: healthy,ileum,control,patient3_1


title: No0544_CTRL, ATRX_sc


title: WT

description: Library name: Sample1


title: healthy,ileum,control,patient6_2


title: END-seq_Canine

description: Library name: Library 1

data_processing:
We developed a Python script, "getTelomereENDseq," to analyze gzipped FASTQ files for the presence of telomeric motifs in DNA sequences on a command-line environment using a Linux-based operating system and the statistical environment RStudio. The script identifies sequences containing G-rich and C-rich telomeric repeats, quantifies their occurrences, and calculates their relative frequencies. It takes a gzipped FASTQ file as input, and the minimum number of telomeric repeats is required. It generates two output files: one with sequences containing G-rich motifs and another with sequences containing C-rich motifs. For this study, we used a minimum of 4 consecutive TTAGGG repeats for G-rich reads and a minimum of 4 consecutive CCCTAA repeats for C-rich reads.
Assembly: hg19, mm10
Supplementary files format and content: The .txt files contain reads corresponding to the G- and C-strands.

organism: Canis lupus familiaris

source_name: Canine cell line

extract_protocol:
Cells were washed with PBS, treated with Trypsin/EDTA, and neutralized with growth media. After pelleting and resuspending in neutralization buffer, cells were processed for END-seq or S1-END-seq. For S1-END-seq, cells were embedded in agarose plugs, lysed with Proteinase K, treated with RNase A, and equilibrated in S1 nuclease buffer. S1 nuclease was added to the plugs, incubated on ice for 15 minutes, then at 37°C for 20 minutes before terminating the reaction with EDTA.
For S1/END-seq, plugs were processed through the standard END-seq protocol.

value: Canine cell line

value: wild-type


title: zebrafish embryo,28C,A40,0hpf,total


title: No0543_CTRL, Input


title: zebrafish embryo,28C,A40,4hpf,total


title: healthy,ileum,control,patient6_1


title: Mouse femur bone marrow - Rep 1

city: Parkville

first: Yunshun

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: 10x Genomics

data_processing: The Xenium Onboard Analysis pipeline (v1.7.1.0) was run directly on the instrument for imaging processing, cell segmentation, image registration, decoding, deduplication, and secondary analysis to generate the processed data files. Information about the output files can be found in https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest.

source_name: Bone marrow

label_protocol: The Mouse Tissue Atlassing gene panel (10x Genomics) was used. Panel content can be found in https://www.10xgenomics.com/products/xenium-panels.

growth_protocol: Long bones were collected from mice and immediately fixed in 10% neutral buffered formalin for at least 24 hours. Samples were then either decalcified with 10% EDTA pH 7.2 solution (Milestone) before paraffin embedding.

extract_protocol: Sectioning was performed at 5 µm on a Leica RM2255 with a water float temperature of 47 °C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were then stored in a sealed dessicator at room temperature for up to a maximum of 14 days.

treatment_protocol: All workstations and equipments were cleaned using RNaseZap™ (ThermoFisher, AM9780) followed by 70% ethanol. All reagents were molecular grade nuclease-free.

value: Bone marrow cells

tag: condition

value: Ctrl

tag: Sex

value: Male


title: AF22_318, H3K9me3

data_processing:
Adaptor was removed and low quality reads were trimmed using Trimmomatic version 0.33.
ChIP-seq and CUT&RUN-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.1.0 with default settings.
Peaks were called using MACS version 3.
Assembly: hg38
Supplementary files format and content: bigwig files were generated using Deeptools (bamCoverage) with the following option --binSize 50 --fragmentLength 200.


title: Human bone marrow trephine of relapse myeloma sample - Rep 1

description: 10x Genomics

data_processing: The Xenium Onboard Analysis pipeline (v1.7.1.0 for Human Multi-Tissue and Cancer gene panel, or v.3.0.0.015 for 5k Human Pan Tissue & Pathways gene panel) was run directly on the instrument for imaging processing, cell segmentation, image registration, decoding, deduplication, and secondary analysis to generate the processed data files. Information about the output files can be found in https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest.

source_name: Trephine

label_protocol: Two pre-designed gene panels (10x Genomics) were used: (i) Human Multi-Tissue and Cancer (377 genes) and (ii) Xenium Prime 5k Human Pan Tissue & Pathways Panel (5,001 genes). Panel content can be found in https://www.10xgenomics.com/products/xenium-panels.

growth_protocol: Bone marrow trephine biopsies from the posterior superior iliac spine were collected from patients undergoing routine investigation of suspected plasma cell disorders. Upon collection, trephines were immediately fixed in 10% neutral buffered formalin for at least 24 hours. Samples were then either embedded directly in paraffin (non-decal) or decalcified with 10% EDTA pH 7.2 solution (Milestone) before paraffin embedding.

value: RM


title: healthy,ileum,control,patient5_2

tag: tissue


title: AF22_318, Input

tag: cell line


title: healthy,ileum,control,patient5_1


title: Human bone marrow trephine of smouldering myeloma  sample - Rep 5

description: 10x Genomics

value: SM


title: healthy,ileum,control,patient3_2


title: AF22_hex15, ATRX_gt


title: No0546_hex15, ATRX_sc


title: Human bone marrow trephine of smouldering myeloma  sample - Rep 4

description: 10x Genomics


title: healthy,ileum,control,patient4_2


title: AF22_hex15, ATRX_sc


title: Human bone marrow trephine of smouldering myeloma  sample - Rep 3

description: 10x Genomics

value: Female


title: AF22_hex15, Input


title: Human bone marrow trephine of smouldering myeloma  sample - Rep 2

description: 10x Genomics


title: healthy,ileum,control,patient1_1


title: healthy,ileum,control,patient1_2


title: AF22_CTRL, ATRX_gt


title: AF22_CTRL, ATRX_sc


title: Human bone marrow trephine of multiple myeloma sample - Rep 10

description: 10x Genomics

value: MM


title: healthy,colon,control,patient12_2

value: colon organoid


title: AF22_CTRL, Input


title: Human bone marrow trephine of smouldering myeloma  sample - Rep 1

description: 10x Genomics


title: healthy,colon,control,patient12_1


title: Human bone marrow trephine of multiple myeloma sample - Rep 9

description: 10x Genomics


title: AF22, Input_v2


title: healthy,colon,control,patient16_1


title: healthy,ileum,control,patient4_1


title: healthy,colon,control,patient16_2


title: AF22, ATRX_sc_v2


title: Human bone marrow trephine of multiple myeloma sample - Rep 8

description: 10x Genomics


title: genomic DNA from SKHep1#2

type: genomic

description:
rep2
SKHep1#2

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to illumina Infinium Human Methylation450 Beadchip using standard Illumina protocolIllumina Infinium protocol

scan_protocol: Illumina Infinium protocol scanned using Illumina HiScan System.

data_processing:
GenomeStudio V2011.1 was used to determine the methylation level at each CpG site as beta value. Normalization to internal controls and background subtraction were applied to determine normalized average beta values.
the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Illumina Infinium protocol

extract_protocol: Phenol-chloroform DNA extraction

value: male

value: cancer HCC cells line


title: Human bone marrow trephine of multiple myeloma sample - Rep 7

description: 10x Genomics


title: healthy,colon,control,patient14_2

value: healthy


title: genomic DNA from SKHep1 5azaCdR#1

description:
rep1
SKHep1_5aza#1

source_name: SKHep1 5azaCdR

tag: sample group

value: inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR)


title: Human bone marrow trephine of multiple myeloma sample - Rep 4

description: 10x Genomics

tag: cell type


title: AF22, ATRX_sc_v1

value: ltNES cells

tag: treatment


title: genomic DNA from SKHep1 5azaCdR#2

description:
rep2
SKHep1_5aza#2


title: genomic DNA from SKHep1 ShDNMT1#2

description:
rep2
SKHep1_Sh1#2

source_name: SKHep1 ShDNMT1

value: DNA methyltransferase (DNMT1) knockdown with shRNA


title: healthy,colon,control,patient14_1

value: control


title: Human bone marrow trephine of multiple myeloma sample - Rep 6

description: 10x Genomics


title: genomic DNA from HepG2 5azaCdR#1

description:
rep1
HepG2_5aza#1

source_name: HepG2 5azaCdR


title: AF22, Input_v1

value: non


title: healthy,colon,control,patient15_2


title: genomic DNA from SKHep1#3

description:
rep3
SKHep1#3


title: genomic DNA from SKHep1#1

description:
rep1
SKHep1#1


title: Human bone marrow trephine of multiple myeloma sample - Rep 5

description: 10x Genomics


title: genomic DNA from HepG2 5azaCdR#2

description:
rep2
HepG2_5aza#2


title: healthy,colon,control,patient13_2


title: genomic DNA from SKHep1 ShDNMT1#3

description:
rep3
SKHep1_Sh1#3


title: Human bone marrow trephine of multiple myeloma sample - Rep 1

description: 10x Genomics


title: SKHep1_ShDNMT1

data_processing:
The reads were aligned to the hg19 genome with Bowtie version 0.12.7
Peaks were called using the MACS2 software with P value<0.05
Duplicate reads were filtered using SAMTools to limit PCR induced biases
Genome_build: hg19

source_name: SKHep1 cell line

growth_protocol: SKHep1 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies), supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco). NorHep were maintained in human hepatocyte cell culture complete medium (Celprogen)

extract_protocol:
ChIP was performed with ChIP-IT High Sensitivity kit (Active Motif), according to manufacturer’s protocol.
A library of the chromatin immunoprecipitated DNA fragments was prepared using the TruSeq DNA kit Protocol (Illumina)

treatment_protocol: SKHep1 and NorHep cells were treated with 1µM 5-azaCdR (Sigma, St. Louis, MO) for 6 days with medium containing 5-azaCdR replaced every second day. For lentiviral ShDNMT1 infection, 1x10^5 cells of interest were plated per well in 6 well plates the day before infection.  The medium was discarded and 0.5 ml of infection medium and containing 4 µg Polybrene (hexadimethrine bromide, Sigma, Canada) was added. Subsequent day, the medium containing virus was replaced with appropriate medium. For selection of infection, 1 ug/ml puromycin was added after 48 hours incubation.

value: SKHep1 cell line

tag: gender

tag: chip antibody

value: RNAPII-Ser5 (Abcam, ab5408)


title: Human bone marrow trephine of multiple myeloma sample - Rep 3

description: 10x Genomics

value: Bone marrow cells


title: genomic DNA from HepG2 ShDNMT1#1

description:
rep1
HepG2_Sh1#1

source_name: HepG2 ShDNMT1

tag: source gender


title: NorHep_5azaCdR

source_name: Liver primary culture

value: Liver primary culture


title: SKHep1_5azaCdR


title: genomic DNA from HepG2#2

description:
rep2
HepG2#2


title: genomic DNA from HepG2#3

description:
rep3
HepG2#3


title: genomic DNA from HepG2#1

description:
rep1
HepG2#1


title: Blastoids_PIPseq_nontarg_c1_R1

city: Stanford

first: Raquel

last: Fueyo

address: 265 Campus Drive

institute: Stanford University

data_processing:
For each sample and replicate, reads obtained from the Novaseq X were analyzed with Fluent Bio’s proprietary software Pipseeker with default parameters and aligning against the GRCh38 transcriptome index. A background removal step was performed in all samples using CellBender with parameters --fpr 0.01 and --epochs 150. Full count matrices with background RNA removed were further analyzed using Seurat. Cells with more than 10% of mitochondrial counts were eliminated and the number of genes detected was also used for filtering the data. Each object was normalized using Seurat’s LogNormalize method and transformed using ScaleData function removing the unwanted variation originated from mitochondrial contamination or the cell cycle stage. Upon examining Elbow plots, 20 Principal Components were considered significant for unsupervised clustering with the FindNeighbors and FindClusters Seurat functions. Cluster identities were assigned based on the genes specifically marking each cluster according to Seurat’s FindMarkers function and comparing them to lineage markers uncovered in human preimplantation datasets. Seurat objects belonging to the nontarg-CARGO or the LTR5Hs-CARGO blastoids were merged.
Assembly: hg38
Supplementary files format and content: Count matrix (dgCMatrix) of all samples and metadata (txt)

source_name: clone 1

growth_protocol: Blastoids were generated following protocol in Kagawa et al. 2022

extract_protocol:
Single cells were obtained by resuspending blastoids in Collagenase IV (StemCell Technologies, 07909) and incubating at 37 degrees with mild agitation for 40 minutes. Blastoids were centrifuged again in N2B27 media and the pellet was resuspended in 0.5% Trypsin-EDTA (Fisher Scientific, 15-400-054) and incubated for 10 minutes at 37 degrees. Two further washes were performed with N2B27 and the dissociated cells were passed through a 40 um Flowmi cell strainer.
Libraries were constructed using the PIP-seq T20 3’ Single Cell RNA Kit

value: clone 1

tag: genotype


title: EBV-CD8rejTs, scRNA-seq

city: Bunkyo

first: Miki

last: Ando

address: Hongo 2-1-1

department: Hematology

institute: Juntendo University

description: Library name: EBV-CD8rejTs

data_processing:
Raw data were demultiplexed and quantified using Cell Ranger (v7.0.0, 10X Genomics). Downstream analyses used the Seurat R package (version 4.1.1).
Assembly: GRCh38
Supplementary files format and content: Barcode, features, matrix, fastq

source_name: Peripheral blood

extract_protocol:
Approximately 0.12 x 106 cells, viability >80%, were used.Sample was suspended in 50 μl of ice - chilled phosphate-buffered saline + 0.04% bovine serum albumin (Thermo Fisher Scientific) and processed to yield scRNA-seq libraries using 10X Chromium Next Gem Single Cell 3’ Reagent Kits v 3.1 (Dual Index) (10x Genomics, Pleasanton, CA) following standard manufacturer protocols. A Bio-Rad T100 thermal cycler (Bio-Rad, Hercules, CA) was used for PCR. After library quality was assessed using Bioanalyzer 2100 (Agilent, Tokyo, Japan), samples were sequenced (Macrogen, Seoul, South Korea) on the HiseqX (Illumina, San Diego, CA) platform at a depth of 2,000,000 pair reads/sample.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v3.1 protocol (10x Genomics).

value: Peripheral blood

value: C3H10T1/2 cells

value: mRNA


title: Human bone marrow trephine of multiple myeloma sample - Rep 2

description: 10x Genomics

value: MM

value: Male


title: NorHep_ShDNMT1

value: male


title: healthy,colon,control,patient13_1

data_processing:
Following base calling adaptor clipping was performed using cutadapt 2.4 (http://journal.embnet.org/index.php/embnetjournal/article/view/200). Data was mapped against the GRCh38 genome and SARS COV2  using STAR v 2.7.5a  (STAR: ultrafast universal RNA-seq aligner.: Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR). Read counts per gene (Gencode Ensembl v 94) were used for further analyses.
Differences in gene expression were analysed using the R package DESeq2 (Love 2014). Two monolayer replicates from a certain patient and treatment were pooled during the analysis after confirming a high correlation (Suppl.Fig.1). The effects of SARS-CoV-2 infection were determined for each group separately and by pairing the infected with the control sample originating from the same patient. If control or infected sample was missing due to low sequencing quality, this patient was removed from the analysis. When assessing the differences in gene expression due to IBD itself, control samples from an IBD group were compared to control samples from the corresponding healthy organ.
Assembly: GRCh98
Supplementary files format and content: Table of genes and read counts per sample and gene.

extract_protocol:
After centrifugation at 2 000 g for 5 minutes, the supernatant was split into two tubes and frozen at -80 °C. 200 µl of TRIzol (Thermo Fisher Scientific) was added to each monolayer well and replicates were collected separately. Cell lysates in TRIzol were vortexed and frozen at -20 °C. Total RNA was isolated according to manufacturer’s protocol. Aliquots were taken from samples originating from different monolayer plates to test for the presence of SARS-CoV-2 RNA.
After initial quality control using Agilent’s Bioanalyzer sequencing libraries were prepared from 25-250ng of total RNA per sample following Roche’s strand specific “KAPA RNA Hyper Prep Kit + RiboErase (HMR)” library preparation protocol for double indexed Illumina libraries:   First, the rRNA fraction was depleted using complementary DNA oligonucleotides. rRNA-DNA hybrids and DNA baits were removed by treatment with RNase H and DNase.  RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A-tailing Illumina sequencing compatible adapters carrying unique dual indices were ligated (NEXTFLEX® Unique Dual Index Barcodes).  Following bead-based clean-up steps the libraries were amplified using 13 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out on an Illumina NovaSeq6000 system in PE100bp mode yielding between 20-40 million fragments per sample.

value: colon organoid

value: healthy


title: Human bone marrow trephine of control sample - Rep 4

description: 10x Genomics

value: Ctrl


title: SKHep1_Scr


title: genomic DNA from HepG2 ShDNMT1#3

description:
rep3
HepG2_Sh1#3

value: cancer HCC cells line

value: DNA methyltransferase (DNMT1) knockdown with shRNA


title: Blastoids_PIPseq_nontarg_c2_R2

source_name: clone 2

value: clone 2


title: Human bone marrow trephine of MGUS sample - Rep 2

description: 10x Genomics

value: MGUS


title: genomic DNA from SKHep1 ShDNMT1#1

description:
rep1
SKHep1_Sh1#1


title: NorHep_Scr

value: RNAPII-Ser5 (Abcam, ab5408)


title: CD8rejTs, scRNA-seq

description: Library name: CD8rejTs


title: genomic DNA from HepG2 ShDNMT1#2

description:
rep2
HepG2_Sh1#2


title: healthy,colon,control,patient15_1

value: control