title: liver_ATAC_800_l2_s1

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
800_peaks.narrowPeak.gz
800_scaled.bw

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.

source_name: liver tissue

extract_protocol:
We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher), homogenized the tissue powder in ice-cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol [pH 7.5]) using a 1-mL dounce for 40 strokes, and rotated for 5 min at 4°C. We filtered the solution through a Miracloth (Calbiochem), centrifuged at 1,100 × g for 10 min at 4°C, washed the pellet with 250 μL NIB containing 0.5% Triton-X, centrifuged at 500 × g for 5 min at 4°C, and resuspended the pellet in 250 μL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 [pH 7.4]). After counting isolated nuclei, we pelleted 50,000 nuclei at 500 × g for 5 min at 4°C
We prepared ATAC-seq libraries using the omni-ATAC protocol with 5 ul Tn5 transposase per reaction, cleaned the transposase reaction and final libraries with Zymo DNA Clean and Concentrator (D4029), visualized and quantified the libraries using a TapeStation, and sequenced 150-bp paired-end reads on either an Illumina HiSeq 4000 or HiSeq X ten.

value: liver tissue


title: 105506-001-070, Lung, BMP6 KO, CS, 24 weeks

status: Public on Feb 01 2025

type: SRA

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

library_source: transcriptomic

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
Assembly: To align the reads of each sample, the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 package 1.34.0 in R studio
Supplementary files format and content: Count files

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Mouse lung tissue was isolated from wild-type or BMP6 KO mice

extract_protocol:
Total RNA from whole lung tissue from wild type (WT) and Bmp6 knockout (Bmp6-/-) mice was isolated using the miRNeasy Mini Kit (Qiagen, 217604).
RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by GenomeScan (https://www.genomescan.nl/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 in R studio

treatment_protocol: Mice were exposed for 4 weeks or for 24 weeks to either air or cigarette smoke (CS)

tag: tissue

value: Lung

tag: genotype

value: BMP6 KO

tag: treatment

value: CS, 24 weeks


title: 105506-001-071, Lung, BMP6 KO, CS, 24 weeks


title: Set2_B12_F_6hr

type: RNA

city: ITHACA

first: Hector

last: Aguilar-Carreno

state: New York

address: T8016A Veterinary Research Tower

department: Microbiology and Immunology

country: USA

institute: Cornell University

description:
F_transfection_6h_B
Gene expression at 6h

hyb_protocol: Hybridization was performed using Agilent Microarray Hybridization Chamber at 65°C for 17 hours.

scan_protocol: Scanning was performed using Agilent Scanner G2505C.

data_processing: Background correction was carried out on microarray samples using the maximum likelihood estimation for the normal-exponential convolution model, with an offset of 50, as implemented in Bioconductor's limma package. Samples were then normalized using quantile normalization and outliers were detected using intensity distribution and a boxplot graph followed by hierarchical clustering and PCA analysis of expression profiles using the MVA package.

organism: Homo sapiens

label_protocol: Cy3 labeling was performed using T7 promoter primer and T7 RNA polymerase.

growth_protocol: HEK293T cells were maintained in complete MDEM media with 10% Fetal Bovine Serum, 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol and quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNAs were converted to cDNAs using AffinityScript reverse transcriptase and oligo-dT promoter primer. The second strand cDNA synthesiswas performed with AffinityScript reverse transcriptase. Cy3 labeled cRNA was synthesized with T7 RNA polymerase mix. cRNAs were purified using RNeasy mini kit. cRNA quantitiy was determined using NanoDrop ND-1000 UV-VIS spectrophotometer and cRNAs were hybridized onto Agilent 4 x 44K human genome microarray slides.

treatment_protocol: For each time-point ten 6-well plates were used, five of them were transfected with HeV genes F, G, and FG combination for 6h, 12h, and 21h time point. Remaining five 6-well plates were used as uninfected controls.

tag: cell line

value: F transfection

tag: time


title: K562, reference, Replicate 1, 2023 screen

city: Princeton

first: Jia

last: Ling

state: NJ

address: Carl Icahn Laboratory, South Drive

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
Library name: 2023 screen, R1_DMSO
DMSO.R1

library_source: genomic

data_processing:
Base-calling was performed using onboard Real Time Analysis (RTA3), v3.4.4. Demultiplexing was performed using deML, a program for maximum likelihood demultiplexing of NGS data, under default parameters. While deML does not indicate a version, commit 036f1c9 from its associated github repository was used for all samples.
To ensure high quality read assignment, we used a two-step aligning and filtering process. Reads consist of 19 nt corresponding to an sgRNA target sequence followed by 21 nt from the associated sgRNA constant region. First, we analyzed the constant region in each read using bowtie2 (v2.3.4.1) to soft trim 19 nt from the 5′ end and map reads to reference constant regions. Reads which mapped constant sequences in the incorrect orientation or which had more than 1 mismatch were discarded using seqtk (v1.3-r117-dirty). We reasoned that these reads represented inactive sgRNAs with defects from cloning. sgRNA target regions from the remaining reads were then analyzed by using bowtie2 to soft trim 21 nt from the 3′ end, isolating only the first 19 nt, and align the remaining read fragments to an sgRNA reference library. Reads with mapping quality ≤ 5 were filtered, and read counts for each position-specific sgRNA pair, or “construct” (denoted by X/Y), were then determined from the remaining aligned reads. For T0 and DMSO-treated samples in the 2022 screen, sequencing was repeated three times due to high percentage of low quality reads caused by incorrect phiX spike-in and reads from three repeats were combined by adding counts from individual runs.
We calculated the median coverage for each sgRNA across replicates in each position and filtered constructs with any sgRNAs demonstrating a median coverage ≤ 35 reads in either position at T0. We then also removed any dual-sgRNA constructs with ＜50 reads in either replicate at T0, and to further avoid effects from low frequency representation, we added a pseudocount of 10 to all surviving construct read counts. Next, we defined an enrichment value for individual constructs as log2 of the fraction of reads (i.e., reference or PARPi) in endpoint samples divided by the fraction of reads for that construct at T0. Enrichments were normalized to non-targeting controls, for γ and τ separately, by subtracting the median enrichment of non-targeting sgRNA pairs (NT/NT) and adjusted by dividing the total number of population doublings that occurred from T0 until endpoint (reference R1 = 8.04, reference R2 = 7.98, PARPi R1 = 5.40, PARPi R2 = 4.98). The resulting values constitute our orientation-dependent γ and τ “construct phenotypes”. To calculate construct ρ phenotypes, we divided the fraction of reads at the PARPi endpoint by the fraction of reads at the reference endpoint, normalized to non-targeting controls, and then adjusted the resulting values by dividing by the difference in the number of population doublings observed in the PARPi-treated and reference arms (R1 = 2.64, R2 = 3.00). To determine individual “sgRNA phenotypes” for each replicate, we averaged the phenotypes of all constructs wherein a given sgRNA was paired with a non-targeting sgRNA, independent of orientation (i.e., including X/NT and NT/X). Similarly, “single-gene phenotypes” were defined as the average of all sgRNA phenotypes for sgRNAs targeting the same gene. Extended discussion of the full analytical process, along with all code for generating genetic interaction scores from counts, is available in an R markdown document in the accompanying Github repository (https://github.com/simpsondl/PARPi_interactions).
Assembly: sgRNA_reference_library.fasta
Supplementary files format and content: For counts files (read_counts2022.txt and read_counts2023.txt), the first two columns contain the guide assigned to each position in the dual-sgRNA construct (FirstPosition and SecondPosition). The remaining six columns give the raw counts (number of reads) assigned to each ordered  combination of guides from each arm/timepoint (T0 [start of screen], DMSO [reference condition], NIRAP [treated with niraparib]) of the relative screen (2022 or 2023) by replicate (R1 or R2).
Supplementary files format and content: For phenotype files (phenotypes2022.txt and phenotypes2023.txt),  the first two columns contain the guide assigned to each position in the dual-sgRNA construct (FirstPosition and SecondPosition). The remaining 9 columns give the 9 calculated phenotypes for each combination of guides. Phenotypes are listed by replicate (R1 or R2) as well as a replicate-averaged value (Avg). Gamma, tau, and rho phenotypes are calculated as described above from raw counts. The file contains only phenotypes for guide combinations passing filters described above.
Supplementary files format and content: sgRNA_reference_library.fasta contains the spacer sequences for all guides in the library.

molecule: genomic DNA

source_name: cell line

growth_protocol: For the 2023 screen, K562 CRISPRi cells were transduced with the dual-sgRNA CRISPRi lentiviral library with more than 400X representation per construct at a low MOI (~0.25) as described above. Two biological replicates were performed. Cells were maintained at 0.5e6 to 0.6e6 per mL in the multitron incubator and were selected with 3 μg/mL puromycin 2 days post transduction. 9 days post transduction, treatment started (T0). T0 samples were collected from each replicate and the remaining cells of each replicate were divided into two populations, one of which was dosed with 2 μM niraparib and the other with vehicle (DMSO). Cells were split with vehicle or niraparib supplemented media for 3 days (the dosage of niraparib was increased to 3 μM from day 2 onwards, roughly the LC35 determined for cells transduced with the interaction sgRNA library) and maintained at densities between 0.5-0.6e6 cells per mL during the treatment. 4 days after dosing, cells were spun down, resuspended in drug-free media and were allowed to grow for an additional 6 days. A 850X representation was maintained for each arm throughout the entire process. 19 days post transduction, cells were collected from the niraparib-treated arms (PARPi endpoint samples) and DMSO-treated arms (reference endpoint samples), respectively. For the 2022 screen, the screen was performed with the same library as described above with the following differences: 1) library was transduced with a 350X representation; 2) the treated arms were dosed with 2 μM niraparib, split with drug-free media and were spun out of drug 3 days after dosing; 3) cells were harvested 18 days post transduction.

extract_protocol:
For the 2023 screen, cell pellets were processed to generate sequencing libraries as follows. Genomic DNA was extracted using the NucleoSpin® Blood XL, Maxi kit for DNA from blood (Macherey-Nagel) with an RNase A treatment step during cell lysis. For the 2022 screen, the extraction was performed as describe above except that the RNase A treatment step was performed separately after extraction of genomic DNA followed by ethanol precipitation.
The sgRNA loci were amplified with an indexing 5′ primer (5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNCAGCACAAAAGGAAACTCACC) and an indexing 3′ primer (5′-CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNGGCGGTAATACGGTTATCCA). Each reaction (100 μL total volume) contained 10 μg of genomic DNA (measured on NanoDrop) and 1 μM of each primer and was run on the Bio-Rad C1000 thermal cycler with the following program: 1 cycle of 30 seconds at 98 °C; 20 cycles of 10 seconds at 98 °C, followed by 75 seconds at 65 °C; 1 cycle of 5 minute at 65 °C; 4 °C hold. At least 400X coverage was maintained for each sample during PCR amplification. Aliquots of the PCR products were purified for sequencing using SPRIselect Reagent (Beckman Coulter) in two double-sided 0.45X-0.8X reactions and two 0.8X reactions. Indexed samples were pooled in equal molar ratio prior to sequencing.

value: cell line

tag: cell type

value: leukemia cell

value: DMSO

tag: batch


title: 105506-001-072, Lung, BMP6 KO, CS, 24 weeks


title: 105506-001-069, Lung, BMP6 KO, CS, 24 weeks


title: Set2_B25_Control_12hr

description:
No_transfection_control_12h_A
Gene expression at 12h

value: control


title: liver_ATAC_800_l1_s1


title: K562, T0, Replicate 2, 2023 screen

description:
Library name: 2023 screen, R2_T0
T0.R2


title: liver_ATAC_798_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
798_peaks.narrowPeak.gz
798_scaled.bw


title: CK-H3K4me3

city: Nanjing

first: huang

middle: ran

last: ran

address: weigang 1

country: China

institute: Nanjing Agricultural College

data_processing:
Sequenced reads were trimmed for adaptor sequences using fastp
Chip-seq clean reads without adaptor sequences were aligned to the maize B73 v4 genome using bowtie2.3.2 with default parameters.
Clean reads were used for peak calling using MACS2 with parameters --nomodel -q 0.01 --broad --broad-cutoff 0.1 -g 2.10434e+09 for H3K27me3 and --nomodel -q 0.01 -g 2.10434e+09 for other histone markers.
Assembly: B73 RefGen_v4
Supplementary files format and content: bw

organism: Zea mays

source_name: seedling

growth_protocol: Uniformly pre-germinated seeds of Maize (Zea mays L. “B73”) were transferred to pots with soil and grown in a growth chamber with 16h light and 8h dark cycle at 25-28℃ for 9 days. Then the plants were equally divided into two halves, one for continuing to grow under the normal conditions, another one for cold treatment (COLD) at 4℃ for 24h.

extract_protocol: The whole seedlings of CK or COLD from 10 individual 10-day-old plants were collected using liquid nitrogen and stored at -80℃ for later use.

value: seedling

value: WT

tag: chip antibody


title: Skeletal sample rep 1, ADT

city: New York

first: Matthew

last: Greenblatt

state: NY

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

library_source: other

data_processing:
Primary processing of rawATACsequencing data from multiplexed sample libraries was done through the standard Cellranger pipeline (10x Genomics), aligning raw reads to mm10 and generating a fragments.tsv file.
Rawsequencing data for protein and hashtag expression were processed through kallisto bustools (Pachter lab) to create count matrices for antibody derived tags.
Mitochondrial DNA variants were genotyped using the mgatk package v0.6.1
Assembly: mm10
Supplementary files format and content: cellranger-atac output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz
Supplementary files format and content: mgatk output files: A.txt.gz, C.txt.gz, G.txt.gz, T.txt.gz, depthTable.txt.gz

molecule: protein

source_name: Femur

extract_protocol:
3-month-old PolGD257A/D257A mouse femurs were extracted and subjected to both mechanical and enzymatic digestion. Cells were co-stained with both FACS antibodies and CITE-seq antibodies and then sorted using a FACS machine for single cell ATAC seq. All skeletal cell population obtained from three mice were kept discrete to run on three individual lanes for sequencing (10X Genomics). Sorted CD45+ hematopoietic cells were polled together to be run on one lane and therefore, hashing was performed to retain the identity of the mouse specimens. Sorted cells were fixed with 1% Paraformaldehyde and cells were gently lyzed (10mM tris-HCl; pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1% BSA) and resuspended in 1X Nuclei buffer (10X Genomics) prior to be subjected to single cell sequencing optimized for mitochondrial DNA capture.
The library was prepared using the ASAP-seq ptotocol , sequenced with NovaSeq 6000, 2X100 bp.
scATAC-seq targeting mitochondrial DNA

value: Femur

tag: library type

value: ADT

value: Skeletal

tag: strain


title: K562, T0, Replicate 1, 2023 screen

description:
Library name: 2023 screen, R1_T0
T0.R1


title: K562, niraparib, Replicate 2, 2023 screen

description:
Library name: 2023 screen, R2_NIRAP
NIRAP.R2

value: niraparib


title: 105506-001-067, Lung, BMP6 KO, CS, 24 weeks


title: Set2_B9_Control_6hr

description:
No_transfection_control_6h_D
Gene expression at 6h


title: Set2_B10_Control_6hr

description:
No_transfection_control_6h_E
Gene expression at 6h


title: liver_ATAC_795_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
795_peaks.narrowPeak.gz
795_scaled.bw


title: Set2_B7_Control_6hr

description:
No_transfection_control_6h_B
Gene expression at 6h


title: 105506-001-066, Lung, BMP6 KO, CS, 24 weeks


title: K562, niraparib, Replicate 1, 2022 screen

description:
Library name: 2022 screen, R1_NIRAP
NIRAP.R1


title: liver_ATAC_794_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
794_peaks.narrowPeak.gz
794_scaled.bw


title: liver_ATAC_794_l2_s1


title: 105506-001-068, Lung, BMP6 KO, CS, 24 weeks


title: K562, niraparib, Replicate 2, 2022 screen

description:
Library name: 2022 screen, R2_NIRAP
NIRAP.R2


title: Set2_B14_F_6hr

description:
F_transfection_6h_D
Gene expression at 6h


title: K562, reference, Replicate 2, 2022 screen

description:
Library name: 2022 screen, R2_DMSO
DMSO.R2


title: 105506-001-064, Lung, BMP6 KO, CS, 24 weeks


title: liver_ATAC_794_l1_s1


title: Set2_B8_Control_6hr

description:
No_transfection_control_6h_C
Gene expression at 6h


title: K562, T0, Replicate 2, 2022 screen

description:
Library name: 2022 screen, R2_T0
T0.R2


title: Set2_B5_Control_0hr

description:
No_transfection_control_0h_E
Gene expression at 0h


title: Set2_B6_Control_6hr

description:
No_transfection_control_6h_A
Gene expression at 6h


title: liver_ATAC_793_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
793_peaks.narrowPeak.gz
793_scaled.bw


title: 105506-001-063, Lung, BMP6 KO, CS, 24 weeks


title: Set2_B4_Control_0hr

description:
No_transfection_control_0h_D
Gene expression at 0h


title: Set2_B2_Control_0hr

description:
No_transfection_control_0h_B
Gene expression at 0h


title: liver_ATAC_793_l1_s1


title: K562, T0, Replicate 1, 2022 screen

description:
Library name: 2022 screen, R1_T0
T0.R1


title: Set2_B16_G_6hr

description:
G_transfection_6h_A
Gene expression at 6h

value: G transfection


title: 105506-001-062, Lung, BMP6 KO, CS, 24 weeks


title: 105506-001-065, Lung, BMP6 KO, CS, 24 weeks


title: VK2/E6E7_HMU_3

city: Seoul

first: Juwon

last: Choi

address: 50 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description: Library name: HMU 3

data_processing:
For quality control of raw sequencing data, FastQC v0.11.7 was used.
Sequence reads were trimmed to remove low-quality bases, adapters, and contaminants using Trimmomatic v0.38.
Trimmed sequence reads were mapped to the GRCh38 genome using HISAT2 version 2.1.0.
Transcript assembly and quantification of gene expression from mapped reads were performed using StringTie version 2.1.3b.
Assembly: GRCh38
Supplementary files format and content: Processed data include gene-level counts and normalized expression values in text format.

growth_protocol: VK2/E6E7 cells were cultured in Keratinocyte Serum-Free Medium (KSFM; Gibco) supplemented with 0.1 ng/mL human recombinant epidermal growth factor (EGF), 0.05 mg/mL bovine pituitary extract (BPE), and antibiotics, in a humid atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol
RNA libraries for RNA sequencing were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocols

treatment_protocol: Cells were treated with PBS (Control) or Lactobacillus salivarius HHuMin-U (HMU) at a concentration of 1×10^8 CFU/mL for 6 hours

value: Vaginal epithelial cell

value: HMU


title: 105506-001-060, Lung, BMP6 KO, Air, 24 weeks

value: Lung

value: Air, 24 weeks


title: liver_ATAC_786_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
786_peaks.narrowPeak.gz
786_scaled.bw

value: liver tissue


title: VK2/E6E7_HMU_2

description: Library name: HMU 2


title: liver_ATAC_786_l1_s1


title: VK2/E6E7_HMU_1

description: Library name: HMU 1


title: Set2_B1_Control_0hr

description:
No_transfection_control_0h_A
Gene expression at 0h


title: liver_ATAC_779_l5_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
779_peaks.narrowPeak.gz
779_scaled.bw


title: VK2/E6E7_PBS_3

description: Library name: Control 3

value: PBS


title: liver_ATAC_783_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
783_peaks.narrowPeak.gz
783_scaled.bw


title: Set1_A64_FG_29hr

description:
FG_transfection_29h_D
Gene expression at 29h

treatment_protocol: For each time-point ten 6-well plates were used, five of them were transfected with NiV genes F, G, and FG combination for 6h, 12h, and 29h time point. Remaining five 6-well plates were used as uninfected controls.

value: FG transfection


title: Set1_A63_FG_29hr

description:
FG_transfection_29h_C
Gene expression at 29h


title: 105506-001-061, Lung, BMP6 KO, Air, 24 weeks

value: BMP6 KO


title: liver_ATAC_786_l3_s1


title: 105506-001-056, Lung, BMP6 KO, Air, 24 weeks


title: VK2/E6E7_PBS_1

description: Library name: Control 1


title: VK2/E6E7_PBS_2

description: Library name: Control 2


title: Set2_B3_Control_0hr

description:
No_transfection_control_0h_C
Gene expression at 0h


title: 105506-001-055, Lung, BMP6 KO, Air, 24 weeks


title: Set1_A62_FG_29hr

description:
FG_transfection_29h_B
Gene expression at 29h


title: 105506-001-059, Lung, BMP6 KO, Air, 24 weeks


title: liver_ATAC_779_l3_s2


title: Set1_A65_FG_29hr

description:
FG_transfection_29h_E
Gene expression at 29h


title: MDA-PCa-2b, input

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

description: DNA-seq

data_processing:
ChIP-seq sequence data was processed using an ENCODE-DC/chip-seq-pipeline2 -based workflow (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Briefly, fastq files were aligned on the hg38 human genome reference using Bowtie2 (v2.2.6) followed by alignment sorting (samtools v1.7) of resulting bam files with filtering out of unmapped reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s MarkDuplicates (v1.126) function, followed by indexation of resulting bam files with samtools. For each bam file, genome coverage was computed with bedtools (v2.26.0), followed by the generation of bigwig (wigToBigWig v377) files. Peaks were called with SPP for each treatment sample using a pooled input alignment (.bam file) as control.
Assembly: GRCh38-2020-A
Supplementary files format and content: bigwig and bed files returned by the encode chip-seq pipeline. They contain information about peak positions.

growth_protocol: MDA-PCa-2b and DU145 cells were obtained from ATCC. MDA-PCa-2b cells were cultured with HCP1 medium (Enzo, catalog number AES-0403), 20% FBS, 1x Glutamine and pen/strep. DU145 was cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
Cells (10 x 10^6) were crosslinked by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator (E220) using the following setup: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: SMARCA4 (ab110641), FOSL1 (PA5-66880 – Invitrogen) and TEAD1 (BD #610923). Antibody chromatin complexes were pulled down with Protein A or Protein A/G magnetic beads and washed twice in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with MinElute PCR purification kit (Qiagen).
Sequencing ready libraries were generated using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina ® (New England Biolabs E7645). Libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and profiled using the D5000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on an Illumina sequencer to generate 25 million paired end 50-base pair reads per library.

treatment_protocol: DU145 and MDA-PCa-2b were treated with 100 nM SMARCA2_4.1 (SMARCA2/4 degrader) or DMSO for 24 hours before cells were harvested for ChIP-seq

value: prostate adenocarcinoma


title: 105506-001-057, Lung, BMP6 KO, Air, 24 weeks


title: Set1_A61_FG_29hr

description:
FG_transfection_29h_A
Gene expression at 29h


title: liver_ATAC_778_l4_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
778_peaks.narrowPeak.gz
778_scaled.bw


title: 105506-001-058, Lung, BMP6 KO, Air, 24 weeks


title: Set1_A60_G_29hr

description:
G_transfection_29h_E
Gene expression at 29h


title: Set1_A59_G_29hr

description:
G_transfection_29h_D
Gene expression at 29h


title: 105506-001-053, Lung, wild-type, CS, 24 weeks

value: wild-type

value: CS, 24 weeks


title: MDA-PCa-2b, SMARCA2/4 degrader, FOXA1, rep2

description: DNA-seq

value: Abcam ab5089


title: Set1_A58_G_29hr

description:
G_transfection_29h_C
Gene expression at 29h


title: MDA-PCa-2b, SMARCA2/4 degrader, FOXA1, rep1

description: DNA-seq


title: liver_ATAC_778_l1_s2


title: 105506-001-054, Lung, BMP6 KO, Air, 24 weeks


title: liver_ATAC_775_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
775_peaks.narrowPeak.gz
775_scaled.bw


title: MDA-PCa-2b, DMSO,  FOXA1, rep1

description: DNA-seq


title: MDA-PCa-2b, DMSO,  FOXA1, rep2

description: DNA-seq


title: 105506-001-050, Lung, wild-type, CS, 24 weeks


title: liver_ATAC_775_l1_s2


title: liver_ATAC_773_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
773_peaks.narrowPeak.gz
773_scaled.bw


title: Set1_A56_G_29hr

description:
G_transfection_29h_A
Gene expression at 29h


title: 105506-001-052, Lung, wild-type, CS, 24 weeks


title: 105506-001-048, Lung, wild-type, CS, 24 weeks


title: 105506-001-049, Lung, wild-type, CS, 24 weeks


title: liver_ATAC_778_l3_s1


title: liver_ATAC_767_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
767_peaks.narrowPeak.gz
767_scaled.bw


title: 105506-001-047, Lung, wild-type, CS, 24 weeks


title: 105506-001-046, Lung, wild-type, CS, 24 weeks


title: liver_ATAC_767_l1_s1


title: Set1_A54_F_29hr

description:
F_transfection_29h_D
Gene expression at 29h

value: F transfection


title: Set1_A55_F_29hr

description:
F_transfection_29h_E
Gene expression at 29h


title: Set1_A57_G_29hr

description:
G_transfection_29h_B
Gene expression at 29h


title: Set1_A51_F_29hr

description:
F_transfection_29h_A
Gene expression at 29h


title: Set1_A52_F_29hr

description:
F_transfection_29h_B
Gene expression at 29h


title: 105506-001-051, Lung, wild-type, CS, 24 weeks


title: Set1_A53_F_29hr

description:
F_transfection_29h_C
Gene expression at 29h


title: MDA-PCa-2b, SMARCA2/4 degrader, SMARCA4, rep2

description: DNA-seq

value: Abcam ab110641


title: Set1_A49_Control_29hr

description:
No_transfection_control_29h_C
Gene expression at 29h

value: control


title: 105506-001-045, Lung, wild-type, CS, 24 weeks


title: MDA-PCa-2b, SMARCA2/4 degrader, SMARCA4, rep1

description: DNA-seq


title: liver_ATAC_773_l1_s2


title: liver_ATAC_753_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
753_peaks.narrowPeak.gz
753_scaled.bw


title: 105506-001-044, Lung, wild-type, CS, 24 weeks


title: MDA-PCa-2b, DMSO,  SMARCA4, rep2

description: DNA-seq


title: liver_ATAC_753_l1_s1


title: MDA-PCa-2b, DMSO,  SMARCA4, rep1

description: DNA-seq


title: 105506-001-043, Lung, wild-type, CS, 24 weeks


title: 105506-001-042, Lung, wild-type, CS, 24 weeks


title: 105506-001-041, Lung, wild-type, Air, 24 weeks


title: 105506-001-040, Lung, wild-type, Air, 24 weeks


title: 3dPI_2

city: Innsbruck

first: Kai

last: Kummer

address: Schoepfstr. 41

department: Institute of Physiology

country: Austria

institute: Medical University of Innsbruck

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt

data_processing:
The quality of sequencing reads was assessed using FastQC
Fastq files were trimmed and adapters removed using skewer (v.0.2.2)
exceRpt small-RNAseq pipeline (https://github.com/gersteinlab/exceRpt) were used including mapping to the genome using STAR.
Reads were quantified using annotation from various databases including miRNAs (miRBase), tRNAs (gtRNAdb), piRNAs (piRNAbank), longRNAs (Genecode v.24 human annotation).
Counts were normalized by library size
Assembly: hg38
Supplementary files format and content: tab-delimited txt file including raw count for each sample
Supplementary files format and content: tab-delimited txt file including counts per million (CPM) for each sample

source_name: bronchial epithelial cells

growth_protocol: Normal human bronchial epithelial cells (NHBE, Lonza, cat# CC-2540 S, upper respiratory tract) are routinely cultured in air liquid interface (ALI). Cells were cultured as a monolayer for 2-4 days until they reached 80% confluence. Cells were detached and seeded onto GrowDexT (UPM)-coated 0.33 cm2 porous (0.4 μm) polyester membrane inserts with a seeding density of 1 × 105 cells per Transwell (Costar, Corning, New York, NY, USA). The cells were grown to near confluence in submerged culture for 3 days in specific epithelial cell growth medium according to the manufacturer´s instructions (Stemcell™). Cultures were maintained in a humidified atmosphere with 5% CO2 at 37 °C and then transferred to ALI culture for another four weeks until cells were fully differentiated. The epithelium was expanded and differentiated using airway media from Stemcell™. The number of days in development was designated relative to initiation of ALI culture, corresponding to day 0.

extract_protocol:
Total RNA of NHBE cells uninfected or infected with SARS-CoV-2 VoCs for 1 hr, 24 hr and 72 hr was extracted using miRNeasy extraction kit (Qiagen) and according to the manual’s instructions.
Small RNA libraries were generated with the Lexogen small RNA-Seq Library Prep Kit (Lexogen GmbH, Vienna, Austria), based on 500 ng total RNA input
Final libraries were multiplexed and sequenced with Illumina NovaSeq 6000  technology, using 150 bp paired-end settings and targeting an average of 20 million read pairs per library (<200nt) (GENEWIZ/Azenta)

treatment_protocol: SARS-CoV-2 variant Delta and Omicron subvariant BA.2 from sequenced COVID-19 positive swabs were propagated and subsequently used to infect cells at a MOI of 0.01.

value: bronchial epithelial cells


title: liver_ATAC_730_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
730_peaks.narrowPeak.gz
730_scaled.bw


title: Set1_A46_Control_29hr

description:
No_transfection_control_29h_A
Gene expression at 29h


title: 3dPI_1

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: liver_ATAC_753_l3_s1


title: liver_ATAC_724_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
724_peaks.narrowPeak.gz
724_scaled.bw


title: Set1_A48_Control_29hr

description:
No_transfection_control_29h_B
Gene expression at 29h


title: 1dPI_3

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: 105506-001-038, Lung, wild-type, Air, 24 weeks


title: Set1_A44_FG_12hr

description:
FG_transfection_12h_D
Gene expression at 12h


title: COLD heavy MNase-seq

data_processing:
Sequenced reads were trimmed for adaptor sequences using fastp
MNase-seq clean reads without adaptor sequences were aligned to the maize B73 v4 genome using bowtie2.3.2 with default parameters.
Nucleosome positions and changes were identified using the dpos function of DANPOS2.bigwig files were generated using deeptools bamCoverage with parameters --centerReads -bs 20 --smoothLength 60 --normalizeUsing RPKM and were transformed to wig files using bigWigtoWig software
Assembly: B73 RefGen_v4
Supplementary files format and content: bw

value: seedling

tag: mnase

value: heavy

value: WT

value: COLD


title: Set1_A45_FG_12hr

description:
FG_transfection_12h_E
Gene expression at 12h


title: Sigma16HBE_1

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

description: Library name: Sigma16HBE_1

data_processing:
Read quality and trimming was performed with Trim Galore 0.6.7 (cutadapt 4.6) with default parameter values.
For gene and isoform level quantification, isoform counts were estimated with Salmon version 1.10.11 using default parameters and using the GENCODE version 45 GTF.
Assembly: Hg38, gtf=gencode.v45.primary_assembly.annotation.gtf.gz
Supplementary files format and content: salmon.merged.gene_tpm.tsv: count data, one column per sample

molecule: polyA RNA

growth_protocol: 16HBE cells were cultured in Eagle's minimal essential medium, supplemented with 10% fetal bovine serum, penicillin (50 units/ml), and streptomycin (50 µg/ml). IMR-90 cells, human fetal lung cells immortalized with human telomerase reverse transcriptase (hTERT), were acquired from Dr. William Hahn’s laboratory at the Dana-Farber Cancer Institute. Culturing was conducted with Eagle's minimum essential medium (EMEM), supplemented with 10% fetal bovine serum, penicillin (50 units/ml), and streptomycin (50 µg/ml).

extract_protocol:
RNA samples from various cell lines were extracted by RNAeasy kit (Qiagen) and measured for quality and quantity by Agilent TapeStation systems with RNA ScreenTape assay. Samples with a RIN over 8 were submitted for sequencing for gene expression.
Paired end cDNA libraries were constructed and sequenced on Illumina platforms for an average read depth of ~50 million reads.

value: plain untreated human bronchial epithelial cell line


title: Set1_A43_FG_12hr

description:
FG_transfection_12h_C
Gene expression at 12h


title: Set1_A42_FG_12hr

description:
FG_transfection_12h_B
Gene expression at 12h


title: 1dPI_2

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: liver_ATAC_720_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
720_peaks.narrowPeak.gz
720_scaled.bw

value: liver tissue


title: liver_ATAC_741_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
741_peaks.narrowPeak.gz
741_scaled.bw


title: 105506-001-037, Lung, wild-type, Air, 24 weeks

value: Lung

value: Air, 24 weeks


title: 3dPI_3

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: Set1_A41_FG_12hr

description:
FG_transfection_12h_A
Gene expression at 12h

value: FG transfection


title: K562, reference, Replicate 1, 2022 screen

description:
Library name: 2022 screen, R1_DMSO
DMSO.R1

value: cell line

value: leukemia cell

value: DMSO


title: liver_ATAC_720_l1_s2


title: Set1_A39_G_12hr

description:
G_transfection_12h_D
Gene expression at 12h

value: G transfection


title: 105506-001-039, Lung, wild-type, Air, 24 weeks

value: wild-type


title: liver_ATAC_733_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
733_peaks.narrowPeak.gz
733_scaled.bw


title: 1dPI_1

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: 1hPI_3

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: 105506-001-036, Lung, wild-type, Air, 24 weeks


title: 105506-001-035, Lung, wild-type, Air, 24 weeks


title: liver_ATAC_713_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
713_peaks.narrowPeak.gz
713_scaled.bw


title: 1hPI_2

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: 1hPI_1

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: Set1_A40_G_12hr

description:
G_transfection_12h_E
Gene expression at 12h


title: liver_ATAC_711_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
711_peaks.narrowPeak.gz
711_scaled.bw


title: Set1_A38_G_12hr

description:
G_transfection_12h_C
Gene expression at 12h


title: liver_ATAC_720_l2_s2


title: Uninf_3

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt

value: 0h (Uninf)


title: liver_ATAC_687_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
687_peaks.narrowPeak.gz
687_scaled.bw


title: 105506-001-032, Lung, wild-type, Air, 24 weeks


title: Set1_A37_G_12hr

description:
G_transfection_12h_B
Gene expression at 12h


title: liver_ATAC_687_l1_s2


title: Uninf_2

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: Set1_A36_G_12hr

description:
G_transfection_12h_A
Gene expression at 12h


title: Uninf_1

description:
COUNT_MATRIX.txt
CPM_MATRIX.txt


title: liver_ATAC_671_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
671_peaks.narrowPeak.gz
671_scaled.bw


title: liver_ATAC_671_l3_s1


title: 105506-001-030, Lung, BMP6 KO, CS, 4 weeks

value: BMP6 KO

value: CS, 4 weeks


title: Set1_A35_F_12hr

description:
F_transfection_12h_E
Gene expression at 12h

value: F transfection


title: Set1_A33_F_12hr

description:
F_transfection_12h_C
Gene expression at 12h


title: HCT16T61AKO2 Ribo-Seq

city: hong kong

first: xiaoting

last: zhang

address: Rm 708, 7/F., Li Ka Shing Medical Science Building , Prince of Wales Hospital, Shatin, N.T., Hong Kong

department: Faculty of Medicine

institute: The Chinese University of Hong Kong

data_processing:
Fastq files were checked with Fastqc (v. 0.11.9) for quality control. Trim-galore (v. 0.6.6) is then used to remove sequencing adaptors and low-quality reads. QC-passed reads are then subjected to bowtie (v. 1.3.0) to remove mycoplasma contamination, and mapped to human ribosome sequences in order to remove rRNA reads. Reads unmapped in this step are collected, subjected to STAR (v. 2.7.8a) and mapped to human reference genome(hg38). Reads mapped to the transcriptome are collected for subsequent analysis. Transcriptome-aligned reads were processed with Ribowaltz (v. 1.2.0), and differences in ribosome binding were analyzed using DESeq2 (v. 1.30.0). Function enrichment was performed using Cluster Profiler (v. 3.18.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: ribo-seq

source_name: colon

extract_protocol:
Cycloheximide (Sigma, St Louis, MO, USA) was added to cell cultures medium to a final concentration of 100 μg/ml and incubated for 2 min.
The clean cell pellet was lysed in 1mL lysis buffer at 4℃ for 10 min followed by incubation of 10μL RNase A (BBI, B600476) at room temperature for 30 min. The RNAs were extracted by Trizol and rRNA was removed with SP-ribo-Pools (Forever Star, FS-R1056-04) followed by clean-up with VAHTS RNA Clean Beads (Vazyme, N412).  The clean RNA samples were then treated with T4 polynucleotide Kinase (PNK, Vazyme, N102) to create RNA fragments with 3’-hydroxyl and a 5’-phosphate that are compatible with the following deep sequencing library construction. Following PNK treatment, the ribosome-protected mRNA fragments (RPFs) were purified by VAHTS RNA Clean Beads followed by library construction with VAHTS Small RNA Library Prep Kit for Illumina (Vazyme, NR801). The libraries were fractioned on 6% PAGE minigel and the bands ranging around 150bp were recovered and purified for quality control. The qualified libraries were sequenced on Illumina Nova Seq 6000.

value: colon

value: Colon epithelial cancer cell

value: TRMT61A knockout


title: 105506-001-029, Lung, BMP6 KO, CS, 4 weeks


title: 105506-001-034, Lung, wild-type, Air, 24 weeks


title: liver_ATAC_671_l1_s1


title: Set1_A34_F_12hr

description:
F_transfection_12h_D
Gene expression at 12h


title: liver_ATAC_669_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
669_peaks.narrowPeak.gz
669_scaled.bw


title: 105506-001-033, Lung, wild-type, Air, 24 weeks


title: 105506-001-028, Lung, BMP6 KO, CS, 4 weeks


title: Set1_A31_F_12hr

description:
F_transfection_12h_A
Gene expression at 12h


title: Set1_A32_F_12hr

description:
F_transfection_12h_B
Gene expression at 12h


title: liver_ATAC_669_l1_s2


title: 105506-001-027, Lung, BMP6 KO, CS, 4 weeks


title: HCT116V21 Ribo-Seq

value: WT


title: 105506-001-026, Lung, BMP6 KO, CS, 4 weeks


title: liver_ATAC_662_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
662_peaks.narrowPeak.gz
662_scaled.bw

value: liver tissue


title: 105506-001-031, Lung, BMP6 KO, CS, 4 weeks

value: Lung


title: liver_ATAC_662_l1_s1


title: Set1_A29_Control_12hr

description:
No_transfection_control_12h_D
Gene expression at 12h

value: control


title: HCT116V22 input

data_processing:
Briefly,MeRIP-seq data analyzed as follows:  Fastqc software to evaluate the quality of the original data; BWA software was used to map reads against the reference genome; Alignment SAM files were sorted by Samtools; Signal distribution (peak calling) was identified by MACS2; Peak and motif annotation results were generated by deeptools; R. achieved statistical analysis and function enrichment analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: MeRIP-seq

extract_protocol:
RNA fragments are first ligated at 3’ end before the chemical reactions.
Briefly, the process involves the following steps: They, whether undergoing biotin pulldown or not, are then subject to reverse transcription before 3’ adaptor ligation to the resulting cDNA. Only those fragments with internal m1A sites are expected to generate misincorporation during reverse transcription that can be further detected using high-throughput sequencing.


title: 105506-001-025, Lung, BMP6 KO, CS, 4 weeks


title: HCT16T61AKO1 input


title: 105506-001-024, Lung, BMP6 KO, Air, 4 weeks

value: Air, 4 weeks


title: liver_ATAC_659_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
659_peaks.narrowPeak.gz
659_scaled.bw


title: HCT16T61AKO1 Ribo-Seq


title: HCT116V22 Ribo-Seq


title: Set1_A26_Control_12hr

description:
No_transfection_control_12h_A
Gene expression at 12h


title: Set1_A27_Control_12hr

description:
No_transfection_control_12h_B
Gene expression at 12h


title: liver_ATAC_659_l2_s2


title: Set1_A28_Control_12hr

description:
No_transfection_control_12h_C
Gene expression at 12h


title: HCT116V21 input


title: 105506-001-023, Lung, BMP6 KO, Air, 4 weeks


title: HCT16T61AKO2 input


title: 105506-001-022, Lung, BMP6 KO, Air, 4 weeks


title: HCT16T61AKO2 MeRIP


title: liver_ATAC_651_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
651_peaks.narrowPeak.gz
651_scaled.bw


title: liver_ATAC_657_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
657_peaks.narrowPeak.gz
657_scaled.bw


title: liver_ATAC_651_l1_s2


title: 105506-001-021, Lung, BMP6 KO, Air, 4 weeks


title: HCT16T61AKO1 MeRIP


title: 105506-001-020, Lung, BMP6 KO, Air, 4 weeks


title: Set1_A24_FG_6hr

description:
FG_transfection_6h_D
Gene expression at 6h

value: FG transfection


title: Set1_A23_FG_6hr

description:
FG_transfection_6h_C
Gene expression at 6h


title: Set1_A20_G_6hr

description:
G_transfection_6h_E
Gene expression at 6h


title: 105506-001-018, Lung, BMP6 KO, Air, 4 weeks


title: Set1_A21_FG_6hr

description:
FG_transfection_6h_A
Gene expression at 6h


title: liver_ATAC_644_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
644_peaks.narrowPeak.gz
644_scaled.bw


title: HCT116V22 MeRIP


title: HCT116V21 MeRIP


title: liver_ATAC_644_l3_s2


title: HCT116siOC21

data_processing:
Quantified libraries were sequenced on Illumina platform Novaseq 6000 using PE150 read length.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
A total amount of 0.4 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA sequencing in CRC cell lines with or without TRMT61A knockout was performed accordingly 6. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H -). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.Over 6G of raw data per sample were generated.

value: ONECUT2 si


title: Set1_A22_FG_6hr

description:
FG_transfection_6h_B
Gene expression at 6h


title: 105506-001-016, Lung, wild-type, CS, 4 weeks


title: HCT116siCTL2


title: liver_ATAC_636_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
636_peaks.narrowPeak.gz
636_scaled.bw


title: liver_ATAC_639_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
639_peaks.narrowPeak.gz
639_scaled.bw


title: 105506-001-015, Lung, wild-type, CS, 4 weeks


title: 105506-001-017, Lung, BMP6 KO, Air, 4 weeks


title: HCT116siOC22


title: liver_ATAC_779_l4_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
779_peaks.narrowPeak.gz
779_scaled.bw


title: Set1_A18_G_6hr

description:
G_transfection_6h_C
Gene expression at 6h


title: liver_ATAC_634_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
634_peaks.narrowPeak.gz
634_scaled.bw


title: Set1_A17_G_6hr

description:
G_transfection_6h_B
Gene expression at 6h


title: HCT116siCTL1


title: liver_ATAC_632_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
632_peaks.narrowPeak.gz
632_scaled.bw


title: 105506-001-014, Lung, wild-type, CS, 4 weeks


title: 105506-001-019, Lung, BMP6 KO, Air, 4 weeks


title: Set1_A15_F_6hr

description:
F_transfection_6h_E
Gene expression at 6h


title: Set1_A14_F_6hr

description:
F_transfection_6h_D
Gene expression at 6h


title: liver_ATAC_632_l1_s2


title: 105506-001-013, Lung, wild-type, CS, 4 weeks


title: HCT16T61AKO2


title: HCT16T61AKO1


title: 105506-001-012, Lung, wild-type, CS, 4 weeks


title: Set1_A19_G_6hr

description:
G_transfection_6h_D
Gene expression at 6h


title: liver_ATAC_630_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
630_peaks.narrowPeak.gz
630_scaled.bw


title: liver_ATAC_629_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
629_peaks.narrowPeak.gz
629_scaled.bw


title: 105506-001-011, Lung, wild-type, CS, 4 weeks


title: HCT116V21


title: 105506-001-010, Lung, wild-type, CS, 4 weeks


title: 105506-001-009, Lung, wild-type, CS, 4 weeks


title: liver_ATAC_629_l2_s2


title: liver_ATAC_629_l1_s2


title: Hela cells, input, rep2 [ChIP-Seq]

city: shanghai

first: heyang

last: wei

address: 131 Dongan Road, Xuhui District

institute: Fudan University

data_processing:
The FASTQ data were trimmed adaptor by trim_galore
ChIP-seq data mapped to human genome hg38 with Bowtie2 in pair-end mode
ChIP-seq peaks were called by MACS3
bigWig files were generated by deepTools
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cervix

growth_protocol: HeLa cells  were cultured in DMEM with 10% fetal bovine serum at 37 ℃ in 5% CO2.

extract_protocol:
Cells were crosslinked in adherent conditions with 1% formaldehyde for 10 minutes at room temperature and quenched with glycine to a final concentration of 125 nM. Fixed cells were lysed in nuclei lysis buffer to extract nuclei and sheared by sonication to 300-500-bp-sized fragments. Sheared chromatin was incubated with antibodies and protein A/G-Dynabeads for 12 hours at 4 ℃. The beads were washed with RIPA150, RIPA500, RIPA-LiCl and TE buffer , respectively. DNA was eluted in elution buffer  with Proteinase K  at 65 ℃ for 6 hours, DNA fragments were digested with RNase A and proteinase K.
ChIP DNA libraries were prepared as directed by protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China).

treatment_protocol: HeLa cells were infected with lentivirus, and stable cell lines were generated by puromycin (2 μg/mL) selection

value: Cervix

value: HeLa

value: Human Cervical Cancer Cells


title: 105506-001-008, Lung, wild-type, Air, 4 weeks

value: wild-type


title: liver_ATAC_627_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
627_peaks.narrowPeak.gz
627_scaled.bw


title: Hela cells, input, rep1 [ChIP-Seq]


title: Set1_A13_F_6hr

description:
F_transfection_6h_C
Gene expression at 6h


title: Hela cells, shMBD2+MBD2KRRE, rep2 [ChIP-Seq]


title: 105506-001-007, Lung, wild-type, Air, 4 weeks


title: HCT116V22


title: Set1_A16_G_6hr

description:
G_transfection_6h_A
Gene expression at 6h

value: G transfection


title: Set1_A10_Control_6hr

description:
No_transfection_control_6h_E
Gene expression at 6h


title: liver_ATAC_623_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
623_peaks.narrowPeak.gz
623_scaled.bw


title: Set1_A12_F_6hr

description:
F_transfection_6h_B
Gene expression at 6h


title: Set1_A11_F_6hr

description:
F_transfection_6h_A
Gene expression at 6h


title: Set1_A9_Control_6hr

description:
No_transfection_control_6h_D
Gene expression at 6h


title: Set1_A8_Control_6hr

description:
No_transfection_control_6h_C
Gene expression at 6h


title: Hela cells, shMBD2+MBD2KRRE, rep1 [ChIP-Seq]


title: 105506-001-006, Lung, wild-type, Air, 4 weeks


title: Hela cells, shMBD2+MBD2WT, rep1 [ChIP-Seq]


title: liver_ATAC_619_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
619_peaks.narrowPeak.gz
619_scaled.bw


title: Set1_A5_Control_0hr

description:
No_transfection_control_0h_C
Gene expression at 0h


title: liver_ATAC_619_l3_s2


title: liver_ATAC_618_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
618_peaks.narrowPeak.gz
618_scaled.bw


title: Hela cells, shMBD2+MBD2WT, rep2 [ChIP-Seq]


title: 105506-001-004, Lung, wild-type, Air, 4 weeks


title: Hela cells, shMBD2, rep2 [ChIP-Seq]


title: Set1_A7_Control_6hr

description:
No_transfection_control_6h_B
Gene expression at 6h


title: 105506-001-005, Lung, wild-type, Air, 4 weeks


title: liver_ATAC_485_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
485_peaks.narrowPeak.gz
485_scaled.bw


title: 105506-001-003, Lung, wild-type, Air, 4 weeks


title: Hela cells, shMBD2, rep1 [ChIP-Seq]


title: liver_ATAC_485_l2_s1


title: 105506-001-001, Lung, wild-type, Air, 4 weeks


title: Hela cells, shCtrl, rep2 [ChIP-Seq]


title: Set1_A6_Control_6hr

description:
No_transfection_control_6h_A
Gene expression at 6h


title: 105506-001-002, Lung, wild-type, Air, 4 weeks


title: HM_8_ZT14_F3_MCC3804A226_S94

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

description: Library name: HM_8_ZT14_F3_MCC3804A226_S94

data_processing:
FASTQC
HTSeq
DESeq2 normalization (median of ratios)
Cosinor modeling
Assembly: Mus musculus Ensembl GRCm38
Supplementary files format and content: .Rdata

source_name: Brain

extract_protocol:
Qiagen Rneasy Plus Micro Kit( (Qiagen)
SMART Stranded Total RNA kit (Takara)

value: Brain

value: Homogenate tissue

value: Wildtype C57BL/6J mice


title: liver_ATAC_485_l1_s1


title: Hela cells, shCtrl, rep1 [ChIP-Seq]


title: HM_7_ZT14_M1_MCC3804A211_S100

description: Library name: HM_7_ZT14_M1_MCC3804A211_S100


title: liver_ATAC_479_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
479_peaks.narrowPeak.gz
479_scaled.bw


title: Mouse 4 - OGN - CCL

description: Mouse 4

growth_protocol: 300,000 freshly isolated mouse Epcam+ cells were mixed in a 1:1 ratio with proliferation-inactivated CCL206 fibroblasts and seeded into 6-well plates as described above. Cultures were exposed to treatments for 72 hours, after which the medium was removed, and Matrigel was digested using 1 mL dispase (Sigma-Aldrich, #SCM133) for 1 hour at 37 °C. Organoids were disrupted by 1 mL trypsin for 5 minutes at 37 °C, and the resulting cells were resorted into Epcam+ and CCL206 fractions using mouse Epcam (CD326) microbeads.

extract_protocol:
Total RNA was isolated using the RNA purification kit NucleoSpin RNA (Macherey-Nagel 740955, Germany) according to the manufacturer’s guide. Cells were lysed by adding a mixture of buffer RA1 and dithiothreitol (Sigma-Aldrich, 3483-12-3). The yield of the isolated RNA was then measured using the NanoDrop 1000 spectrophotometer.
RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by GenomeScan (https://www.genomescan.nl/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 in R studio

treatment_protocol: Organoids were exposed to either vehicle, OGN (10 ug/ml), MRC5-derived extracellular vesicles or MRC5-derived soluble factors.

value: OGN


title: Hela cells, FLAG-MBD2, CUT&Tag, rep2

data_processing:
The FASTQ data were trimmed adaptor by trim_galore
CUT&Tag data mapped to human genome hg38 with Bowtie2 in pair-end mode
The aligned reads were processed by MACS3 to call peaks
bigWig files were generated by bamCoverage function in Deeptools
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag experiments were performed using CUT&Tag Assay Kit (pAG-Tn5) for illumina(ABclonal, RK20265) according to the manufacturer’s instructions.
Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000

value: FLAG


title: HM_60_ZT22_F2_MCC3804A239_S132

description: Library name: HM_60_ZT22_F2_MCC3804A239_S132


title: Hela cells, FLAG-MBD2, CUT&Tag, rep1


title: Mouse 3 - OGN - CCL

description: Mouse 3


title: liver_ATAC_479_l1_s2

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.

extract_protocol:
We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher), homogenized the tissue powder in ice-cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol [pH 7.5]) using a 1-mL dounce for 40 strokes, and rotated for 5 min at 4°C. We filtered the solution through a Miracloth (Calbiochem), centrifuged at 1,100 × g for 10 min at 4°C, washed the pellet with 250 μL NIB containing 0.5% Triton-X, centrifuged at 500 × g for 5 min at 4°C, and resuspended the pellet in 250 μL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 [pH 7.4]). After counting isolated nuclei, we pelleted 50,000 nuclei at 500 × g for 5 min at 4°C
We prepared ATAC-seq libraries using the omni-ATAC protocol with 5 ul Tn5 transposase per reaction, cleaned the transposase reaction and final libraries with Zymo DNA Clean and Concentrator (D4029), visualized and quantified the libraries using a TapeStation, and sequenced 150-bp paired-end reads on either an Illumina HiSeq 4000 or HiSeq X ten.


title: Mouse 2 - OGN - CCL

description: Mouse 2

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
Assembly: To align the reads of each sample, the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 package 1.34.0 in R studio
Supplementary files format and content: Count files


title: HM_9_ZT18_M1_MCC3804A213_S115

description: Library name: HM_9_ZT18_M1_MCC3804A213_S115


title: Hela cells, FLAG-GATAD2A, CUT&Tag, rep2


title: HM_58_ZT18_F3_MCC3804A217_S85

description: Library name: HM_58_ZT18_F3_MCC3804A217_S85


title: liver_ATAC_465_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
465_peaks.narrowPeak.gz
465_scaled.bw


title: liver_ATAC_459_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
459_peaks.narrowPeak.gz
459_scaled.bw


title: HM_6_ZT10_F3_MCC3804A205_S114

description: Library name: HM_6_ZT10_F3_MCC3804A205_S114


title: Mouse 1 - OGN - CCL

description: Mouse 1


title: HM_59_ZT22_M3_MCC3804A207_S128

description: Library name: HM_59_ZT22_M3_MCC3804A207_S128


title: HM_57_ZT18_M1_MCC3804A208_S135

description: Library name: HM_57_ZT18_M1_MCC3804A208_S135


title: liver_ATAC_459_l2_s1


title: liver_ATAC_459_l1_s1


title: HM_56_ZT14_F3_MCC3804A219_S101

description: Library name: HM_56_ZT14_F3_MCC3804A219_S101


title: Mouse 2 - SFs - CCL

description: Mouse 2

value: SFs


title: Mouse 3 - SFs - CCL

description: Mouse 3


title: Set1_A4_Control_0hr

description:
No_transfection_control_0h_B
Gene expression at 0h

data_processing: Background correction was carried out on microarray samples using the maximum likelihood estimation for the normal-exponential convolution model, with an offset of 50, as implemented in Bioconductor's limma package. Samples were then normalized using quantile normalization and outliers were detected using intensity distribution and a boxplot graph followed by hierarchical clustering and PCA analysis of expression profiles using the MVA package.


title: Hela cells, shMBD2+MBD2WT, rep2 [ATAC-seq]

data_processing:
The FASTQ data were trimmed adaptor by trim_galore
The ATAC-seq data were mapped to the hg38 using bowtie2 with the default parameters.
ATAC-seq peaks were called by MACS3
bigWig files were generated by deepTools
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
50,000 viable cells were  disrupted in cold resuspension buffer for 2 min on ice. The lysis reaction was stopped with the addition of 1 mL wash buffer. After a centrifugation step at 500g for 10 min, pelleted nuclei were resuspended in 50 μL of transposition buffer (25 μL 2× TD buffer, 2.5 μL transposase (100 nM final), 16.5 μL PBS, 2×TD Buffer for 30 min at 37 ℃ with 1000 rpm mixing. DNA was purified on AMPure XP beads.
Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000


title: Mouse 1 - SFs - CCL

description: Mouse 1


title: liver_ATAC_458_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
458_peaks.narrowPeak.gz
458_scaled.bw

value: liver tissue


title: Hela cells, shMBD2+MBD2WT, rep1 [ATAC-seq]


title: Hela cells, FLAG-GATAD2A, CUT&Tag, rep1


title: HM_53_ZT10_M1_MCC3804A259_S106

description: Library name: HM_53_ZT10_M1_MCC3804A259_S106


title: Mouse 4 - EVs - CCL

description: Mouse 4

value: Lung

value: EVs


title: Hela cells, shMBD2, rep2 [ATAC-seq]


title: liver_ATAC_457_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
457_peaks.narrowPeak.gz
457_scaled.bw


title: Mouse 3 - EVs - CCl

description: Mouse 3


title: Hela cells, shMBD2, rep1 [ATAC-seq]


title: Hela cells, shMBD2+MBD2KRRE, rep1 [ATAC-seq]


title: HM_51_ZT6_M2_MCC3804A251_S105

description: Library name: HM_51_ZT6_M2_MCC3804A251_S105


title: liver_ATAC_458_l3_s2


title: Set1_A3_Control_0hr

description:
No_transfection_control_0h_A
Gene expression at 0h

extract_protocol: Total RNA was extracted using Trizol and quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNAs were converted to cDNAs using AffinityScript reverse transcriptase and oligo-dT promoter primer. The second strand cDNA synthesiswas performed with AffinityScript reverse transcriptase. Cy3 labeled cRNA was synthesized with T7 RNA polymerase mix. cRNAs were purified using RNeasy mini kit. cRNA quantitiy was determined using NanoDrop ND-1000 UV-VIS spectrophotometer and cRNAs were hybridized onto Agilent 4 x 44K human genome microarray slides.

value: control


title: HM_52_ZT6_F1_MCC3804A247_S133

description: Library name: HM_52_ZT6_F1_MCC3804A247_S133


title: Mouse 2 - EVs - CCL

description: Mouse 2


title: liver_ATAC_457_l1_s1


title: Hela cells, shCtrl, rep2 [ATAC-seq]


title: Hela cells, shMBD2+MBD2KRRE, rep2 [ATAC-seq]


title: Hela cells, shCtrl, rep1 [ATAC-seq]


title: HM_5_ZT10_M1_MCC3804A252_S113

description: Library name: HM_5_ZT10_M1_MCC3804A252_S113


title: liver_ATAC_439_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
439_peaks.narrowPeak.gz
439_scaled.bw


title: liver_ATAC_438_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
438_peaks.narrowPeak.gz
438_scaled.bw


title: Mouse 1 - EVs - CCL

description: Mouse 1


title: HM_50_ZT2_F2_MCC3804A214_S122

description: Library name: HM_50_ZT2_F2_MCC3804A214_S122


title: Mouse 4 - control - CCL

description: Mouse 4

value: Control


title: HM_55_ZT14_M2_MCC3804A255_S134

description: Library name: HM_55_ZT14_M2_MCC3804A255_S134


title: Hela cells, shMBD2+MBD2KRR/E, rep3

data_processing:
The FASTQ data were trimmed adaptor by trim_galore ,RNA-seq data were mapped to the human genome hg38 using hisat2
Assembly: hg38
Supplementary files format and content: text file include raw counts for each Sample

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizolreagent. Illumina TruSeqRNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: shRNA


title: Mouse 3 - control - CCL

description: Mouse 3


title: HM_49_ZT2_M3_MCC3804A245_S119

description: Library name: HM_49_ZT2_M3_MCC3804A245_S119


title: liver_ATAC_438_l2_s1


title: HM_48_ZT22_F3_MCC3804A204_S107

description: Library name: HM_48_ZT22_F3_MCC3804A204_S107


title: Hela cells, shMBD2+MBD2KRR/E, rep2


title: Mouse 2 - control - CCL

description: Mouse 2


title: liver_ATAC_440_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
440_peaks.narrowPeak.gz
440_scaled.bw


title: liver_ATAC_438_l1_s1


title: Hela cells, shMBD2+MBD2KRR/E, rep1


title: HM_47_ZT22_M1_MCC3804A256_S141

description: Library name: HM_47_ZT22_M1_MCC3804A256_S141


title: HM_46_ZT18_F4_MCC3804A244_S112

description: Library name: HM_46_ZT18_F4_MCC3804A244_S112


title: Mouse 1 - control - CCL

description: Mouse 1


title: Hela cells, shMBD2+MBD2WT, rep3


title: liver_ATAC_437_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
437_peaks.narrowPeak.gz
437_scaled.bw


title: Mouse 4 - OGN - Epcam

description: Mouse 4

value: CD45-/CD31-/Epcam+ cells


title: HM_45_ZT18_M2_MCC3804A237_S118

description: Library name: HM_45_ZT18_M2_MCC3804A237_S118


title: Hela cells, shMBD2+MBD2WT, rep2

value: Cervix


title: Mouse 4 - SFs - CCL

description: Mouse 4


title: HM_44_ZT_14_F1_MCC3804A203_S99

description: Library name: HM_44_ZT_14_F1_MCC3804A203_S99


title: liver_ATAC_437_l2_s2


title: Mouse 3 - OGN - Epcam

description: Mouse 3


title: liver_ATAC_435_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
435_peaks.narrowPeak.gz
435_scaled.bw


title: Hela cells, shMBD2, rep3

value: HeLa


title: Hela cells, shMBD2+MBD2WT, rep1

value: Human Cervical Cancer Cells


title: HM_43_ZT14_M1_MCC3804A216_S136

description: Library name: HM_43_ZT14_M1_MCC3804A216_S136


title: liver_ATAC_433_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
433_peaks.narrowPeak.gz
433_scaled.bw


title: Hela cells, shMBD2, rep2


title: HM_42_ZT10_F3_MCC3804A202_S91

description: Library name: HM_42_ZT10_F3_MCC3804A202_S91


title: Mouse 4 - SFs - Epcam

description: Mouse 4


title: Hela cells, shMBD2, rep1


title: liver_ATAC_418_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
418_peaks.narrowPeak.gz
418_scaled.bw


title: HM_41_ZT10_M2_MCC3804A243_S104

description: Library name: HM_41_ZT10_M2_MCC3804A243_S104


title: Mouse 3 - SFs - Epcam

description: Mouse 3


title: liver_ATAC_418_l2_s1


title: HM_40_ZT6_F2_MCC3804A223_S130

description: Library name: HM_40_ZT6_F2_MCC3804A223_S130


title: liver_ATAC_435_l3_s2


title: Hela cells, shCtrl, rep3

value: shCtrl


title: liver_ATAC_418_l1_s1


title: Mouse 2 - SFs - Epcam

description: Mouse 2


title: Mouse 2 - OGN - Epcam

description: Mouse 2


title: Mouse 1 - OGN - Epcam

description: Mouse 1


title: Hela cells, shCtrl, rep1


title: liver_ATAC_414_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
414_peaks.narrowPeak.gz
414_scaled.bw


title: HM_39_ZT6_M1_MCC3804A253_S120

description: Library name: HM_39_ZT6_M1_MCC3804A253_S120


title: DND1-NANOS3-dKO,hPGCLC,day4,rep2

city: Haining

first: zhaoyu

last: Gu

state: Zhejiang

address: 718 East Haizhou Road

department: ZJE

institute: Zhejiang University

data_processing:
Step 1: Data preprocessing using Cutadapt. - Software: Cutadapt - Version: 4.1 - Parameters: -j 20 -u 20 -U 20
Step 2: Quality control and trimming using Trim Galore. - Software: Trim Galore - Version: 0.6.7 - Parameters: -q 25 --phred33 -e 0.1 --stringency 4 --gzip --trim-n
Step 3: Read alignment using STAR. - Software: STAR - Version: 2.7.10a - Parameters: --runThreadN 15 --runMode alignReads --readFilesCommand zcat --twopassMode Basic --outSAMtype BAM SortedByCoordinate --genomeDir /home/data/genome/STAR_RNA_UCSCfa_GENCODEgtf_hg38_index --readFilesIn ${i}/02_trimmed/${i}_1_cut_val_1.fq.gz ${i}/02_trimmed/${i}_2_cut_val_2.fq.gz --outFileNamePrefix ${i}/03_mapped/
Step 4: Sorting using Samtools. - Software: Samtools - Version: 1.6 - Parameters: sort -@ 20
Step 5: Counting using FeatureCounts. - Software: FeatureCounts - Version: 2.0.1 - Parameters: -T 10 -a /home/data/genome/GENCODE/gencode_v41_gtf/gencode.v41.annotation.gtf -p -C -t exon -g gene_name
Assembly: hg38
Supplementary files format and content: The "Geneid" column contains the gene identifiers, while the "Chr", "Start", "End", "Strand", and "Length" columns provide genomic information about each gene.  The remaining columns contain the read counts for each sample, indicating the number of reads mapped to each gene in the specified sample.

growth_protocol: The H1 hESCs (46, XY) were cultured in the Nuwacell® ncTarget hPSC medium (Nuwacell, RP01020) supplemented with 50ng/ml Primocin (InvivoGen, ant-pm-2) on Matrigel (Corning, 354234)-coated plates. The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.  For the induction of iMeLC and hPGCLCs, hESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) in basic DMEM/F-12 (1:1) medium (GIBCO, C11330500BT) supplemented with 20% KnockOut Serum (GIBCO, 10828028), 1% non-essential amino acids (GIBCO, 11140-050), 0.1 nM β-mercaptoethanol (GIBCO, 21985023), 1× Penicillin-Streptomycin-Glutamine (Invitrogen, 10378016) and 10 ng/ml FGF2 (Peprotech, 100-18B). The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.

extract_protocol:
The cells were pelleted down and snap frozen until use. RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For hPGCLCs, to enrich mRNA from extracted total RNA, VAHTS mRNA Capture Beads (Vazyme, N401) was applied. After enrichment, VAHTS universal V8 RNA-seq library Prep Kit for Illumina (Vazyme, NR605) was utilized to prepare libraries for sequencing, which briefly contains fragmentation, cDNA synthesis, adapter ligation, PCR amplification and purification. For hESCs and three different germ lyers,after the RNA sample passes the test, magnetic beads with Oligo(dT) are used to enrich eukaryotic mRNA. Then fragmentation buffer is added to break the mRNA into short fragments. Using the mRNA as a template, six-base random primers (random hexamers) are used to synthesize one-strand cDNA. Then buffer, dNTPs, and DNA polymerase I and RNase H are added to synthesize two-strand cDNA. Double-stranded cDNA was then purified using AMPure XP beads. The purified double-stranded cDNA is first subjected to end repair, A-tailing and ligation of sequencing adapters, and then AMPure XP beads are used for fragment size selection. Finally, PCR amplification was performed, and the PCR product was purified with AMPure XP beads to obtain the final sequencing library.

value: hPGCLCs


title: HM_38_ZT2_F3_MCC3804A229_S117

description: Library name: HM_38_ZT2_F3_MCC3804A229_S117

value: Brain


title: Mouse 4 - EVs - Epcam

description: Mouse 4


title: Mouse 3 - EVs - Epcam

description: Mouse 3


title: DND1-NANOS3-dKO,hPGCLC,day4,rep1

treatment_protocol: For the induction of iMeLC and hPGCLCs, hESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) in basic DMEM/F-12 (1:1) medium (GIBCO, C11330500BT) supplemented with 20% KnockOut Serum (GIBCO, 10828028), 1% non-essential amino acids (GIBCO, 11140-050), 0.1 nM β-mercaptoethanol (GIBCO, 21985023), 1× Penicillin-Streptomycin-Glutamine (Invitrogen, 10378016) and 10 ng/ml FGF2 (Peprotech, 100-18B). The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.


title: liver_ATAC_390_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
390_peaks.narrowPeak.gz
390_scaled.bw


title: liver_ATAC_399_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
399_peaks.narrowPeak.gz
399_scaled.bw


title: HM_37_ZT2_M2_MCC3804A220_S109

description: Library name: HM_37_ZT2_M2_MCC3804A220_S109

value: Homogenate tissue


title: Mouse 1 - EVs - Epcam

description: Mouse 1


title: Control H1,ectoderm,day5,rep2

value: ectoderm

value: WT control


title: liver_ATAC_390_l1_s1


title: Mouse 2 - EVs - Epcam

description: Mouse 2


title: HM_36_ZT22_F3_MCC3804A221_S116

description: Library name: HM_36_ZT22_F3_MCC3804A221_S116

value: Wildtype C57BL/6J mice


title: Mouse 1 - SFs - Epcam

description: Mouse 1

value: SFs


title: liver_ATAC_390_l2_s1

value: liver tissue


title: Mouse 4 - control - Epcam

description: Mouse 4

value: Lung


title: liver_ATAC_39_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
39_peaks.narrowPeak.gz
39_scaled.bw


title: Hela cells, shCtrl, rep2


title: Control H1,mesoderm,day5,rep2

value: mesoderm


title: Control H1,ectoderm,day5,rep1


title: Control H1,mesoderm,day5,rep1


title: HM_35_ZT22_M2_MCC3804A231_S131

description: Library name: HM_35_ZT22_M2_MCC3804A231_S131


title: liver_ATAC_39_l1_s2


title: Mouse 3 - control - Epcam

description: Mouse 3


title: HM_33_ZT18_M3_MCC3804A258_S98

description: Library name: HM_33_ZT18_M3_MCC3804A258_S98


title: liver_ATAC_387_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
387_peaks.narrowPeak.gz
387_scaled.bw


title: HM_32_ZT14_F2_MCC3804A246_S126

description: Library name: HM_32_ZT14_F2_MCC3804A246_S126


title: Control H1,endoderm,day5,rep2

value: endoderm


title: HM_31_ZT14_M3_MCC3804A227_S102

description: Library name: HM_31_ZT14_M3_MCC3804A227_S102


title: Mouse 2 - control - Epcam

description: Mouse 2

value: Control


title: liver_ATAC_387_l2_s1


title: liver_ATAC_383_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
383_peaks.narrowPeak.gz
383_scaled.bw


title: Control H1,endoderm,day5,rep1


title: NANOS3-ADAR,hPGCLC,day4,rep2


title: liver_ATAC_383_l1_s2


title: HM_30_ZT10_F2_MCC3804A230_S124

description: Library name: HM_30_ZT10_F2_MCC3804A230_S124


title: NANOS3-ADAR,hPGCLC,day4,rep1


title: DND1-ADAR,hPGCLC,day4,rep2


title: Resis_Warfarin1_scRNA

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
scRNA.Warfarin.Vehicle.rds
scRNA.NSCLC.all.rds
scRNA.onlyT.Warfarin.Vehicle.rds

library_source: transcriptomic single cell

data_processing:
we add the exogenous sequence of plasmids into mm10 genome reference. The cellranger (v5.0.1) was used to generate the index of genome reference and to align the raw data with the mm10 genome reference, removing duplicated reads by adjusting unique molecules identities (UMIs), estimating single-cell by splitting barcodes, quantify the gene counts on single-cell levels and summarize the sequencing reads information, mapping ratio, and cells and genes’ detection.
The FindVariableFeatures was implemented to identify 4,000 high-variable genes with vst model for data scaling and subsequent clustering and dimension reducing. The 25 principal component analysis factors were used to embedding calculation and the 20 principal component analysis factors were used to neighbors’ estimation. The openTSNE, t-SNE, UMAP and force atlas2 (fa2) were used to reduce the dimension following previously reported methods. The major population and subpopulation were identified by classical signatures, and top markers were calculated by FindAllMarkers with wilcox.test.
Assembly: mm10
Supplementary files format and content: MTX
Supplementary files format and content: RDS

source_name: NSCLC

extract_protocol:
The lung cancers tissues were collected from sensitive (n=2), sensitive+anti-PD1(n=2), resistant (n=2) and resistant+anti-PD1 (n=2), resistant dKO (n=2), resistant + ant-PD1+veh (n=1), resistant + ant-PD1+warfarin (n=1) groups and washed with PBS supplemented with 2% fetal bovine serum (FBS). The lung tumors were digested by Collagenase I and IV into single cells and filtered through a 100um filter to obtain a single-cell suspension. Cell numbers were counted and the concentration of single-cell suspension was about 1000 cells/μl. The cell activity of single-cell suspension was more than 85%.
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.
10X 3' scRNA

value: NSCLC

tag: group


title: HM_34_ZT18_F2_MCC3804A222_S123

description: Library name: HM_34_ZT18_F2_MCC3804A222_S123


title: HM_4_ZT6_F1_MCC3804A257_S90

description: Library name: HM_4_ZT6_F1_MCC3804A257_S90


title: HM_29_ZT10_M3_MCC3804A254_S127

description: Library name: HM_29_ZT10_M3_MCC3804A254_S127


title: Resis_veh1_scRNA

value: immunotherapy-resistant + anti-PD1+veh


title: liver_ATAC_383_l1_s1


title: DND1-ADAR,hPGCLC,day4,rep1


title: dKO_ICI2_scRNA

description:
scRNA.NSCLC.with.dKO.rds
scRNA.NSCLC.all.rds
scRNA.onlyT.with.dKO.rds

value: immunotherapy-resistant dKO+anti-PD1


title: HM_28_ZT6_F3_MCC3804A228_S110

description: Library name: HM_28_ZT6_F3_MCC3804A228_S110


title: NANOS3-KO,hPGCLC,day4,rep2


title: Mouse 1 - control - Epcam

description: Mouse 1

value: CD45-/CD31-/Epcam+ cells


title: HM_27_ZT6_M3_MCC3804A210_S92

description: Library name: HM_27_ZT6_M3_MCC3804A210_S92


title: dKO_ICI1_scRNA


title: liver_ATAC_382_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
382_peaks.narrowPeak.gz
382_scaled.bw


title: HM_26_ZT2_F2_MCC3804A218_S93

description: Library name: HM_26_ZT2_F2_MCC3804A218_S93