title: CHIP066, H3K9me2, FRDA, rep1

description: H3K9me2_PT_1_AK132_AK134.inpLg2_1kb.woTNR.e100.S10Kb.bw

source_name: FRDA fibroblast

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms
Libraries were quantified and pooled for sequencing; input libraries were always run with associated ChIP samples. If possible, replicate samples were run together on the same sequencing run.

value: FRDA fibroblast

value: H3K9me2 (Active Motif, #39239)

value: FRDA


title: patient infected with Male patient infected with meningioma WHO grade I

status: Public on Jun 24 2026

type: SRA

city: Wuhan

first: Haobin

last: Ren

state: Hubei

address: G9P7+CP8, Wuchang District

country: China

institute: Wuhan University

description: Library name: MG101

library_source: other

data_processing:
FastQC for QC
Trim Galore for trimming
BWA-MEM for alignment
Circle-Map for ecDNA detection
Assembly: hg38
Supplementary files format and content: txt for identified ecDNA

molecule: other

organism: Homo sapiens

source_name: Frontal lobe

extract_protocol:
ecDNA purification was performed on DNA extracted from meningioma, glioblastoma, pituitary adenoma and vestibular schwannoma. After confirming the successful enrichment of ecDNA from total DNA samples, Phi29-assisted ecDNA rolling circle amplification was performed before DNA library preparation.
Amplicon was sonicated into DNA fragments with average size as 350bp using Bioruptor. Library preparation was performed using Vazyme DNA library preparation kit (Vazyme) following the standard protocol starting with 300 ng of sonicated DNA per sample. Library quality and fragment size distribution were assessed using the Qsep400 system (BiOptic).

tag: tissue

value: Frontal lobe

tag: infection


title: gD2-gC1 rep3

city: Tianjin

first: Zhao

last: Wenying

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: Library name: SAMPLES 9

library_source: transcriptomic

data_processing:
lllumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al.,Nucleic Acids Research,2009.In short, exons from all isoforms.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM yalues for each Sample

molecule: total RNA

organism: Mus musculus

source_name: draining lymph nodes

extract_protocol:
RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: draining lymph nodes

tag: strain

value: BABL/c

tag: time

tag: treatment

value: 10μg gD2 + 10μg gC1


title: gD2-gC1 rep2

description: Library name: SAMPLES 8


title: A549 cells, 8 Gy C-ions, chronic hypoxia, 4 h, replicate 4

city: Koeln

first: Christine

middle: Elisabeth

last: Hellweg

state: Nordrhein-Westfalen

address: Linder Hoehe

department: r, IInstitute of Aerospace Medicine

country: Germany

institute: German Aerospace Center

description: Library name: H-8Gy-4h-4

data_processing:
trimming by GENEWIZ
mapping by GENEWIZ
differential gene expression by GENEWIZ
DESeq2 package in R
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: tab-delimited text files include GeneID,  Chr, Start, End, Strand, Length for each Sample

growth_protocol: A549 were seeded in 25 cm2 cell culture flasks at a density of 5000 cells/cm2. The cells were incubated at 37 °C and saturated humidity, either under normoxia (20% O2) in a CO2 incubator (5% CO2; Heraeus HERAcell 150, Thermo Fisher Scientific, Karlsruhe, Germany) or under hypoxia (1% O2) in an InvivO2 400 hypoxia workstation (Baker Ruskinn, South Wales, UK) flushed with 5% CO2, 1% O2, and 94% N2.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen). At least 3 µg total RNA per sample (4 biological repeats per condition, with RNA Integrity Numbers (RIN) above 9.0) were sent on dry ice to GENEWIZ (Leipzig, Germany) for mRNA sequencing in the same run after Poly(A) selection using the Illumina NovaSeq6000 platform (configuration: 2x150 bp, 350M read pairs)
RNA libraries for RNA-seq were prepared by GENEWIZ.

treatment_protocol: After 48 h, cells were irradiated with 0 or 8 Gy of C-ions (at GANIL, Caen, France; 35 MeV/n, LET ~75 keV/µm) at a dose rate of 1 Gy/min and room temperature. Incubation was continued after irradiation under normoxia (normoxia, N, or transient hypoxia /reoxygenation, R) or hypoxia (chronic hypoxia, H). Cells were lysed for RNA extraction 4 h after irradiation. For more details: https://doi.org/10.3390/ijms25021010

tag: cell line

tag: cell type

value: non small cell lung cancer

tag: genotype

value: hypotriploid, p53 wild-type, KRAS mutated

value: hypoxia 48 h, 8 Gy C-ions, hypoxia 4 h

tag: batch


title: A549 cells, 0 Gy C-ions, chronic hypoxia, 4 h, replicate 4

description: Library name: H-0Gy-4h-4

value: hypoxia 48 h, 0 Gy C-ions, hypoxia 4 h


title: gD2-gC1 rep1

description: Library name: SAMPLES 7


title: A549 cells, 8 Gy C-ions, transient hypoxia, 4 h, replicate 4

description: Library name: R-8Gy-4h-4

value: hypoxia 48 h, 8 Gy C-ions, normoxia 4 h


title: gD2 rep3

description: Library name: SAMPLES 6

value: 10μg gD2


title: A549 cells, 0 Gy C-ions, transient hypxia, 4 h, replicate 4

description: Library name: R-0Gy-4h-4

value: hypoxia 48 h, 0 Gy C-ions, normoxia 4 h


title: gD2 rep2

description: Library name: SAMPLES 5


title: gD2 rep1

description: Library name: SAMPLES 4


title: A549 cells, 8 Gy C-ions, normoxia, 4 h, replicate 4

description: Library name: N-8Gy-4h-4

value: normoxia 48 h, 8 Gy C-ions, normoxia 4 h


title: A549 cells, 0 Gy C-ions, normoxia, 4 h, replicate 4

description: Library name: N-0Gy-4h-4

value: normoxia 48 h, 0 Gy C-ions, normoxia 4 h


title: A549 cells, 8 Gy C-ions, chronic hypoxia, 4 h, replicate 3

description: Library name: H-8Gy-4h-3


title: PBS rep3

description: Library name: SAMPLES 3

value: 100μl PBS


title: BxPC3, IgG, plus IFNγ, Replicate1, CUT&RUN

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center/New York University

description:
Library name: BxPC3_IgG_plusIFNγ_Rep1_Rep1
BxPC3_CUTRUN_IgG_plusIFNγ_3reps.bw
BxPC3_CUTRUN_IgG_plusIFNγ_3reps_peaks.narrowPeak

library_source: genomic

data_processing:
The fastq files were trimmed and quality-controlled with Trim Galore (version 0.6.10 with the default options in a pair-end mode. The resulting reads were aligned to hg38 using bowtie2 (version 2.4.4) with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 (Langmead & Salzberg, 2012). The alignment files were sorted by coordinate, then unpaired reads were removed, and indexed with samtools (version 1.14) (Danecek et al., 2021).
For reads visualization on genome tracks, the processed bam files were merged with samtools and visualized via the Integrative Genomics Viewer (version 2.16.1) (Robinson et al., 2011).
For peak identification, peaks and summits were called with MACS2 (version 2.2.7.1) using all three individual bam files for all replicates targeting the protein of interest (-t) and all three targeting IgG as controls (-c) with options --format BAMPE --gsize 2.7e9 --keep-dup all (Zhang et al., 2008).sortRegions descend (Ramirez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
We performed CUT&RUN in BxPC-3 cells using CUTANA ChIC/CUT&RUN Kit (EpiCypher) following the manufacturer’s protocol (Skene & Henikoff, 2017). In brief, 500,000 cells were trypsinized, washed, and bound to activated Concanavalin A-conjugated paramagnetic beads (EpiCypher). The cell-bead conjugates were then resuspended in recommended buffer with 0.5 μg antibody targeting the protein of interest: Anti-H3K27ac (Active Motif 39135), Anti-H3K4me3 (EpiCypher 13-0041k) as positive control, and Anti-IgG (EpiCypher 13-0042k) as negative control. The suspensions were incubated overnight at 4 °C with gentle shaking. Then, the cell-bead conjugates were washed twice with the kit’s permeabilization buffer, and incubated with pAG-MNase (Epicypher 15-1016) for 10 min at room temperature. Subsequently, the unbound pAG-MNase was washed away, and the MNase was activated by adding CaCl2 to a final concentration of 2 mM. The reaction was stopped after the pAG-MNase was allowed to digest and release the antibody-bound chromatin for 2 hours at 4 °C. Finally, the released DNA was purified with the spin columns provided by the kit (EpiCypher).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). The libraries were sequenced on a IlluminaNovaSeq 6000  SP using 2x50 bp reads.

value: PDAC

tag: cut&run antibody

value: IgG (EpiCypher 13-0042k)

value: plus IFNγ


title: CREFLOX-15

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: Library name: CREFLOX-15

data_processing:
Raw fastq was trimmed using TrimGalore! And cutadapt to remove standard Illumina adapters. The trimmed reads were aligned to mouse reference genome GRCm38 with hisat2 v2.1.0 [1].  Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Mus_musculus.GRCm38.102.
Assembly: GRCm38
Supplementary files format and content: raw counts from featureCounts

molecule: polyA RNA

source_name: lung

growth_protocol: Cx3cr1-CreERT2; Casp11^WT/WT (Cx3cr1-Cre control) and Cx3cr1-CreERT2; Casp11^flox/flox (Cx3cr1-MPS-Casp11⁻/⁻) mice were housed under standard specific-pathogen-free conditions at The Ohio State University. Both groups are homozygous for the Cx3cr1-CreERT2 knock-in allele. To induce Cre-mediated recombination, mice were administered tamoxifen at 75 mg/kg dissolved in corn oil via intraperitoneal injection for 7 consecutive days, followed by a 3-day washout period. Mice were 3–4 months of age at the time of infection. Food and water were provided ad libitum.

extract_protocol:
Total RNA was extracted from the left lung lobe using TRIzol reagent (Thermo Fisher Scientific, Cat. 15596026) according to the manufacturer's instructions. RNA cleaning and concentration were performed using the Zymo Research RNA Clean & Concentrator-5 kit (Cat. R1015). RNA integrity and quantity were assessed using an RNA Biochip and Qubit RNA Fluorescence Dye (Invitrogen).
The RNA sample received was quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Mice were anesthetized by isoflurane induction at 2–3% concentration in an induction chamber for approximately 5 minutes. Mice were infected intranasally with 5×10⁵ TCID50 of mouse-adapted SARS-CoV-2 strain MA10 in 50 μL sterile PBS (25 μL per nare). Lungs were harvested at day 4 post-infection. The left lung lobe was snap frozen in liquid nitrogen and stored at −80°C prior to RNA extraction.

value: lung

value: Cx3cr1-CreERT2; Casp11^flox/flox


title: CREFLOX-16

description: Library name: CREFLOX-16


title: PBS rep2

description: Library name: SAMPLES 2

value: draining lymph nodes

value: BABL/c


title: A549 cells, 0 Gy C-ions, chronic hypoxia, 4 h, replicate 3

description: Library name: H-0Gy-4h-3

value: non small cell lung cancer


title: CREFLOX-10

description: Library name: CREFLOX-10


title: PBS rep1

description: Library name: SAMPLES 1


title: BxPC3, IgG, no IFNγ, Replicate2, CUT&RUN

description:
Library name: BxPC3_IgG_noIFNγ_Rep1_Rep2
BxPC3_CUTRUN_IgG_noIFNγ_3reps.bw
BxPC3_CUTRUN_IgG_noIFNγ_3reps_peaks.narrowPeak

value: no IFNγ


title: 6

description: Library name: 6

data_processing:
Raw paired-end reads were assessed for quality using FastQC and trimmed for adapter sequences and low-quality bases prior to alignment.
Reads were quantified against the Mus musculus GRCm39 reference transcriptome (Ensembl release 109) using Salmon (v1.10.3) with sequence-bias correction enabled.
Transcript-level quantifications were imported into R and summarized to gene-level counts using the tximport package (v1.30.0) with transcript-to-gene mappings derived from the GRCm39.109 GTF annotation via GenomicFeatures.
Assembly: Mus musculus GRCm39 (Ensembl release 109)
Supplementary files format and content: Tab-delimited text file containing gene-level count matrix (raw counts) for all samples, with Ensembl gene IDs and gene symbols.

source_name: Lung

growth_protocol: C57BL/6 wild-type (WT) and Casp11⁻/⁻ mice were housed under standard specific-pathogen-free conditions at The Ohio State University. Mice were 3–4 months of age at the time of infection. Food and water were provided ad libitum.

value: Lung

value: WT

value: MA10 SARS-CoV-2 infection


title: A549 cells, 8 Gy C-ions, transient hypoxia, 4 h, replicate 3

description: Library name: R-8Gy-4h-3

value: hypotriploid, p53 wild-type, KRAS mutated

value: hypoxia 48 h, 8 Gy C-ions, normoxia 4 h


title: Mx1-T3

city: BERKELEY

first: DANICA

last: CHEN

state: CA

address: 119 Morgan Hall

department: NST

institute: UC BERKELEY

description: Library name: Mx1-T3

library_source: genomic single cell

data_processing:
Sequencing data were processed using the Cell Ranger ARC pipeline (v2.0.2, 10x Genomics), which included demultiplexing of cells with cell barcodes, alignment to the GRCm39 mouse reference genome, and removal of empty droplets, cell debris, and low-quality cells. Filtered peak data were imported into Seurat (v4.1.0) and Signac (v1.11.0) for further quality control. Cells were retained if they had 2,300–40,000 peaks, >25% fragments in peaks, <5% of reads mapping to blacklist regions, nucleosome signal <4, and TSS enrichment score >3. A total of 7,196 nuclei (Cre) and 5,538 nuclei (T3) passed QC. Dimensionality reduction was performed by TF-IDF normalization followed by singular value decomposition (SVD) on peak features. Low-dimensional visualization was performed using UMAP on LSI components 2–50, followed by clustering with FindNeighbors and FindClusters in Seurat. Gene activities were inferred from accessibility peaks using GeneActivity (Signac), and cell type identification was performed manually using curated gene markers from the literature. Differential peak occupancy analysis was conducted using FindMarkers (Seurat).
Assembly: GRCm39
Supplementary files format and content: atac_fragments.*tsv.gz

source_name: lineage-negative bone marrow cells

extract_protocol:
Bone marrow cells were lysed with ACK buffer to remove red blood cells. Lineage-negative cells were enriched using the Lineage Cell Depletion Kit (Miltenyi Biotec), stained with a lineage antibody cocktail and propidium iodide, and live lineage-negative cells were sorted using a BD Aria cell sorter. Nuclei isolation from sorted cells was performed following the manufacturer’s instructions for the Single Cell Multiome protocol (10x Genomics).
Single-nuclei droplets and ATAC-seq libraries were prepared according to the 10x Genomics Chromium Single Cell Multiome ATAC protocol. Libraries were sequenced on an Illumina NovaSeq 6000 SP flow cell (100 cycles, paired-end, 2 × 50 bp).

value: lineage-negative bone marrow cells


title: A549 cells, 0 Gy C-ions, transient hypxia, 4 h, replicate 3

description: Library name: R-0Gy-4h-3

value: hypoxia 48 h, 0 Gy C-ions, normoxia 4 h


title: 16

description: Library name: 16

value: Caspase 11 KO


title: BxPC3, IgG, no IFNγ, Replicate1, CUT&RUN

description:
Library name: BxPC3_IgG_noIFNγ_Rep1_Rep1
BxPC3_CUTRUN_IgG_noIFNγ_3reps.bw
BxPC3_CUTRUN_IgG_noIFNγ_3reps_peaks.narrowPeak

value: PDAC


title: Mx1-Cre

description: Library name: Mx1-Cre


title: A549 cells, 8 Gy C-ions, normoxia, 4 h, replicate 3

description: Library name: N-8Gy-4h-3

value: normoxia 48 h, 8 Gy C-ions, normoxia 4 h


title: T3_6_8

description: Library name: T3_6_8

data_processing:
Data analysis was processed within the Galaxy public server (usegalaxy.org)74. In brief, after removing low-quality reads and adaptor sequences, data were mapped against mouse genome (mm10) using “HISAT2” (Galaxy Version 2.2.1)71. Gene expression levels were measured from feature counts using “HTSeq” (Galaxy Version 0.9.1)75. Differential gene expression was analyzed using “DESeq2” (Galaxy Version 1.34.0)67. GSEA of gene ontology (gseGO) was performed with ClusterProfiler (v4.6.2).
Assembly: mm10
Supplementary files format and content: .xlsx File include geneID and raw read counts.

source_name: Gastrocnemius muscle

extract_protocol:
The total RNA of gastrocnemius muscle was isolated with RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
The polyA enrichment library was prepared by Novogene and sequencing was performed on NovaSeq PE150.

value: Gastrocnemius muscle


title: A549 cells, 0 Gy C-ions, normoxia, 4 h, replicate 3

description: Library name: N-0Gy-4h-3

value: normoxia 48 h, 0 Gy C-ions, normoxia 4 h


title: BxPC3, H3K27ac, no IFNγ, Replicate2, CUT&RUN

description:
Library name: BxPC3_H3K27ac_noIFNγ_Rep2
BxPC3_CUTRUN_H3K27ac_noIFNγ_3reps.bw
BxPC3_CUTRUN_H3K27ac_noIFNγ_3reps_peaks.narrowPeak

value: H3K27ac (Active Motif 39135)


title: COLXIV_KO_ZT_4 biol rep 2

status: Public on Jun 25 2026

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Library name: K_4_2

data_processing:
Adapters from reads were removed using TrimGalore with default parameters.
Reads were aligned to the mm10 version of musmusculus using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package using the Entrez gene annotation
Assembly: GRCm38.102
Supplementary files format and content: Count matrix in excel format

source_name: epidermis

extract_protocol:
RNA was extracted from epidermal cell pellets frozen in Trizol using the NZY Total RNA Isolation Kit (NZY Tech)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (20020595, Illumina) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 500 ng of total RNA were used for polyA‐mRNA selection using Oligo‐dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, which was performed using reverse transcriptase (SuperScript II; 18064‐014, Invitrogen). Then, second strand cDNA was synthesised, incorporating dUTP in place of dTTP and generating blunt‐ended ds cDNA. A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments (A‐tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (A63882, Beckman Coulter). Final libraries were analysed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (5067‐1504 or DNF‐473, Agilent) to estimate the quantity and validate the size distribution and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (07960204001, Roche).

treatment_protocol: Epidermal cells suspensions were obtained from the skin of 47 weeks old ColXIV KO and WT mice that were sacrificed at different times of the day (ZT0, 4, 8, 12, 16, 20).

value: epidermis

value: ColXIV KO


title: A549, Kaempferol, CA10, 6h, B04

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description: Library name: CA10_T7_D1_B04

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: lung

value: epithelial cell

value: Adenocarcinoma

value: test


title: GFP-RIP_Pir2-GFP_pir1∆

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description:
Library name: RIPseq_27
Tgs1-GFP_pir1∆

data_processing:
Normalization done to reads per million for each sample. Normalized samples were subtracted from untagged controls
Samples 1, 7, 12 , 23, 24 uses sample 2 as untagged; Samples 3, 25 and 26 uses sample 5 as untagged; Sample 4 uses sample 6 as untagged; Sample 8 uses sample 9 as untagged; Sample 10 uses sample 11 as untagged; Sample 13 uses sample 14 as untagged; Sample 15, 17 and 20 uses sample 16 as untagged; Sample 18 uses sample 19 as untagged; Sample 21 uses sample 22 as untagged; Sample 27 uses sample 29 as untagged; Sample 28 uses sample 30 as untagged; Sample 31 uses sample 33 as untagged; Sample 32 uses sample 34 as untagged
Sample 18 uses sample 19 as untagged; Sample 21 uses sample 22 as untagged; Sample 29 uses sample 31 as untagged; Sample 30 uses sample 32 as untagged
Sample 33 uses sample 35 as untagged; Sample 34 uses sample 36 as untagged

Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM) (untagged controls) or RPM-normalized counts for the IP minus RPM counts of an untagged control (IPs).
Supplementary files format and content: Figure 3a,3b: Samples 3,4 for Tf2-3, Samples 7,8,9 for other genes
Supplementary files format and content: Figure 4j: Samples 23,24
Supplementary files format and content: Figure 5e: Samples 17,18
Supplementary files format and content: Figure 7a: Samples 27,28

organism: Schizosaccharomyces pombe

source_name: Yeast Whole Cells

growth_protocol: Cells were grown on YEA rich media at 30°C  for all cases except for experiments performed to check meiotic targets. For meiotic targets, cells grown to 0.1 OD600 at 30°C in YEA was shifted to 18°C for 24 hrs

extract_protocol:
Immunoprecipitation of epitope tagged protein, Proteinase treatment to remove protein; DNAse treatment to remove DNA and acid phenol-chloroform extraction to isolate associated RNA followed by ethanol precipitation
For RIP Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
RNA coimmunoprecipitated with epitope tagged proteins were used for library preparation.

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1 /ura4DS/E  Pir2-GFP<<KanMX pir1D::KanMX

value: Yeast Whole Cells

tag: rip antibody

value: Anti-GFP Ab290

tag: growth

value: Growth in YEA 30°C, shifted to 18°C for 24 hrs


title: T3_6_7

description: Library name: T3_6_7


title: 11

description: Library name: 11

value: Lung

value: MA10 SARS-CoV-2 infection


title: A549 cells, 8 Gy C-ions, chronic hypoxia, 4 h, replicate 2

description: Library name: H-8Gy-4h-2

value: non small cell lung cancer

value: hypotriploid, p53 wild-type, KRAS mutated

value: hypoxia 48 h, 8 Gy C-ions, hypoxia 4 h


title: T3_6_3

description: Library name: T3_6_3

value: Gastrocnemius muscle


title: A549 cells, 0 Gy C-ions, chronic hypoxia, 4 h, replicate 2

description: Library name: H-0Gy-4h-2

value: hypoxia 48 h, 0 Gy C-ions, hypoxia 4 h


title: T3_2_3

description: Library name: T3_2_3


title: A549 cells, 8 Gy C-ions, transient hypoxia, 4 h, replicate 2

description: Library name: R-8Gy-4h-2

value: hypoxia 48 h, 8 Gy C-ions, normoxia 4 h


title: BxPC3, H3K27ac, no IFNγ, Replicate1, CUT&RUN

description:
Library name: BxPC3_H3K27ac_noIFNγ_Rep1
BxPC3_CUTRUN_H3K27ac_noIFNγ_3reps.bw
BxPC3_CUTRUN_H3K27ac_noIFNγ_3reps_peaks.narrowPeak

value: PDAC

value: H3K27ac (Active Motif 39135)

value: no IFNγ


title: scRNA-seq of C2

city: Shanghai

first: Lei

last: Shi

state: 请选择

address: 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiaotong university

description: Library name: C2

library_source: transcriptomic single cell

data_processing:
The raw reads were mapped to the rat reference genome (refdata-gex-Rnor6-2022/Rnor_6) using DNBC4Tools (v 2.1.2) with default parameters, the digital expression matrix was extracted from the“filtered_feature_bc_matrix” folder outputted by the DNBC4Tools count pipeline.
Assembly: MM39
Supplementary files format and content: matrix

source_name: Knee joint synovial tissue

extract_protocol:
Samples were minced with a sterile scalpel into 1 mm3 fragments, suspended in 5ml of digestion buffer consisting of 2 mg/mL Collagenase type I (Sigma，C0130)，2 mg/mL Collagenase type II (Sigma, C6885) and 200U/ml DNase I (Worthington, LS006344) in RPMI medium (Coring,10-040-CV), and incubated in 37℃ water bath with shaking for 60 min. The suspension was passed through a 100 μm filter (Falcon,3523260) and centrifugated (400g, 10 min, 4℃). Pelleted cells were resuspended in red blood cell lysis buffer (Solarbio,R1010), incubated for 2 min, passed through a 40 μm filter (Falcon,3523240), collected by centrifugation (400g, 10 min, 4℃) and resuspended in PBS (BI, 02-024-1ACS)  containing 0.04% BSA (Sigma,B2064). Cells were manually counted by Trypan blue (Thermo, T10282) and AO-PI (LUNA, D23001) after each centrifugation (400g, 10 min, 4℃) and resuspended.
Single-cell libraries were constructed with the DNBelab C Series Single-Cell Library Prep Kit (MGI, Cat. # 940-001818-00). Briefly, single-cell suspensions were subjected to droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Library quantification and quality control were performed using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Q33216) and an Agilent 4200 TapeStation (Agilent, G2991AA), respectively. Finally, DNA nanoballs (DNBs) were loaded into patterned nanoarrays and sequenced on a DNBSEQ platform. The sequencing run was configured with the following read lengths: 30 bp for read 1, inclusive of 10 bp cell barcode 1, 10 bp cell barcode 2, and 10 bp unique molecular identifier (UMI), 100 bp of transcript sequence for read 2, and 10 bp for sample index.

value: Knee joint synovial tissue

tag: group

value: control


title: scRNA-seq of C3

description: Library name: C3


title: Mx1_6_2

description: Library name: Mx1_6_2

value: WT


title: A549 cells, 0 Gy C-ions, transient hypxia, 4 h, replicate 2

description: Library name: R-0Gy-4h-2

value: hypoxia 48 h, 0 Gy C-ions, normoxia 4 h


title: Mx1_3_1

description: Library name: Mx1_3_1


title: Mx1_2_2

description: Library name: Mx1_2_2


title: A549 cells, 8 Gy C-ions, normoxia, 4 h, replicate 2

description: Library name: N-8Gy-4h-2

value: normoxia 48 h, 8 Gy C-ions, normoxia 4 h


title: A549 cells, 0 Gy C-ions, normoxia, 4 h, replicate 2

description: Library name: N-0Gy-4h-2

value: normoxia 48 h, 0 Gy C-ions, normoxia 4 h


title: Mx1-T3-3

description: Library name: Mx1-T3-3

data_processing:
Sequencing reads were aligned to the mouse reference genome using BWA (v0.7.12). Peaks were called using MACS (v3.0.0) with a p-value cutoff of 1e−7, without a control file, and with the –nomodel option. Peaks overlapping the ENCODE blacklist regions were removed. Differential accessibility analysis was performed using DESeq2, and pathway enrichment analysis was performed with GSEAPY (v0.10.3) in Python.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: HSC

extract_protocol:
HSCs were sorted using a BD Aria cell sorter. A total of 50,000 HSCs were resuspended in ice-cold cryopreservation solution (50% FBS, 40% growth media, 10% DMSO). Growth media contained StemSpan SFEM (StemCell Technologies) supplemented with 10% ES-Cult FBS (StemCell Technologies), 1% penicillin/streptomycin (Invitrogen), IL-3 (20 ng/ml), IL-6 (20 ng/ml), TPO (50 ng/ml), Flt3L (50 ng/ml), and SCF (100 ng/ml) (Peprotech). HSCs were frozen in a pre-chilled Mr. Frosty container, placed at −80 °C overnight to complete cryopreservation, and then submitted to Active Motif (Carlsbad, CA, USA) for ATAC-seq.
ATAC-seq libraries were prepared by Active Motif following their standard workflow and sequenced on an Illumina NovaSeq 6000 platform, generating paired-end 42 bp reads (2 × 42 bp).

value: HSC


title: Mx1-T3-2

description: Library name: Mx1-T3-2


title: A549 cells, 8 Gy C-ions, chronic hypoxia, 4 h, replicate 1

description: Library name: H-8Gy-4h-1


title: A549 cells, 8 Gy C-ions, transient hypoxia, 4 h, replicate 1

description: Library name: R-8Gy-4h-1


title: A549 cells, 0 Gy C-ions, chronic hypoxia, 4 h, replicate 1

description: Library name: H-0Gy-4h-1


title: Mx1-T3-1

description: Library name: Mx1-T3-1


title: A549 cells, 0 Gy C-ions, transient hypxia, 4 h, replicate 1

description: Library name: R-0Gy-4h-1


title: Mx1_1_2

description: Library name: Mx1_1_2


title: Mx1-Cre-3

description: Library name: Mx1-Cre-3


title: A549 cells, 8 Gy C-ions, normoxia, 4 h, replicate 1

description: Library name: N-8Gy-4h-1


title: Mx1-Cre-2

description: Library name: Mx1-Cre-2


title: patient infected with Recurrent right vestibular schwannoma

description: Library name: VS103

source_name: Right cerebellopontine angle

value: Right cerebellopontine angle

value: Recurrent right vestibular schwannoma


title: A549 cells, 0 Gy C-ions, normoxia, 4 h, replicate 1

description: Library name: N-0Gy-4h-1

value: non small cell lung cancer

value: hypotriploid, p53 wild-type, KRAS mutated


title: Gadd45a knockout mice, TET1 ChIP, Prefrontal cortex, biol rep2

city: CHENGDU

first: Tian

last: Tang

state: Sichuan

address: No. 20, Section 3,Renmin South Road

institute: Sichuan university

description:
Library name: Gadd45a knockout mice biol rep2, ChIP
KO_2_IP

data_processing:
The clean reads were employed for analyzing protein binding sites in Mus musculus by mapping them to the reference genome with STAR software (version 2.5.3a). Reads distribution analysis was conducted using RSeQC (version 2.6). Peak calling was performed with MACS2 software (Version 2.1.1), while peaks annotation and distribution analysis were carried out using bedtools (Version 2.25.0).
Assembly: GRCm38
Supplementary files format and content: bigwig  (WT_1_Input, WT_1_IP, WT_2_Input, WT_2_IP, KO_1_Input, KO_1_IP, KO_2_Input, KO_2_IP)

source_name: prefrontal cortex

extract_protocol:
Tissue fixation was carried out using 1% formaldehyde for 10 minutes at room temperature under a vacuum pump. The crosslinking reaction was terminated by adding 0.125 M glycine and allowing the mixture to settle for 5 minutes. Subsequently, the tissue was collected, frozen in liquid nitrogen, and processed using a tissue lyser. The resulting powder underwent treatment with cell lysis buffer, and the nucleus was isolated by centrifugation at 2000g for 5 minutes. The isolated nucleus was then subjected to nucleus lysis buffer treatment and sonication to fragment the chromatin DNA. Following sonication, 10% of the lysed chromatin was stored as “input,” while 45% was utilized in immunoprecipitation reactions with an anti-TET1 antibody (GeneTex, GTX124207) and labeled as “IP.” Additionally, 45% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control, labeled as “IgG.” Subsequently, DNA extraction from both input and IP samples was performed using the phenol-chloroform method.
High-throughput DNA sequencing libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme).

value: prefrontal cortex

value: Gadd45a knockout

tag: age

value: 12 weeks old

tag: Sex

value: male

tag: chip antibody

value: TET1(GeneTex, GTX124207)


title: Mx1-Cre-1

description: Library name: Mx1-Cre-1


title: A549 cells, 8 Gy X-rays, transient hypoxia, 4 h, replicate 4

description: Library name: R-8Gy-4h-4

treatment_protocol: After 48 h, cells were irradiated with 0 or 8 Gy of X-rays (200 kV, X-ray source RS225, Gulmay Medical, now: X-Strahl, Surrey, UK) at a dose rate of 1 Gy/min and room temperature, at DLR, Cologne. Incubation was continued after irradiation under normoxia (normoxia, N, or transient hypoxia /reoxygenation, R, samples) or hypoxia (chronic hypoxia, H). Cells were lysed for RNA extraction 4 h after irradiation. For more details: https://doi.org/10.3390/ijms25021010

value: hypoxia 48 h, 8 Gy X-rays, normoxia 4 h


title: A549 cells, 0 Gy X-rays, chronic hypoxia, 4 h, replicate 4

description: Library name: H-0Gy-4h-4

value: hypoxia 48 h, 0 Gy X-rays, hypoxia 4 h


title: A549 cells, 8 Gy X-rays, chronic hypoxia, 4 h, replicate 4

description: Library name: H-8Gy-4h-4

value: hypoxia 48 h, 8 Gy X-rays, hypoxia 4 h


title: Gadd45a knockout mice, TET1 ChIP, Prefrontal cortex, biol rep1

description:
Library name: Gadd45a knockout mice biol rep1, ChIP
KO_1_IP


title: Gadd45a knockout mice, Input, Prefrontal cortex, biol rep2

description:
Library name: Gadd45a knockout mice biol rep2, Input
KO_2_Input


title: A549 cells, 0 Gy X-rays, transient hypxia, 4 h, replicate 4

description: Library name: R-0Gy-4h-4

value: hypoxia 48 h, 0 Gy X-rays, normoxia 4 h


title: Gadd45a knockout mice, Input, Prefrontal cortex, biol rep1

description:
Library name: Gadd45a knockout mice biol rep1, Input
KO_1_Input


title: A549 cells, 8 Gy X-rays, normoxia, 4 h, replicate 4

description: Library name: N-8Gy-4h-4

value: normoxia 48 h, 8 Gy X-rays, normoxia 4 h


title: Wildtype mice, Input, Prefrontal cortex, biol rep2

description:
Library name: Wildtype mice biol rep2, Input
WT_2_Input

value: wildtype


title: Wildtype mice, TET1 ChIP, Prefrontal cortex, biol rep2

description:
Library name: Wildtype mice biol rep2, ChIP
WT_2_IP


title: A549 cells, 8 Gy X-rays, chronic hypoxia, 4 h, replicate 3

description: Library name: H-8Gy-4h-3


title: A549 cells, 0 Gy X-rays, normoxia, 4 h, replicate 4

description: Library name: N-0Gy-4h-4

value: normoxia 48 h, 0 Gy X-rays, normoxia 4 h


title: Wildtype mice, TET1 ChIP, Prefrontal cortex, biol rep1

description:
Library name: Wildtype mice biol rep1, ChIP
WT_1_IP


title: A549 cells, 0 Gy X-rays, chronic hypoxia, 4 h, replicate 3

description: Library name: H-0Gy-4h-3


title: A549 cells, 8 Gy X-rays, transient hypoxia, 4 h, replicate 3

description: Library name: R-8Gy-4h-3


title: KP cells, shDmap1, replicate 3

first: Kan

last: Huang

address: 130, Dongan Road

institute: Fudan University

description:
Library name: shDm_3
Column name in raw.TPM.csv: shDm_3

data_processing:
Raw read counts quality were checked using fastqc v0.12.1
Sequence reads were pseudo-aligned to GrCM38/mm10 using Kallisto v0.50.1 (parameters - default parameter, -t 10)
Read counts and TPM file were extracted using tximport v1.36.1 in R v4.5.1
Read count normalization and downstream analysis were performed using edgeR v4.6.3 and limma v3.64.1
Assembly: mm10
Supplementary files format and content: csv file includes raw TPM for each Sample

source_name: lung adenocarcinoma

growth_protocol: KP lung adenocarcinoma cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5% CO2 at 37℃

extract_protocol:
Cell total RNA was harvested using TRNzol Universal Reagent (TIANGEN #DP424). RNA purity and concentration were then examined using NanoDrop 2000; RNA integrity and quantity were measured using the Agilent 2100/2400 system
RNA library was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcripbed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: lung adenocarcinoma

value: KP

value: lung adenocarcinoma cells

value: Dmap1 knockdown


title: KP cells, shDmap1, replicate 2

description:
Library name: shDm_2
Column name in raw.TPM.csv: shDm_2


title: A549 cells, 8 Gy X-rays, normoxia, 4 h, replicate 3

description: Library name: N-8Gy-4h-3

value: non small cell lung cancer

value: hypotriploid, p53 wild-type, KRAS mutated


title: A549 cells, 0 Gy X-rays, transient hypxia, 4 h, replicate 3

description: Library name: R-0Gy-4h-3


title: KP cells, shDmap1, replicate 1

description:
Library name: shDm_1
Column name in raw.TPM.csv: shDm_1


title: KP cells, shLacZ, replicate 2

description:
Library name: shLacZ_2
Column name in raw.TPM.csv: shLacZ_2

value: WT

value: shLacZ


title: KP cells, shLacZ, replicate 3

description:
Library name: shLacZ_3
Column name in raw.TPM.csv: shLacZ_3


title: A549 cells, 0 Gy X-rays, chronic hypoxia, 4 h, replicate 2

description: Library name: H-0Gy-4h-2


title: A549 cells, 0 Gy X-rays, normoxia, 4 h, replicate 3

description: Library name: N-0Gy-4h-3


title: A549 cells, 8 Gy X-rays, chronic hypoxia, 4 h, replicate 2

description: Library name: H-8Gy-4h-2


title: KP cells, shLacZ, replicate 1

description:
Library name: shLacZ_1
Column name in raw.TPM.csv: shLacZ_1


title: A549 cells, 8 Gy X-rays, transient hypoxia, 4 h, replicate 2

description: Library name: R-8Gy-4h-2


title: D7_Naive_LN_3

city: Huntington

first: Mohit

last: Verma

state: WV

address: 1676 3rd Ave, 4th Floor, Suite #4109

department: Department of Biomedical Sciences

institute: Marshall University

description:
Library name: D7_NAiVE_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_NAiVE_LN_3

data_processing:
Illumina NovaSeq 6000
Sdequence reads were trimmed for adapter/ low quality reads using multiQC
Trimmed sequence reads were mapped on GRCm39 using HISAT2 tool
Reat count extraction and normalization were performed
cudiff was using to perform differential expression analysis
Assembly: GCRm39
Supplementary files format and content: Text files includes raw reads counts for each samples
Supplementary files format and content: Tab delimeted text file includes FPKM counts for each samples

source_name: C57BL/6 Mouse Lymph Node Tissue

growth_protocol: C57BL/6 mice (4–6 weeks old) were obtained from Jackson Laboratory and maintained under standard housing conditions in accordance with protocols approved by the Institutional Animal Care and Use Committee. SA-4-1BBL recombinant protein was produced and validated in-house, while the 3H3 agonistic antibody to CD137 was purchased from BioXcell.

extract_protocol:
Tissues stored in TRIzol reagent were homogenized using a handheld microtissue homogenizer. After phase separation with chloroform, the aqueous phase was mixed with ethanol and total RNA was extracted using the RNeasy Mini Kit (Qiagen) per manufacturer’s instructions. RNA quality and quantity were assessed using a Nanodrop One spectrophotometer and Agilent Bioanalyzer.
Batches of RNA were shipped to LC Sciences (Houston, TX) for poly(A) RNA sequencing. cDNA library was prepared followed by Illumina TrueSeq-standard sample preparation protocol.

treatment_protocol: Mice received subcutaneous injections of either SA-4-1BBL, 3H3 agonist antibody, or PBS (control). Treatments were administered once or twice, two weeks apart. Tissues were collected at 3 or 7 days after the final injection for RNA extraction.

value: Lymph Node

value: C57BL/6 WT

value: Saline


title: A549 cells, 0 Gy X-rays, normoxia, 4 h, replicate 2

description: Library name: N-0Gy-4h-2


title: A549 cells, 8 Gy X-rays, normoxia, 4 h, replicate 2

description: Library name: N-8Gy-4h-2


title: D7_Naive_LN_1

description:
Library name: D7_NAiVE_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_NAiVE_LN_1


title: A549 cells, 0 Gy X-rays, transient hypxia, 4 h, replicate 2

description: Library name: R-0Gy-4h-2


title: A549 cells, 8 Gy X-rays, chronic hypoxia, 4 h, replicate 1

description: Library name: H-8Gy-4h-1


title: D7_Naive_IS_3

description:
Library name: D7_NAiVE_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_NAiVE_IS_3

source_name: C57BL/6 Mouse Skin Tissue

value: Skin


title: D7_Naive_IS_2

description:
Library name: D7_NAiVE_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_NAiVE_IS_2


title: A549 cells, 0 Gy X-rays, chronic hypoxia, 4 h, replicate 1

description: Library name: H-0Gy-4h-1

value: hypoxia 48 h, 0 Gy X-rays, hypoxia 4 h


title: D7_SA-4-1BBL_LN_3

description:
Library name: D7_41BBL_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_41BBL_LN_3


title: A549 cells, 0 Gy X-rays, transient hypxia, 4 h, replicate 1

description: Library name: R-0Gy-4h-1

value: hypoxia 48 h, 0 Gy X-rays, normoxia 4 h


title: D7_Naive_IS_1

description:
Library name: D7_NAiVE_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_NAiVE_IS_1


title: D7_SA-4-1BBL_IS_3

description:
Library name: D7_41BBL_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_41BBL_IS_3


title: A549 cells, 0 Gy X-rays, normoxia, 4 h, replicate 1

description: Library name: N-0Gy-4h-1


title: D7_SA-4-1BBL_IS_2

description:
Library name: D7_41BBL_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_41BBL_IS_2


title: P5624, high resolution spatial transcriptomics

city: St Louis

first: Thomas

middle: F

last: Barrett

state: MO

address: 660 Euclid Ave

department: Otolaryngology

institute: Washington University

description:
Library name: P5624_hd
FFPE section for high resolution spatial transcriptomic sequencing

data_processing:
Raw sequencing data were prepared with 10X genomics Space Ranger pipeline to generate FastQ files. 16 micrometer bins were used for downsream analyses.
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files
After sequencing, the resulting FASTQ files were aligned to grch38 reference genome
Assembly: grch38
Supplementary files format and content: tissue_positions_list.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Library strategy: spatial transcriptomics

source_name: Head and neck mucosal squamous cell carcinoma

extract_protocol:
Clinically obtained FFPE tissue samples were assessed for tumor purity and DV200 value and cut to 5 micron sections.
Spatial transcriptome sequencing libraries were prepared according to the 10X Genomics CytAssist Probe Release & Capture protocol.

tag: hpv-related

value: No


title: P5684, high resolution spatial transcriptomics

description:
Library name: P5684_hd
FFPE section for high resolution spatial transcriptomic sequencing

tag: tissue

value: Head and neck mucosal squamous cell carcinoma


city: Frankfurt am Main

first: Josep

last: Biayna Rodriguez

state: Hessen

address: Theodor-Stern-Kai 7

institute: Institute of Cardiovascular Regeneration

description:
Library name: Lib_CYTOB_4h5
RNA-seq of GM25256 iPSC cytoplasmic fraction 4.5h Sample B

data_processing:
VAST-TOOLS
Raw RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 2.5.1 (Tapial et al., (2017)), which is available on github (https://github.com/vastgroup/vast-tools).
Assembly: Human (GRCm38)
Supplementary files format and content: iPS_ActD_INCLUSION_LEVELS_FULL-hg38-16 are primary vast-tools output files for human IPS cells samples in tab-delimited format

molecule: cytoplasmic RNA

growth_protocol: hiPSCs WTC-11 (Coriell Institute) were cultured on Vitronectin (Thermo Fisher Scientific) coated plates or 18 mm round glass coverslips (for smRNA FISH and IF) in StemFlex basal medium (Thermo Fisher Scientific) with StemFlex supplement (Thermo Fisher Scientific), RevitaCell supplement with Rock inhibitor (Thermo Fisher Scientific) and 2.5% penicillin-streptomycin

extract_protocol:
hiPSCs were rinsed twice with ice-cold PBS, scraped, and centrifuged at 500 g for 5’. Cell pellets were lysed with 175 μl/106 cells of ice-cold lysis buffer (50 mM Tris-HCl pH 8.0, 140 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1:200 dilution of 20 U/μL SUPERase RNase inhibitor), and incubated on ice for 10’. The lysate was centrifuged at 300 g for 3’ at 4°C to pellet the nuclei and the supernatant was collected as the cytoplasmic fraction. Finally, the nuclear and the cytoplasmic fractions were processed for RNA extraction as described below. The efficiency of RNA fractionation was assessed by quantitative polymerase chain reaction (qPCR) using GAPDH as a marker for the cytoplasm fraction, 45s rRNA for the nuclear fraction
The quantity, quality and integrity of the RNA samples were assessed using Bioanalyzer 5400 (Agilent Technologies, USA). After isolation, RNA was sent to Novogene for sequencing. Briefly, poly(A) RNA was enrichmed with oligo d(T) magnetic beads. Subsequently, RNA was randomly fragmented, and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. After purification, the resulting products followed end-repair, A-tailing and adapter ligation steps. Fragments of the appropriate size were enriched by PCR, where indexed P5 and P7 primers were introduced, and final products were purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 5400 for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000/Novaseq X Plus platforms. The qualified libraries were sequenced Next Generation Sequencing (NGS) based on Illumina's Sequencing Technology by Synthesis (SBS)- detection by fluorescence of the nucleotide added during the synthesis of the complementary chain - and in a parallelized and massive way. The Novaseq6000/Novaseq X Plus sequencing systems were used to sequence the libraries. The strategy was paired-end 150bp.

treatment_protocol: Actinomycin D (ActD, Sigma-Aldrich) was used at a final concentration of 5 μg/mL in complete growth media. Cell pellets and coverslips were harvested at 0 h, 0.5 h, 2 h and 4.5 h after adding ActD

tag: biomaterial provider

value: hiPSCs

value: ActD 4.5h


description:
Library name: Lib_CYTOA_4h5
RNA-seq of GM25256 iPSC cytoplasmic fraction 4.5h Sample A


title: D7_SA-4-1BBL_IS_1

description:
Library name: D7_41BBL_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_41BBL_IS_1


title: D7_3H3_LN_3

description:
Library name: D7_3H3_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_3H3_LN_3

value: anti-4-1BB Ab (3H3)


title: D7_3H3_LN_2

description:
Library name: D7_3H3_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_3H3_LN_2


description:
Library name: Lib_CYTOB_2h
RNA-seq of GM25256 iPSC cytoplasmic fraction 2h Sample B

value: ActD 2h


title: D7_3H3_LN_1

description:
Library name: D7_3H3_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_3H3_LN_1


description:
Library name: Lib_CYTOB_30
RNA-seq of GM25256 iPSC cytoplasmic fraction 30 min Sample B

value: ActD 30 min


title: D7_3H3_IS_1

description:
Library name: D7_3H3_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_3H3_IS_1


description:
Library name: Lib_CYTOA_30
RNA-seq of GM25256 iPSC cytoplasmic fraction 30 min Sample A


description:
Library name: Lib_CYTOB_UT
RNA-seq of GM25256 iPSC cytoplasmic fraction untreated Sample B

value: untreated


title: D7_2X_SA-4-1BBL_LN_3

description:
Library name: D7_2X_41BBL_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_LN_3


description:
Library name: Lib_NUCA_4h5
RNA-seq of GM25256 iPSC nuclear fraction 4.5h Sample A

molecule: nuclear RNA


title: D7_2X_SA-4-1BBL_LN_2

description:
Library name: D7_2X_41BBL_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_LN_2


description:
Library name: Lib_NUCB_2h
RNA-seq of GM25256 iPSC nuclear fraction 2h Sample B


title: D7_2X_SA-4-1BBL_LN_1

description:
Library name: D7_2X_41BBL_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_LN_1


description:
Library name: Lib_NUCB_30
RNA-seq of GM25256 iPSC nuclear fraction 30 min Sample B


title: D7_2X_SA-4-1BBL_IS_2

description:
Library name: D7_2X_41BBL_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_IS_2


description:
Library name: Lib_NUCB_UT
RNA-seq of GM25256 iPSC nuclear fraction untreated Sample B


title: D7_2X_SA-4-1BBL_IS_1

description:
Library name: D7_2X_41BBL_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_IS_1


title: D7_2X_3H3_LN_3

description:
Library name: D7_2X_3H3_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_LN_3


title: Placenta sample X31303.520

city: New York

first: Corina

last: Lesseur

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine

description:
Library name: X31303.520
Column name in counts_nhbcs.csv.gz : X31303.520

data_processing:
Reads aligned with Splice Transcripts Alignment to a Reference (STAR) with GENCODE v47 (GRCh38) and quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv gzipped file with raw counts for each sample

source_name: Placenta villis fetal side

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany, cat. No. 74106), and the Norgen Tissue RNA Purification Kit (Norgen Biotek, Thorold, ON, Canada, Cat. No. 25700), following the manufacturer’s protocols.
Ribosomal RNA depletion was used to prepare RNA-sequencing (RNA-seq) libraries, transcriptome-wide RNA-sequencing was performed with paired-end 75 bp reads on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) .

value: Placenta villis fetal side

tag: maternal smoking

tag: baby race

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

value: SGA

tag: delivery method

value: Vaginal delivery

tag: infant sex

value: Male

tag: maternal age

tag: rna integrity_number


title: Placenta sample X31303.519

description:
Library name: X31303.519
Column name in counts_nhbcs.csv.gz : X31303.519

value: AGA

value: Female


title: D7_2X_3H3_LN_1

description:
Library name: D7_2X_3H3_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_LN_1

value: Lymph Node

tag: genotype

value: C57BL/6 WT

tag: treatment


title: Placenta sample X31303.518

description:
Library name: X31303.518
Column name in counts_nhbcs.csv.gz : X31303.518

value: Yes

value: C-section


title: D7_2X_3H3_IS_4

description:
Library name: D7_2X_3H3_IS_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_IS_4

value: Skin


title: A549 cells, 8 Gy X-rays, transient hypoxia, 4 h, replicate 1

description: Library name: R-8Gy-4h-1

data_processing:
trimming by GENEWIZ
mapping by GENEWIZ
differential gene expression by GENEWIZ
DESeq2 package in R
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: tab-delimited text files include GeneID,  Chr, Start, End, Strand, Length for each Sample

tag: cell line

tag: cell type

value: non small cell lung cancer

value: hypotriploid, p53 wild-type, KRAS mutated

value: hypoxia 48 h, 8 Gy X-rays, normoxia 4 h

tag: batch


title: A549 cells, 8 Gy X-rays, normoxia, 4 h, replicate 1

description: Library name: N-8Gy-4h-1

value: normoxia 48 h, 8 Gy X-rays, normoxia 4 h


title: Placenta sample X31303.517

description:
Library name: X31303.517
Column name in counts_nhbcs.csv.gz : X31303.517

value: No


title: D7_2X_3H3_IS_3

description:
Library name: D7_2X_3H3_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_IS_3

value: anti-4-1BB Ab (3H3)


title: D7_3H3_IS_3

description:
Library name: D7_3H3_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_3H3_IS_3


title: D7_2X_3H3_IS_2

description:
Library name: D7_2X_3H3_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_IS_2


title: D7_3H3_IS_2

description:
Library name: D7_3H3_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_3H3_IS_2


title: Placenta sample X31303.514

description:
Library name: X31303.514
Column name in counts_nhbcs.csv.gz : X31303.514

value: Placenta villis fetal side

value: White


title: D7_2X_3H3_IS_1

description:
Library name: D7_2X_3H3_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_IS_1


title: Placenta sample X31303.513

description:
Library name: X31303.513
Column name in counts_nhbcs.csv.gz : X31303.513

value: SGA

value: Vaginal delivery


title: D7_2X_SA-4-1BBL_LN_4

description:
Library name: D7_2X_41BBL_LN_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_LN_4


title: D3_SA-4-1BBL_LN_3

description:
Library name: D3_41BBL_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_41BBL_LN_3


title: Placenta sample X31303.510

description:
Library name: X31303.510
Column name in counts_nhbcs.csv.gz : X31303.510

value: LGA

value: Male


title: Placenta sample X31303.508

description:
Library name: X31303.508
Column name in counts_nhbcs.csv.gz : X31303.508

value: AGA

value: Female


title: D3_SA-4-1BBL_LN_2

description:
Library name: D3_41BBL_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_41BBL_LN_2

value: Lymph Node

value: C57BL/6 WT


title: D7_2X_SA-4-1BBL_IS_3

description:
Library name: D7_2X_41BBL_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_IS_3

value: Skin


title: D3_SA-4-1BBL_LN_1

description:
Library name: D3_41BBL_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_41BBL_LN_1


title: Placenta sample X31303.507

description:
Library name: X31303.507
Column name in counts_nhbcs.csv.gz : X31303.507

value: C-section


title: D3_SA-4-1BBL_IS_3

description:
Library name: D3_41BBL_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_41BBL_IS_3


title: D7_2X_3H3_LN_4

description:
Library name: D7_2X_3H3_LN_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_LN_4


title: Placenta sample X31303.505

description:
Library name: X31303.505
Column name in counts_nhbcs.csv.gz : X31303.505


title: D3_SA-4-1BBL_IS_1

description:
Library name: D3_41BBL_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_41BBL_IS_1


title: D3_3H3_LN_3

description:
Library name: D3_3H3_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_3H3_LN_3


title: Placenta sample X31303.500

description:
Library name: X31303.500
Column name in counts_nhbcs.csv.gz : X31303.500


title: Placenta sample X31303.501

description:
Library name: X31303.501
Column name in counts_nhbcs.csv.gz : X31303.501

value: Yes


title: D3_3H3_LN_2

description:
Library name: D3_3H3_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_3H3_LN_2


title: D7_2X_3H3_LN_2

description:
Library name: D7_2X_3H3_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_3H3_LN_2


title: Placenta sample X31303.499

description:
Library name: X31303.499
Column name in counts_nhbcs.csv.gz : X31303.499


title: D3_3H3_LN_1

description:
Library name: D3_3H3_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_3H3_LN_1


title: Placenta sample X31303.498

description:
Library name: X31303.498
Column name in counts_nhbcs.csv.gz : X31303.498


title: Placenta sample X31303.497

description:
Library name: X31303.497
Column name in counts_nhbcs.csv.gz : X31303.497


title: D3_3H3_IS_3

description:
Library name: D3_3H3_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_3H3_IS_3


title: D3_3H3_IS_2

description:
Library name: D3_3H3_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_3H3_IS_2


title: Placenta sample X31303.491

description:
Library name: X31303.491
Column name in counts_nhbcs.csv.gz : X31303.491


title: D3_3H3_IS_1

description:
Library name: D3_3H3_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_3H3_IS_1


title: Placenta sample X31303.487

description:
Library name: X31303.487
Column name in counts_nhbcs.csv.gz : X31303.487


title: D3_2X_SA-4-1BBL_LN_4

description:
Library name: D3_2X_41BBL_LN_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_LN_4


title: Placenta sample X31303.484

description:
Library name: X31303.484
Column name in counts_nhbcs.csv.gz : X31303.484


title: D3_2X_SA-4-1BBL_LN_3

description:
Library name: D3_2X_41BBL_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_LN_3


title: Placenta sample X31303.482

description:
Library name: X31303.482
Column name in counts_nhbcs.csv.gz : X31303.482


title: D3_2X_SA-4-1BBL_LN_2

description:
Library name: D3_2X_41BBL_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_LN_2


title: Placenta sample X31303.481

description:
Library name: X31303.481
Column name in counts_nhbcs.csv.gz : X31303.481


title: Placenta sample X31303.516

description:
Library name: X31303.516
Column name in counts_nhbcs.csv.gz : X31303.516


title: D3_2X_SA-4-1BBL_LN_1

description:
Library name: D3_2X_41BBL_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_LN_1


title: Placenta sample X31303.478

description:
Library name: X31303.478
Column name in counts_nhbcs.csv.gz : X31303.478


title: Placenta sample X31303.476

description:
Library name: X31303.476
Column name in counts_nhbcs.csv.gz : X31303.476


title: D3_2X_SA-4-1BBL_IS_4

description:
Library name: D3_2X_41BBL_IS_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_IS_4


title: D3_2X_SA-4-1BBL_IS_3

description:
Library name: D3_2X_41BBL_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_IS_3


title: Placenta sample X31303.474

description:
Library name: X31303.474
Column name in counts_nhbcs.csv.gz : X31303.474


title: D3_2X_SA-4-1BBL_IS_2

description:
Library name: D3_2X_41BBL_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_IS_2


title: Placenta sample X31303.475

description:
Library name: X31303.475
Column name in counts_nhbcs.csv.gz : X31303.475


title: D3_2X_SA-4-1BBL_IS_1

description:
Library name: D3_2X_41BBL_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_41BBL_IS_1


title: Placenta sample X31303.473

description:
Library name: X31303.473
Column name in counts_nhbcs.csv.gz : X31303.473


title: Placenta sample X31303.471

description:
Library name: X31303.471
Column name in counts_nhbcs.csv.gz : X31303.471


title: D3_2X_3H3_LN_4

description:
Library name: D3_2X_3H3_LN_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_LN_4


title: Placenta sample X31303.467

description:
Library name: X31303.467
Column name in counts_nhbcs.csv.gz : X31303.467


title: Placenta sample X31303.465

description:
Library name: X31303.465
Column name in counts_nhbcs.csv.gz : X31303.465


title: D3_2X_3H3_LN_2

description:
Library name: D3_2X_3H3_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_LN_2


title: Placenta sample X31303.506

description:
Library name: X31303.506
Column name in counts_nhbcs.csv.gz : X31303.506


title: D3_2X_3H3_LN_3

description:
Library name: D3_2X_3H3_LN_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_LN_3


title: Placenta sample X31303.464

description:
Library name: X31303.464
Column name in counts_nhbcs.csv.gz : X31303.464


title: D3_2X_3H3_LN_1

description:
Library name: D3_2X_3H3_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_LN_1


title: D3_SA-4-1BBL_IS_2

description:
Library name: D3_41BBL_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_41BBL_IS_2


title: D3_2X_3H3_IS_4

description:
Library name: D3_2X_3H3_IS_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_IS_4


title: Placenta sample X31303.462

description:
Library name: X31303.462
Column name in counts_nhbcs.csv.gz : X31303.462


title: Wildtype mice, Input, Prefrontal cortex, biol rep1

description:
Library name: Wildtype mice biol rep1, Input
WT_1_Input

value: prefrontal cortex

value: wildtype

tag: age

value: 12 weeks old

tag: Sex

value: male

tag: chip antibody


title: D3_2X_3H3_IS_3

description:
Library name: D3_2X_3H3_IS_3_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_IS_3

tag: tissue

value: anti-4-1BB Ab (3H3)


title: Placenta sample X31303.461

description:
Library name: X31303.461
Column name in counts_nhbcs.csv.gz : X31303.461

value: Placenta villis fetal side

tag: maternal smoking

value: No

tag: baby race

value: White


title: D3_2X_3H3_IS_2

description:
Library name: D3_2X_3H3_IS_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_IS_2


title: Placenta sample X31303.460

description:
Library name: X31303.460
Column name in counts_nhbcs.csv.gz : X31303.460

tag: gestational age

tag: birthweight percentile

value: Vaginal delivery


title: Placenta sample X31303.459

description:
Library name: X31303.459
Column name in counts_nhbcs.csv.gz : X31303.459

tag: birthweight fenton_group

tag: delivery method


title: D3_2X_3H3_IS_1

description:
Library name: D3_2X_3H3_IS_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D3_2X_3H3_IS_1


title: POND-GFP_mESC_rep-2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

source_name: V6.5 mouse embryonic stem cells

growth_protocol: HEK293T, Huh-7, and A549 cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml). V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor. H1 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2.

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

value: V6.5 mouse embryonic stem cells


title: Placenta sample X31303.458

description:
Library name: X31303.458
Column name in counts_nhbcs.csv.gz : X31303.458

value: AGA

tag: infant sex

tag: maternal age


title: POND-GFP_mESC_rep-1

tag: genotype


title: Placenta sample X31303.456

description:
Library name: X31303.456
Column name in counts_nhbcs.csv.gz : X31303.456

value: Female

tag: rna integrity_number


title: D7_Naive_LN_2

description:
Library name: D7_NAiVE_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_NAiVE_LN_2

value: Lymph Node

tag: treatment

value: Saline


title: POND-mLin28A_mESC_rep-2

tag: cell line


title: POND-mLin28A_mESC_rep-1


title: Placenta sample X31303.455

description:
Library name: X31303.455
Column name in counts_nhbcs.csv.gz : X31303.455

value: SGA

value: Male


title: Placenta sample X31303.454

description:
Library name: X31303.454
Column name in counts_nhbcs.csv.gz : X31303.454

value: C-section


title: EAP, prostate, LIT927, 14d, rep4

city: Hefei

first: Yi

last: Zhang

address: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, People’s Republic of China.

institute: the First Affiliated Hospital of Anhui Medical University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Prostate

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Prostate


title: Placenta sample X31303.452

description:
Library name: X31303.452
Column name in counts_nhbcs.csv.gz : X31303.452


title: EAP, prostate, LIT927, 14d, rep3


title: EAP, prostate, LIT927, 14d, rep2


title: Placenta sample X31303.449

description:
Library name: X31303.449
Column name in counts_nhbcs.csv.gz : X31303.449


title: Placenta sample X31303.450

description:
Library name: X31303.450
Column name in counts_nhbcs.csv.gz : X31303.450


title: EAP, prostate, LIT927, 14d, rep1


title: Placenta sample X31303.448

description:
Library name: X31303.448
Column name in counts_nhbcs.csv.gz : X31303.448


title: D7_SA-4-1BBL_LN_2

description:
Library name: D7_41BBL_LN_2_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_41BBL_LN_2

value: C57BL/6 WT


title: BxPC3, IgG, no IFNγ, Replicate3, CUT&RUN

description:
Library name: BxPC3_IgG_noIFNγ_Rep1_Rep3
BxPC3_CUTRUN_IgG_noIFNγ_3reps.bw
BxPC3_CUTRUN_IgG_noIFNγ_3reps_peaks.narrowPeak

data_processing:
The fastq files were trimmed and quality-controlled with Trim Galore (version 0.6.10 with the default options in a pair-end mode. The resulting reads were aligned to hg38 using bowtie2 (version 2.4.4) with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 (Langmead & Salzberg, 2012). The alignment files were sorted by coordinate, then unpaired reads were removed, and indexed with samtools (version 1.14) (Danecek et al., 2021).
For reads visualization on genome tracks, the processed bam files were merged with samtools and visualized via the Integrative Genomics Viewer (version 2.16.1) (Robinson et al., 2011).
For peak identification, peaks and summits were called with MACS2 (version 2.2.7.1) using all three individual bam files for all replicates targeting the protein of interest (-t) and all three targeting IgG as controls (-c) with options --format BAMPE --gsize 2.7e9 --keep-dup all (Zhang et al., 2008).sortRegions descend (Ramirez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

extract_protocol:
We performed CUT&RUN in BxPC-3 cells using CUTANA ChIC/CUT&RUN Kit (EpiCypher) following the manufacturer’s protocol (Skene & Henikoff, 2017). In brief, 500,000 cells were trypsinized, washed, and bound to activated Concanavalin A-conjugated paramagnetic beads (EpiCypher). The cell-bead conjugates were then resuspended in recommended buffer with 0.5 μg antibody targeting the protein of interest: Anti-H3K27ac (Active Motif 39135), Anti-H3K4me3 (EpiCypher 13-0041k) as positive control, and Anti-IgG (EpiCypher 13-0042k) as negative control. The suspensions were incubated overnight at 4 °C with gentle shaking. Then, the cell-bead conjugates were washed twice with the kit’s permeabilization buffer, and incubated with pAG-MNase (Epicypher 15-1016) for 10 min at room temperature. Subsequently, the unbound pAG-MNase was washed away, and the MNase was activated by adding CaCl2 to a final concentration of 2 mM. The reaction was stopped after the pAG-MNase was allowed to digest and release the antibody-bound chromatin for 2 hours at 4 °C. Finally, the released DNA was purified with the spin columns provided by the kit (EpiCypher).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). The libraries were sequenced on a IlluminaNovaSeq 6000  SP using 2x50 bp reads.

tag: cell type

value: PDAC

tag: cut&run antibody

value: IgG (EpiCypher 13-0042k)

value: no IFNγ


title: D7_SA-4-1BBL_LN_1

description:
Library name: D7_41BBL_LN_1_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_41BBL_LN_1


title: Placenta sample X31303.447

description:
Library name: X31303.447
Column name in counts_nhbcs.csv.gz : X31303.447

value: Placenta villis fetal side


title: EAP, prostate, methyl-β-cyclodextrin, 14d, rep4


title: Placenta sample X31303.444

description:
Library name: X31303.444
Column name in counts_nhbcs.csv.gz : X31303.444

value: Yes


title: EAP, prostate, methyl-β-cyclodextrin, 14d, rep1


title: EAP, prostate, methyl-β-cyclodextrin, 14d, rep3


title: Placenta sample X31303.443

description:
Library name: X31303.443
Column name in counts_nhbcs.csv.gz : X31303.443

value: No

value: White


description:
Library name: Lib_CYTOA_2h
RNA-seq of GM25256 iPSC cytoplasmic fraction 2h Sample A

tag: biomaterial provider

value: hiPSCs

value: WT

value: ActD 2h

tag: batch


title: si-IFITM3-RH

city: Fuzhou

first: Yanlong

last: Gu

address: 15 Xiadian Road, Cangshan District, Fujian Agriculture and Forestry University

description: Library name: sample 8

data_processing:
Raw sequencing reads were first quality controlled using FastQC (v0.11.9). Adapter sequences and low-quality reads (Phred quality score < 20) were trimmed using Trimmomatic (v0.39). Clean reads were aligned to the Chlorocebus sabaeus reference genome (ChlSab1.1, GCF_000409795.2) using HISAT2 (v2.2.1) with default parameters. Gene-level read counts were quantified using featureCounts (v2.0.1) based on the Ensembl gene annotation.
Assembly: GCF_000409795.2
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all 8 samples, generated by featureCounts (v2.0.1) based on Ensembl gene annotation.

organism: Chlorocebus sabaeus

source_name: Kidney

extract_protocol:
cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. illumina TruSeq RNA Sample Prep Kit il
mRNA was enriched from total RNA using oligo(dT) magnetic beads. The enriched mRNA was fragmented into 200-300 bp fragments using fragmentation buffer. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The double-stranded cDNA was subjected to end repair, A-tailing, and ligation with Illumina sequencing adapters. The ligated products were purified and amplified by PCR for 12-15 cycles. The final libraries were quantified using Qubit 3.0 Fluorometer and validated for size distribution using Agilent 2100 Bioanalyzer.

tag: tissue

value: Kidney

value: Vero

value: Epithelial cell

tag: transfection

value: IFITM3 overexpression vector

tag: infection

value: Toxoplasma gondii


title: Placenta sample X31303.441

description:
Library name: X31303.441
Column name in counts_nhbcs.csv.gz : X31303.441

tag: maternal smoking

tag: baby race

tag: gestational age

value: AGA

value: C-section

value: Female


title: Placenta sample X31303.439

description:
Library name: X31303.439
Column name in counts_nhbcs.csv.gz : X31303.439

tag: birthweight percentile

tag: birthweight fenton_group

tag: delivery method


title: si-IFITM3

institute: Fujian Agriculture and Forestry University

description: Library name: sample 7

value: uninfected


title: si-IFITM2-RH

description: Library name: sample 6

value: IFITM2 overexpression vector


title: Placenta sample X31303.438

description:
Library name: X31303.438
Column name in counts_nhbcs.csv.gz : X31303.438

value: Placenta villis fetal side

value: Vaginal delivery

tag: infant sex

tag: maternal age


title: si-IFITM2

description: Library name: sample 5


title: Placenta sample X31303.433

description:
Library name: X31303.433
Column name in counts_nhbcs.csv.gz : X31303.433

value: No

value: Male

tag: rna integrity_number


title: pVAX1-IFITM3-RH

description: Library name: sample 4

tag: cell line

value: empty vector control


title: Placenta sample X31303.435

description:
Library name: X31303.435
Column name in counts_nhbcs.csv.gz : X31303.435

value: White


description:
Library name: Lib_NUCB_4h5
RNA-seq of GM25256 iPSC nuclear fraction 4.5h Sample B

tag: cell type

value: hiPSCs

tag: genotype

value: WT

tag: treatment

value: ActD 4.5h


description:
Library name: Lib_CYTOA_UT
RNA-seq of GM25256 iPSC cytoplasmic fraction untreated Sample A

tag: biomaterial provider

value: untreated

tag: batch


title: pVAX1-IFITM3

description: Library name: sample 3

tag: tissue

value: Kidney

value: Vero

value: Epithelial cell

tag: transfection


title: Placenta sample X31303.430

description:
Library name: X31303.430
Column name in counts_nhbcs.csv.gz : X31303.430

tag: maternal smoking

value: AGA

value: C-section


title: Placenta sample X31303.429

description:
Library name: X31303.429
Column name in counts_nhbcs.csv.gz : X31303.429

tag: baby race

value: Female


title: pVAX1-IFITM2-RH

description: Library name: sample 2

tag: infection

value: Toxoplasma gondii


title: pVAX1-IFITM2

description: Library name: sample 1

value: uninfected


title: Placenta sample X31303.428

description:
Library name: X31303.428
Column name in counts_nhbcs.csv.gz : X31303.428

value: Placenta villis fetal side

tag: gestational age

tag: birthweight percentile

value: Vaginal delivery


title: FMR1-RIPseq_Mock-rep2

description:
Library name: Sample124
fig7_192

source_name: HEK293T cell line

value: HEK293T cell line


title: Placenta sample X31303.427

description:
Library name: X31303.427
Column name in counts_nhbcs.csv.gz : X31303.427

value: No

tag: birthweight fenton_group

tag: delivery method


description:
Library name: Lib_NUCA_2h
RNA-seq of GM25256 iPSC nuclear fraction 2h Sample A

value: ActD 2h


title: D7_2X_SA-4-1BBL_IS_4

description:
Library name: D7_2X_41BBL_IS_4_Clean_Data1.fq.gz
column name in mouse_gene_fpkm.txt D7_2X_41BBL_IS_4

value: Skin

value: C57BL/6 WT


title: Placenta sample X31303.425

description:
Library name: X31303.425
Column name in counts_nhbcs.csv.gz : X31303.425

value: White

tag: infant sex

value: Male

tag: maternal age


title: FMR1-RIPseq_E280K-rep2

description:
Library name: Sample122
fig7_190

tag: cell line


title: FMR1-RIPseq_E280K-rep1

description:
Library name: Sample121
fig7_189


title: FMR1-RIPseq_Mock-rep1

description:
Library name: Sample123
fig7_191

value: WT


title: Placenta sample X31303.423

description:
Library name: X31303.423
Column name in counts_nhbcs.csv.gz : X31303.423

tag: rna integrity_number


title: FMR1-RIPseq_G266E-rep2

description:
Library name: Sample120
fig7_188

tag: genotype


title: Placenta sample X31303.417

description:
Library name: X31303.417
Column name in counts_nhbcs.csv.gz : X31303.417

value: Yes


title: FMR1-RIPseq_G266E-rep1

description:
Library name: Sample119
fig7_187

tag: treatment


title: FMR1-RIPseq_WT-rep2

description:
Library name: Sample118
fig7_186


title: Placenta sample X31303.414

description:
Library name: X31303.414
Column name in counts_nhbcs.csv.gz : X31303.414


title: PABPC1-POND-Huh-7-Separate-D4_rep2

description:
Library name: Sample116
fig5_42

source_name: Huh-7 cell line

value: Huh-7 cell line


title: Placenta sample X31303.415

description:
Library name: X31303.415
Column name in counts_nhbcs.csv.gz : X31303.415

value: AGA


title: PABPC1-POND-Huh-7-Separate-D4_rep1

description:
Library name: Sample115
fig5_41


title: Placenta sample X31303.410

description:
Library name: X31303.410
Column name in counts_nhbcs.csv.gz : X31303.410


title: Placenta sample X31303.412

description:
Library name: X31303.412
Column name in counts_nhbcs.csv.gz : X31303.412

value: C-section


title: PABPC1-POND-Huh-7-Separate-D2_rep2

description:
Library name: Sample114
fig5_40


title: PABPC1-POND-Huh-7-Separate-D2_rep1

description:
Library name: Sample113
fig5_39


title: Placenta sample X31303.408

description:
Library name: X31303.408
Column name in counts_nhbcs.csv.gz : X31303.408

value: LGA

value: Female


title: Placenta sample X31303.407

description:
Library name: X31303.407
Column name in counts_nhbcs.csv.gz : X31303.407


title: PABPC1-POND-Huh-7-Separate-D1_rep1

description:
Library name: Sample111
fig5_37


title: Placenta sample X31303.406

description:
Library name: X31303.406
Column name in counts_nhbcs.csv.gz : X31303.406


title: PABPC1-POND-Huh-7-Coculture-D4_rep2

description:
Library name: Sample110
fig5_36


title: Placenta sample X31303.405

description:
Library name: X31303.405
Column name in counts_nhbcs.csv.gz : X31303.405


title: Placenta sample X31303.403

description:
Library name: X31303.403
Column name in counts_nhbcs.csv.gz : X31303.403


title: Placenta sample X31303.402

description:
Library name: X31303.402
Column name in counts_nhbcs.csv.gz : X31303.402

value: SGA


title: PABPC1-POND-Huh-7-Coculture-D2_rep1

description:
Library name: Sample107
fig5_33


title: Placenta sample X31303.397

description:
Library name: X31303.397
Column name in counts_nhbcs.csv.gz : X31303.397

value: Placenta villis fetal side


title: Placenta sample X31303.395

description:
Library name: X31303.395
Column name in counts_nhbcs.csv.gz : X31303.395

value: Vaginal delivery


title: PABPC1-POND-Huh-7-Coculture-D1_rep2

description:
Library name: Sample106
fig5_32


title: PABPC1-POND-Huh-7-Coculture-D1_rep1

description:
Library name: Sample105
fig5_31


title: Placenta sample X31303.394

description:
Library name: X31303.394
Column name in counts_nhbcs.csv.gz : X31303.394


title: PABPC1-POND-Huh-7-D0_rep2

description:
Library name: Sample104
fig5_30


title: Placenta sample X31303.390

description:
Library name: X31303.390
Column name in counts_nhbcs.csv.gz : X31303.390


title: PABPC1-POND-Huh-7-D0_rep1

description:
Library name: Sample103
fig5_29


title: Placenta sample X31303.384

description:
Library name: X31303.384
Column name in counts_nhbcs.csv.gz : X31303.384


title: PABPC1-POND-A549-StableCell_rep2

description:
Library name: Sample102
fig5_16

source_name: A549 cell line

value: A549 cell line

value: 0.2 μM doxycycline


title: Placenta sample X31303.385

description:
Library name: X31303.385
Column name in counts_nhbcs.csv.gz : X31303.385

value: No


title: Placenta sample X31303.383

description:
Library name: X31303.383
Column name in counts_nhbcs.csv.gz : X31303.383


title: Placenta sample X31303.382

description:
Library name: X31303.382
Column name in counts_nhbcs.csv.gz : X31303.382


title: PABPC1-POND-Huh7-StableCell_rep1

description:
Library name: Sample99
fig5_13


title: PABPC1-POND-A549-Bezonase_rep2

description:
Library name: Sample98
fig5_12


title: Placenta sample X31303.379

description:
Library name: X31303.379
Column name in counts_nhbcs.csv.gz : X31303.379


title: Placenta sample X31303.378

description:
Library name: X31303.378
Column name in counts_nhbcs.csv.gz : X31303.378


title: Placenta sample X31303.381

description:
Library name: X31303.381
Column name in counts_nhbcs.csv.gz : X31303.381


title: PABPC1-POND-A549-Bezonase_rep1

description:
Library name: Sample97
fig5_11


title: PABPC1-POND-Huh7-Bezonase_rep2

description:
Library name: Sample96
fig5_10


title: Placenta sample X31303.376

description:
Library name: X31303.376
Column name in counts_nhbcs.csv.gz : X31303.376


title: Placenta sample X31303.375

description:
Library name: X31303.375
Column name in counts_nhbcs.csv.gz : X31303.375


title: A549-Mock_supernatant_rep2

description:
Library name: Sample94
fig5_8


title: Placenta sample X31303.372

description:
Library name: X31303.372
Column name in counts_nhbcs.csv.gz : X31303.372


title: A549-Mock_supernatant_rep1

description:
Library name: Sample93
fig5_7


title: Huh-7-Mock_supernatant_rep2

description:
Library name: Sample92
fig5_6


title: Placenta sample X31303.371

description:
Library name: X31303.371
Column name in counts_nhbcs.csv.gz : X31303.371


title: Placenta sample X31303.370

description:
Library name: X31303.370
Column name in counts_nhbcs.csv.gz : X31303.370


title: Placenta sample X31303.369

description:
Library name: X31303.369
Column name in counts_nhbcs.csv.gz : X31303.369


title: Placenta sample X31303.368

description:
Library name: X31303.368
Column name in counts_nhbcs.csv.gz : X31303.368


title: Placenta sample X31303.366

description:
Library name: X31303.366
Column name in counts_nhbcs.csv.gz : X31303.366


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1R2_rep2

description:
Library name: Sample88
fig4_70

value: HEK293T cell line


title: Placenta sample X31303.365

description:
Library name: X31303.365
Column name in counts_nhbcs.csv.gz : X31303.365


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1R2_rep1

description:
Library name: Sample87
fig4_69


title: Placenta sample X31303.361

description:
Library name: X31303.361
Column name in counts_nhbcs.csv.gz : X31303.361


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1R1_rep2

description:
Library name: Sample86
fig4_68


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1R1_rep1

description:
Library name: Sample85
fig4_67


title: Placenta sample X31303.357

description:
Library name: X31303.357
Column name in counts_nhbcs.csv.gz : X31303.357


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1_rep2

description:
Library name: Sample84
fig4_66

value: 50ng/ml TNFα plus 0.2 μM doxycycline


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1_rep1

description:
Library name: Sample83
fig4_65


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T0_rep2

description:
Library name: Sample82
fig4_64


title: Placenta sample X31303.352

description:
Library name: X31303.352
Column name in counts_nhbcs.csv.gz : X31303.352

value: White


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T0_rep1

description:
Library name: Sample81
fig4_63


title: Placenta sample X31303.351

description:
Library name: X31303.351
Column name in counts_nhbcs.csv.gz : X31303.351

value: Male


title: PABPC1-POND-293T-3h-T1R3_rep2

description:
Library name: Sample80
fig4_62


title: Placenta sample X31303.350

description:
Library name: X31303.350
Column name in counts_nhbcs.csv.gz : X31303.350


title: PABPC1-POND-293T-3h-T1R3_rep1

description:
Library name: Sample79
fig4_61


title: Placenta sample X31303.349

description:
Library name: X31303.349
Column name in counts_nhbcs.csv.gz : X31303.349


title: PABPC1-POND-293T-3h-T1R2_rep1

description:
Library name: Sample77
fig4_59


title: Placenta sample X31303.347

description:
Library name: X31303.347
Column name in counts_nhbcs.csv.gz : X31303.347


title: PABPC1-POND-293T-3h-T1R1_rep2

description:
Library name: Sample76
fig4_58


title: Placenta sample X31303.344

description:
Library name: X31303.344
Column name in counts_nhbcs.csv.gz : X31303.344


title: Placenta sample X31303.343

description:
Library name: X31303.343
Column name in counts_nhbcs.csv.gz : X31303.343


title: PABPC1-POND-293T-3h-T1R1_rep1

description:
Library name: Sample75
fig4_57


title: Placenta sample X31303.342

description:
Library name: X31303.342
Column name in counts_nhbcs.csv.gz : X31303.342


title: PABPC1-POND-293T-3h-T1_rep1

description:
Library name: Sample73
fig4_55


title: Placenta sample X31303.341

description:
Library name: X31303.341
Column name in counts_nhbcs.csv.gz : X31303.341


title: PABPC1-POND-293T-3h-T0_rep2

description:
Library name: Sample72
fig4_54


title: PABPC1-POND-293T-3h-T1R2_rep2

description:
Library name: Sample78
fig4_60


title: Placenta sample X31303.340

description:
Library name: X31303.340
Column name in counts_nhbcs.csv.gz : X31303.340


title: PABPC1-POND-293T-3h-T0_rep1

description:
Library name: Sample71
fig4_53


title: Placenta sample X31303.339

description:
Library name: X31303.339
Column name in counts_nhbcs.csv.gz : X31303.339


title: RNA-seq_293T-PABPC1-POND-TNFα-3h_celllysate-3h-T0_rep2

description:
Library name: Sample70
fig4_52


title: Placenta sample X31303.337

description:
Library name: X31303.337
Column name in counts_nhbcs.csv.gz : X31303.337


title: Placenta sample X31303.424

description:
Library name: X31303.424
Column name in counts_nhbcs.csv.gz : X31303.424


title: Placenta sample X31303.419

description:
Library name: X31303.419
Column name in counts_nhbcs.csv.gz : X31303.419


title: RNA-seq_293T-PABPC1-POND-TNFα-3h_celllysate-3h-T0_rep1

description:
Library name: Sample69
fig4_51


title: Placenta sample X31303.416

description:
Library name: X31303.416
Column name in counts_nhbcs.csv.gz : X31303.416


title: FMR1-RIPseq_WT-rep1

description:
Library name: Sample117
fig7_185


title: Placenta sample X31303.335

description:
Library name: X31303.335
Column name in counts_nhbcs.csv.gz : X31303.335


title: RNA-seq_293T-PABPC1-POND-TNFα-1h_celllysate-3h-T0_rep2

description:
Library name: Sample68
fig4_50


title: PABPC1-POND-Huh-7-Separate-D1_rep2

description:
Library name: Sample112
fig5_38


title: PABPC1-POND-293T-3h-T1_rep2

description:
Library name: Sample74
fig4_56


title: Placenta sample X31303.334

description:
Library name: X31303.334
Column name in counts_nhbcs.csv.gz : X31303.334


title: Placenta sample X31303.332

description:
Library name: X31303.332
Column name in counts_nhbcs.csv.gz : X31303.332


title: PABPC1-POND-Huh-7-Coculture-D4_rep1

description:
Library name: Sample109
fig5_35


title: Placenta sample X31303.331

description:
Library name: X31303.331
Column name in counts_nhbcs.csv.gz : X31303.331


title: RNA-seq_293T-PABPC1-POND-TNFα-1h_celllysate-3h-T0_rep1

description:
Library name: Sample67
fig4_49


title: RNA-seq_293T-PABPC1-POND-TNFα-0.5h_celllysate-3h-T0_rep2

description:
Library name: Sample66
fig4_48


title: RNA-seq_293T-PABPC1-POND-TNFα-0.5h_celllysate-3h-T0_rep1

description:
Library name: Sample65
fig4_47


title: PABPC1-POND-Huh-7-Coculture-D2_rep2

description:
Library name: Sample108
fig5_34


title: Placenta sample X31303.329

description:
Library name: X31303.329
Column name in counts_nhbcs.csv.gz : X31303.329


title: RNA-seq_293T-PABPC1-POND-untreated_celllysate-3h-T0_rep2

description:
Library name: Sample64
fig4_46


title: Placenta sample X31303.327

description:
Library name: X31303.327
Column name in counts_nhbcs.csv.gz : X31303.327


title: RNA-seq_293T-PABPC1-POND-untreated_celllysate-3h-T0_rep1

description:
Library name: Sample63
fig4_45


title: PABPC1-POND-A549-StableCell_rep1

description:
Library name: Sample101
fig5_15


title: Placenta sample X31303.326

description:
Library name: X31303.326
Column name in counts_nhbcs.csv.gz : X31303.326


title: Placenta sample X31303.325

description:
Library name: X31303.325
Column name in counts_nhbcs.csv.gz : X31303.325


title: PABPC1-POND-293T-TNFα-3h_rep1

description:
Library name: Sample61
fig4_43


title: Placenta sample X31303.324

description:
Library name: X31303.324
Column name in counts_nhbcs.csv.gz : X31303.324


title: PABPC1-POND-293T-TNFα-3h_rep2

description:
Library name: Sample62
fig4_44


title: PABPC1-POND-293T-TNFα-1h_rep2

description:
Library name: Sample60
fig4_42


title: PABPC1-POND-Huh7-StableCell_rep2

description:
Library name: Sample100
fig5_14


title: Placenta sample X31303.322

description:
Library name: X31303.322
Column name in counts_nhbcs.csv.gz : X31303.322


title: Placenta sample X31303.321

description:
Library name: X31303.321
Column name in counts_nhbcs.csv.gz : X31303.321


title: Placenta sample X31303.320

description:
Library name: X31303.320
Column name in counts_nhbcs.csv.gz : X31303.320


title: PABPC1-POND-293T-TNFα-1h_rep1

description:
Library name: Sample59
fig4_41


title: PABPC1-POND-293T-TNFα-0.5h_rep2

description:
Library name: Sample58
fig4_40


title: PABPC1-POND-Huh7-Bezonase_rep1

description:
Library name: Sample95
fig5_9


title: PABPC1-POND-293T-TNFα-0.5h_rep1

description:
Library name: Sample57
fig4_39


title: Placenta sample X31303.318

description:
Library name: X31303.318
Column name in counts_nhbcs.csv.gz : X31303.318


title: PABPC1-POND-293T-3h_rep2

description:
Library name: Sample56
fig4_38