title: patient3_day100

description:
Library name: sample_116
Column name in counts.csv: sample_116


title: F123 GAM library f123_1NP_GAM180116_B07_2_S146_R1_001

status: Public on Jan 29 2025

type: SRA

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip

library_source: genomic

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse F123 ESCs (a male, hybrid cell line, derived from S129/Jae and Cast) (Gribnau et al., 2003) were cultured in a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol , 1000 U / ml LIF). Before harvesting, mESCs were passaged onto feeder free 0.1% gelatin coated plates for at least 2 passages to remove feeder cells. As feeder-removal results in reduced levels of LIF in the culture, the LIF concentration in the media was doubled when the cells were in feeder-free culture conditions. Cells were harvested after ~ 48 h at 70 – 80 % confluency.

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Hybrid F1 S129/Jae and Cast

tag: Sex

value: male


title: PBMC from BatchC (10 hashed donors, chip2 lane1) during ART, GEX

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

country: USA

institute: Walter Reed Army Institute of Research

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchC_Lane1_barcodes.tsv.gz
BatchC_Lane1_features.tsv.gz
BatchC_Lane1_matrix.mtx.gz

library_source: transcriptomic

data_processing:
Sequencing reads were generated from bcl files using cellranger mkfastq
Matched gene expression and HTO libraries for each chip well from both sequencing runs at a time were aligned to the Homo sapiens genome (GRCh38; Ensembl annotation 93) using cellranger count v3.1.0
Gene expression and HTO counts per cell barcode were quantified using cellranger count v3.1.0
Assembly: GRCh38
Supplementary files format and content: Processed files are gzipped barcode/features/matrix files that include raw gene expression and HTO counts
Library strategy: CITE-seq

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMC from 38 participants were washed then individually hashed with TotalSeq-C anti-human hashtag antibodies (BioLegend). Uniquely-hashed participant PBMC were pooled into 4 batches of 9 or 10 participants and cells from each batch were loaded into 4 different wells of a Chromium chip (10x Genomics), with targeted recoveries of 16,000 cells/well, for subsequent library construction.
Library constructions were processed for CITE-seq using the Chromium Next GEM 5’ Single Cell V(D)J Reagent Kit with Feature Barcode v1.1 (10x Genomics) per manufacturer’s instructions.

tag: tissue

value: PBMC

tag: library type

value: mRNA


title: PDSD-3

city: Luzhou

first: Fengtian

last: Li

address: Zhongshan Road

country: China

institute: Southwest Medical University

data_processing:
Filtering of Clean Reads Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp(version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA) Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
Alignment with reference genome An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 (version 2.1.0) with “-rna-strandness RF” and other parameters set as a default.
Transcripts Reconstruction The reconstruction of transcripts was carried out with software Stringtie (version 1.3.4), which together with HISAT2, allow biologists to identify new genes and new splice variants of known ones.
Novel Transcripts Identification and Annotation To identify the new transcripts, all of the reconstructed transcripts were aligned to reference genome and were divided into twelve categories by using Cuffcompare. Transcripts with one of the classcodes “u,i,j,x,c,e,o” were defined as novel transcripts. We used the following parameters to identify reliable novel genes: the length of transcript was longer than 200bp and the exon number was more than 2 (plants more than 1). Novel transcripts were then aligned to the Nr, KEGG, and GO database to obtain protein functional annotation.
lncRNA Prediction Two softwares CNCI (version 2) and CPC (version 0.9-r2) ( http://cpc.cbi.pku.edu.cn/) were used to assess the protein-coding potential of novel transcripts by default parameters. The intersection of both non protein-coding potential results were chosen as long non-coding RNAs.
lncRNA type classification lncRNAs were classified into five classes according to their location relative to protein-coding genes: intergenic lncRNAs, bidirectional lncRNAs, intronic lncRNAs, antisense lncRNAs, and sense overlapping lncRNAs. Different types of lncRNAs may have different biological functions.
Quantification of Transcripts Abundance Transcripts abundances were quantified by software StringTie in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Assembly: Ensembl_release104
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

source_name: Colorectal tumor

extract_protocol:
Tumor samples stored in RNA-later buffer were used for RNA extraction. Total RNA was extracted using RNAiso Plus (9109, TaKaRa, Japan) following the manufacturer's protocol.
The RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and confirmed through RNase-free agarose gel electrophoresis. Following RNA extraction, rRNAs were depleted to enrich mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short segments using a fragmentation buffer and then reverse transcribed into cDNA with random primers. Subsequently, second-strand cDNA synthesis was carried out using DNA polymerase I, RNase H, dNTPs (with dUTP substituted for dTTP), and buffer. The resulting cDNA fragments were purified with the QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), subjected to end repair, poly(A) tail addition, and ligation to Illumina sequencing adapters. Subsequently, Uracil-N-Glycosylase (UNG) was employed to degrade the second-strand cDNA. The digested products underwent size selection via agarose gel electrophoresis, PCR amplification, and sequencing on the Illumina HiSeq TM 4000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: Colorectal tumor

tag: treatment

value: Neoadjuvant therapy


title: PDSD-2


title: patient41_day100

city: Oslo

first: Maria

middle: Dehli

last: Vigeland

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

description:
Library name: sample_113
Column name in counts.csv: sample_113

data_processing:
The reads were mapped to the human genome (GRCh38.p10) using HISAT2 v2.1.0 and counted with featureCounts from Subread v1.6.3, using gene coordinates from Ensembl 88.
Assembly: GRCh38.p10 and Ensembl 88
Supplementary files format and content: Csv file "counts.csv" includes gene counts for each sample

source_name: whole blood

extract_protocol:
Total RNA was isolated from the blood using the Preserved Blood RNA Purification Kit I (Norgen Biotek, Thorold, Canada) according to the manufacturer’s instructions. DNAse treatment was included as recommended.
RNA was prepared for sequencing using TruSeq RNA library prep kits (Illumina) and sequenced with 2×75 bp paired-end configuration on the HiSeq3000 platform (Illumina)

value: whole blood

value: placebo sugar pills


title: F123 GAM library f123_1NP_GAM180116_B06_2_S138_R1_001


title: PBMC from BatchB (9 hashed donors, chip1 lane2) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchB_Lane2_barcodes.tsv.gz
BatchB_Lane2_features.tsv.gz
BatchB_Lane2_matrix.mtx.gz

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-C0251 anti-human Hashtag 1, TotalSeq-C0252 anti-human Hashtag 2, TotalSeq-C0253 anti-human Hashtag 3, TotalSeq-C0254 anti-human Hashtag 4, TotalSeq-C0255 anti-human Hashtag 5, TotalSeq-C0256 anti-human Hashtag 6, TotalSeq-C0257 anti-human Hashtag 7, TotalSeq-C0258 anti-human Hashtag 8, TotalSeq-C0259 anti-human Hashtag 9


title: F123 GAM library f123_1NP_GAM180116_B11_1_S82_R1_001


title: F123 GAM library f123_1NP_GAM180116_B12_1_S90_R1_001


title: F123 GAM library f123_1NP_GAM180116_B05_2_S130_R1_001


title: patient3_1y

description:
Library name: sample_117
Column name in counts.csv: sample_117


title: PBMC from BatchB (9 hashed donors, chip1 lane4) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchB_Lane4_barcodes.tsv.gz
BatchB_Lane4_features.tsv.gz
BatchB_Lane4_matrix.mtx.gz


title: PDSD-4


title: patient41_day0

description:
Library name: sample_112
Column name in counts.csv: sample_112


title: PR-4


title: PBMC from BatchB (9 hashed donors, chip1 lane2) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchB_Lane2_barcodes.tsv.gz
BatchB_Lane2_features.tsv.gz
BatchB_Lane2_matrix.mtx.gz


title: F123 GAM library f123_1NP_GAM180116_B08_2_S154_R1_001


title: patient40_day100

description:
Library name: sample_110
Column name in counts.csv: sample_110


title: patient40_1y

description:
Library name: sample_111
Column name in counts.csv: sample_111


title: PBMC from BatchA (10 hashed donors, chip1 lane7) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchA_Lane7_barcodes.tsv.gz
BatchA_Lane7_features.tsv.gz
BatchA_Lane7_matrix.mtx.gz

value: TotalSeq-C0251 anti-human Hashtag 1, TotalSeq-C0252 anti-human Hashtag 2, TotalSeq-C0253 anti-human Hashtag 3, TotalSeq-C0254 anti-human Hashtag 4, TotalSeq-C0255 anti-human Hashtag 5, TotalSeq-C0256 anti-human Hashtag 6, TotalSeq-C0257 anti-human Hashtag 7, TotalSeq-C0258 anti-human Hashtag 8, TotalSeq-C0259 anti-human Hashtag 9, TotalSeq-C0260 anti-human Hashtag 10


title: F123 GAM library f123_1NP_GAM180116_B04_2_S122_R1_001


title: PR-3


title: PBMC from BatchA (10 hashed donors, chip1 lane7) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchA_Lane7_barcodes.tsv.gz
BatchA_Lane7_features.tsv.gz
BatchA_Lane7_matrix.mtx.gz


title: PR-2


title: F123 GAM library f123_1NP_GAM180116_B02_2_S106_R1_001


title: PR-1


title: patient19_1y

description:
Library name: sample_108
Column name in counts.csv: sample_108


title: S6004

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
Reads were aligned to GRCh38 and GRCm38 chromosomes concurrently using HISAT2v2.2.1 to separate human and mouse reads.
Human reads were further processed and normalized using DESeq2.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PDX HCC

growth_protocol: Fresh tumor tissues from mice bearing established primary human liver cancer (PDX models LI6280, LI6716, LI6688, LI6723, LI1055 and LI1068) were harvested and cut into small pieces (approximately 2-3 mm in diameter) and inoculated subcutaneously at the upper right dorsal flank into female BALB/c nude mice for tumor development

extract_protocol:
Liver tissue was lysed in TRI-reagent (Molecular Research Center), and RNA was purified using Direct-zol RNA MiniPrep (Zymo Research) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Randomization into treatment groups started when the mean tumor size reached 100 mm3. A total of 5 mice were enrolled in each model. Randomization into groups receiving CLDN1 mAb (10 mg/kg, 10 mL/kg, once weekly (QW), n=3 mice) or vehicle control (10 mL/kg, QW, n=2 mice) was performed based on "Matched distribution" method. The date of grouping was denoted as day 1 (5/12/2020). Dosing was started on day 1 and continued through day 25.

value: vehicle

tag: donor

value: PDX tumor


title: PBMC from BatchA (10 hashed donors, chip1 lane5) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchA_Lane5_barcodes.tsv.gz
BatchA_Lane5_features.tsv.gz
BatchA_Lane5_matrix.mtx.gz


title: F123 GAM library f123_1NP_GAM180116_B01_2_S98_R1_001


title: patient40_day0

description:
Library name: sample_109
Column name in counts.csv: sample_109


title: patient19_day100

description:
Library name: sample_107
Column name in counts.csv: sample_107


title: F123 GAM library f123_1NP_GAM180116_A12_2_S185_R1_001


title: patient19_day0

description:
Library name: sample_106
Column name in counts.csv: sample_106


title: patient18_1y

description:
Library name: sample_105
Column name in counts.csv: sample_105


title: PBMC from BatchA (10 hashed donors, chip1 lane3) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchA_Lane3_barcodes.tsv.gz
BatchA_Lane3_features.tsv.gz
BatchA_Lane3_matrix.mtx.gz


title: S6001


title: F123 GAM library f123_1NP_GAM180116_A12_1_S89_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: F123 GAM library f123_1NP_GAM180116_A11_2_S177_R1_001


title: S6002

value: CLDN1 mAb


title: F123 GAM library f123_1NP_GAM180116_B03_2_S114_R1_001


title: PBMC from BatchA (10 hashed donors, chip1 lane3) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchA_Lane3_barcodes.tsv.gz
BatchA_Lane3_features.tsv.gz
BatchA_Lane3_matrix.mtx.gz


title: PBMC from BatchA (10 hashed donors, chip1 lane1) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchA_Lane1_barcodes.tsv.gz
BatchA_Lane1_features.tsv.gz
BatchA_Lane1_matrix.mtx.gz


title: S5998


title: PBMC from BatchA (10 hashed donors, chip1 lane5) during ART, HTO

description:
HTO library: R1 contains cell barcode and UMI; R2 contains Hashtag Antibody Derived Tag reads
BatchA_Lane5_barcodes.tsv.gz
BatchA_Lane5_features.tsv.gz
BatchA_Lane5_matrix.mtx.gz


title: patient18_day0

description:
Library name: sample_103
Column name in counts.csv: sample_103


title: F123 GAM library f123_1NP_GAM180116_A11_1_S81_R1_001


title: patient17_1y

description:
Library name: sample_102
Column name in counts.csv: sample_102


title: patient18_day100

description:
Library name: sample_104
Column name in counts.csv: sample_104


title: S5092


title: F123 GAM library f123_1NP_GAM180116_A09_2_S161_R1_001


title: S5088


title: F123 GAM library f123_1NP_GAM180116_A10_1_S73_R1_001


title: PBMC from BatchA (10 hashed donors, chip1 lane1) during ART, GEX

description:
GEX (5' mRNA) library: R1 contains cell barcode and UMI; R2 contains transcript
BatchA_Lane1_barcodes.tsv.gz
BatchA_Lane1_features.tsv.gz
BatchA_Lane1_matrix.mtx.gz


title: XC-13150_PBM_NELF_YKL_1

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-13150_2022_10_12_PBM_NELF_YKL_1

data_processing:
Single-end reads are pre-processed using fastp which supports adapter trimming, low quality base trimming, and calculation of additional quality control metrics.
Trimmed reads were aligned to the mm10 genome using bowtie2  with --very-sensitive-local -q -p options set. Low quality, improper, multimapping alignments, and PCR duplicates are filtered using SAMtools .
Peaks are called on each sample (replicas are not pooled) with MACS2  sing macs2 callpeak --nomodel --shift -100 --extsize 200 -q 0.05 options. After peak calling, all peaks from all samples called separately were combined and adjacent peaks (within 10bp) were merged. Reads from each sample within the combined set of peaks are then counted using featureCounts to produce an initial reads-per-peak count matrix
Assembly: mm10(mouse samples), hg38(human samples)
Supplementary files format and content: bigwig files for each sample

source_name: Blood

growth_protocol:
Mouse bone marrow derived macrophages: 1.YKL, LPS Mouse  time course experiment: Bone marrow derived Macrophages from tibiae and femora were flushed and incubated for 5 days in DMEM (Corning, 1 g/L glucose) supplemented with 20% FBS and 20% L-Cell conditioned media. Adherent cells were then scraped, seeded into 150 mm or 6-well plates in DMEM -20% FBS and treated the following day
PBMC-derived macrophages: Deidentified human buffy coats were purchased from New York Blood Center. PBMC were isolated by gradient centrifugation of buffy coats with Lymphoprep (STEMCELL Technologies, 07851). Human monocytes were purified from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec, 130-050-201) as recommended by the manufacturer. Purified human monocytes were seeded into 150 mm plates (1.5 x 107 cells/ plate) or 6-well plates (2x106 cells/well) and cultured for 5 days in DMEM supplemented with 20% heat-inactivated FBS, penicillin/streptomycin, L-glutamine, with 20 ng/ml human macrophage colony-stimulating factor (hM-CSF) added fresh every other day.

extract_protocol:
Mouse BMM and hM were crosslinked with 1% formaldehyde, scraped, PBS-washed and lysed as previously described 52. Crude nuclei were prepared, lysed 52 and sonicated for 6 cycles (hM) or 8 cycles (BMM) of 30 s on/ 30 s off in Diagenode Bioruptor Pico system. Sonicated samples are cleared with protein A/G agarose beads (Santa Cruz) and incubated with BSA-blocked protein A/G agarose beads (Santa Cruz) and antibody overnight. For control, rabbit IgG (Thermo Fisher Scientific) is used with concentration matching other antibodies. Samples were then washed 2x with Szac RIPA (150 mM NaCl, 1% v/v Nonidet P-40, 0.5% w/v Na deoxycholate, 0.1% w/v SDS, 50 mM Tris-Cl pH 8.0, 5 mM EDTA pH 8.0), 4x with Szac IP wash buffer (100 mM Tris-Cl pH 8.5, 500 mM LiCl, 1% v/v Nonidet P-40, 1% w/v Na deoxycholate), 2x with Szac RIPA buffer, and 2x with ChIP-TE buffer (100 mM Tris-Cl pH 7.5, 100 mM EDTA, 500 mM NaCl). Washed samples were next incubated with decrosslinking buffer (0.5% SDS and 0.1% v/v proteinase K in TE buffer) for 2 h at 55°C followed by overnight incubation at 65°C. DNA fragments were purified using Qiagen QIAquick PCR Purification Kit
For ChIPseq, libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s protocol and multiplexed with index primers (NEB E7335, E7500, E7600).

treatment_protocol:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages : Mouse bone marrow derived macrophages were treated  with LPS (10 ng/ml) for 30 and 60 min and compared with PBS-treated control.
Pol II and Ser5-P PolII ChIPseq in  untreated or TNF+IFNg-polarized macrophages treated with YKL: human macrophages were untreated or polarized for 24h with human TNF (Abcam, ab259410) and IFNγ (ab259377) used at 20 ng/ml and 5 ng/ml, respectively, with YKL-5-124 (250 nM final concentration) or DMSO vehicle added for the last 5h of polarization.
NELF-E ChiPseq in YKL-treated mouse macrophages: BMDM were treated with YKL-5-124 (250 nM) or DMSO vehical for 6h and processed for ChIP.
NELF-E ChiPseq in YKL- or THZ1-treated PBMC-derived human macrophages: hMF were treated with THZ1, YKL-5-124 (250 nM each) or DMSO vehicle for 3h and processed for ChIP.

value: Blood

value: primary

value: PBMC-derived macrophages

tag: age

tag: batch

tag: antibodies

value: 4 mkg NELF-E (Santa Cruz, sc-377052)


title: F123 GAM library f123_1NP_GAM180116_A08_2_S153_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: patient17_day0

description:
Library name: sample_100
Column name in counts.csv: sample_100


title: XC-13150_PBM_NELF_THZ1_2

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-13150_2022_10_12_PBM_NELF_THZ1_2


title: F123 GAM library f123_1NP_GAM180116_A07_2_S145_R1_001


title: S5085


title: S5087


title: patient17_day100

description:
Library name: sample_101
Column name in counts.csv: sample_101


title: F123 GAM library f123_1NP_GAM180116_A06_2_S137_R1_001


title: XC-13150_PBM_NELF_THZ1_1

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-13150_2022_10_12_PBM_NELF_THZ1_1


title: S4422


title: patient39_1y

description:
Library name: sample_99
Column name in counts.csv: sample_99


title: S4383


title: patient39_day0

description:
Library name: sample_97
Column name in counts.csv: sample_97


title: F123 GAM library f123_1NP_GAM180116_A05_2_S129_R1_001


title: XC-13150_PBM_NELF_DMSO_2

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-13150_2022_10_12_PBM_NELF_DMSO_2


title: patient39_day100

description:
Library name: sample_98
Column name in counts.csv: sample_98


title: S5095


title: S4318


title: F123 GAM library f123_1NP_GAM180116_A04_2_S121_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: XC-13150_PBM_NELF_YKL_2

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-13150_2022_10_12_PBM_NELF_YKL_2


title: F123 GAM library f123_1NP_GAM180116_A03_2_S113_R1_001


title: XC-11769_PBM_NELF_YKL_1

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-11769_2022_01_12_PBM_NELF_YKL_1


title: patient38_1y

description:
Library name: sample_96
Column name in counts.csv: sample_96


title: XC-11769_PBM_NELF_THZ1_1

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-11769_2022_01_12_PBM_NELF_THZ1_1


title: F123 GAM library f123_1NP_GAM180116_A02_2_S105_R1_001


title: patient38_day100

description:
Library name: sample_95
Column name in counts.csv: sample_95


title: S2771


title: F123 GAM library f123_1NP_GAM180116_A01_2_S97_R1_001


title: patient38_day0

description:
Library name: sample_94
Column name in counts.csv: sample_94


title: XC-11769_PBM_NELF_DMSO_1

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-11769_2022_01_12_PBM_NELF_DMSO_1


title: DD-10264_PBM_NELF_YKL_2

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-DD-10264_2021_03_26_PBM_NELF_YKL_2


title: F123 GAM library f123_1NP_GAM171221_G09_1_S71_R1_001


title: S2767


title: S2757


title: patient37_day100

description:
Library name: sample_92
Column name in counts.csv: sample_92


title: F123 GAM library f123_1NP_GAM171221_H09_1_S72_R1_001


title: DD-10264_PBM_NELF_THZ1_2

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-DD-10264_2021_03_26_PBM_NELF_THZ1_2


title: patient37_1y

description:
Library name: sample_93
Column name in counts.csv: sample_93


title: S2760


title: patient37_day0

description:
Library name: sample_91
Column name in counts.csv: sample_91


title: DD-10264_PBM_NELF_DMSO_2

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-DD-10264_2021_03_26_PBM_NELF_DMSO_2


title: XC-13150_PBM_NELF_DMSO_1

description:
NELF-E ChIPseq in YKL treated human PBMC-derived macrophages
Rogatsky-XC-13150_2022_10_12_PBM_NELF_DMSO_1


title: S2751


title: F123 GAM library f123_1NP_GAM171221_E09_1_S69_R1_001


title: YKL_pPolii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_YKL_pPolii_3

value: 2 mkg, Abcam, Ab5131


title: F123 GAM library f123_1NP_GAM171221_F09_1_S70_R1_001


title: patient30_1y

description:
Library name: sample_90
Column name in counts.csv: sample_90


title: YKL_Polii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_YKL_Polii_3

value: 2 mkg, Bethyl, A304-405A


title: S2749


title: S2772


title: patient30_day100

description:
Library name: sample_89
Column name in counts.csv: sample_89

value: whole blood


title: S2742


title: F123 GAM library f123_1NP_GAM171221_D09_1_S68_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: S2744


title: TNF-IFN-YKL_pPolii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_TNF-IFN-YKL_pPolii_3


title: patient30_day0

description:
Library name: sample_88
Column name in counts.csv: sample_88

value: placebo sugar pills


title: TNF-IFN-YKL_Polii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_TNF-IFN-YKL_Polii_3


title: S2736


title: patient28_1y

description:
Library name: sample_87
Column name in counts.csv: sample_87


title: patient28_day100

description:
Library name: sample_86
Column name in counts.csv: sample_86


title: TNF-IFN_pPolii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_TNF-IFN_pPolii_3


title: patient28_day0

description:
Library name: sample_85
Column name in counts.csv: sample_85


title: TNF-IFN_Polii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_TNF-IFN_Polii_3


title: S2412


title: F123 GAM library f123_1NP_GAM171130_H05_1_S40_R1_001


title: S2408


title: F123 GAM library f123_1NP_GAM171221_A09_1_S65_R1_001


title: DMSO_pPolii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_DMSO_pPolii_3


title: F123 GAM library f123_1NP_GAM171130_H04_1_S32_R1_001


title: patient16_day0

description:
Library name: sample_83
Column name in counts.csv: sample_83


title: S2398


title: patient16_1y

description:
Library name: sample_84
Column name in counts.csv: sample_84


title: DMSO_Polii_3

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-13150_2022_10_12_DMSO_Polii_3


title: YKL_pPolii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_YKL_pPolii_2


title: F123 GAM library f123_1NP_GAM171221_C09_1_S67_R1_001


title: patient15_1y

description:
Library name: sample_82
Column name in counts.csv: sample_82


title: S1209


title: F123 GAM library f123_1NP_GAM171130_H03_1_S24_R1_001


title: F123 GAM library f123_1NP_GAM171130_H02_1_S16_R1_001


title: F123 GAM library f123_1NP_GAM171221_B09_1_S66_R1_001


title: S2397


title: patient15_day100

description:
Library name: sample_81
Column name in counts.csv: sample_81


title: YKL_pPolii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_YKL_pPolii_1


title: F123 GAM library f123_1NP_GAM171130_H01_1_S8_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: patient15_day0

description:
Library name: sample_80
Column name in counts.csv: sample_80


title: YKL_Polii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_YKL_Polii_1


title: S1199


title: S1190


title: S1189


title: patient29_day0

description:
Library name: sample_77
Column name in counts.csv: sample_77


title: F123 GAM library f123_1NP_GAM171130_G03_1_S23_R1_001


title: S1191


title: F123 GAM library f123_1NP_GAM171130_G10_1_S79_R1_001


title: patient29_1y

description:
Library name: sample_79
Column name in counts.csv: sample_79


title: F123 GAM library f123_1NP_GAM171130_G11_1_S87_R1_001


title: TNF-IFN-YKL_pPolii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN-YKL_pPolii_2


title: patient29_day100

description:
Library name: sample_78
Column name in counts.csv: sample_78


title: TNF-IFN-YKL_Polii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN-YKL_Polii_1


title: YKL_Polii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_YKL_Polii_2


title: F123 GAM library f123_1NP_GAM171130_G04_1_S31_R1_001


title: F123 GAM library f123_1NP_GAM171130_G01_1_S7_R1_001


title: F123 GAM library f123_1NP_GAM171130_G02_1_S15_R1_001


title: TNF-IFN-YKL_pPolii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN-YKL_pPolii_1


title: patient14_1y

description:
Library name: sample_76
Column name in counts.csv: sample_76


title: TNF-IFN-YKL_Polii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN-YKL_Polii_2


title: patient14_day100

description:
Library name: sample_75
Column name in counts.csv: sample_75


title: R4KO_MEF_biol_rep_2

city: Montreal

first: Lisa

middle: M

last: Munter

state: QC

address: 3649 Sir-William-Osler Promenade

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description:
Library name: Sample_5
column name in raw counts: R4KO-2_SR44-1_B5-1

data_processing:
Alignment to mm10 was performed with the STAR aligner (v2.5.3a) using default parameters on FASTQ files. RNA-SeQC analyzed the resulting Bam files to confirm library quality. Read counts were computed with htseq-count, and RPKM values were determined using cufflinks (v2.2.1) with default settings. Principal component analysis (PCA) was conducted using the prcomp function in R and visualized with the ggfortify package. Genes with RPKM values below 2 in all samples were excluded from subsequent analysis. Differential expression between RHBDL4 KO and WT MEFs was computed from transcript counts for each gene using the DEseq2 software package. Log2FC and the FDR-adjusted p-value were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: mm10

source_name: embryo

growth_protocol: Mouse embryonic fibroblasts were cultured in DMEM with 10% FCS at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using the QIAGEN RNeasy Micro Kit .
mRNA enrichment was carried out on 500 ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module Kit, followed by library generation using the Swift RNA Library Kit.

treatment_protocol: Cells were grown for 48 h under standard conditions.

value: embryo

value: mouse embryonic fibroblasts

value: KO

value: standard cultivation for 48 h


title: F123 GAM library f123_1NP_GAM171130_F11_1_S86_R1_001


title: WT_MEF_biol_rep_3

description:
Library name: Sample_3
column name in raw counts: WT-3_SR44-2_B6_WT

value: WT


title: R4KO_MEF_biol_rep_1

description:
Library name: Sample_4
column name in raw counts: R4KO-1_B5


title: TNF-IFN_pPolii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN_pPolii_2


title: patient14_day0

description:
Library name: sample_74
Column name in counts.csv: sample_74


title: TNF-IFN_pPolii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN_pPolii_1


title: patient2_1y

description:
Library name: sample_73
Column name in counts.csv: sample_73


title: TNF-IFN_Polii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN_Polii_2


title: F123 GAM library f123_1NP_GAM171130_F08_1_S62_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: patient2_day100

description:
Library name: sample_72
Column name in counts.csv: sample_72


title: R4KO_MEF_biol_rep_3

description:
Library name: Sample_6
column name in raw counts: R4KO-3_SR44-2_B5_KO


title: WT_MEF_biol_rep_1

description:
Library name: Sample_1
column name in raw counts: WT-1_B6


title: F123 GAM library f123_1NP_GAM171130_F04_1_S30_R1_001


title: Postnatal day 20 female oocyte, Classified as SN, Rep2

city: Athens

first: Claudia

last: Baumann

state: GA

address: 501 DW Brooks Drive

department: College of Veterinary Medicine - Physiology and Pharmacology

institute: University of Georgia

data_processing:
Data retrieved from RNA-Seq on DNBseq platform was filtered by removing reads mapped to rRNA and low-quality, adaptor-polluted and high content of unknown base (N) reads
Mapped clean reads to reference genome using HISAT2, using paramters --phred33 --sensitive --no-discordant --no-mixed -I 1 -X1000
Novel coding transcripts were merged with reference transcripts to obtain the complete reference, and then Bowtie2 was used to map clean reads to this reference (Bowtie2 parameter: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X1000 --nomixed --no-discordant -p 1 -k 200)
Gene expression level was calculated for each sample by the RSEM software (RSEM parameter: -p 8 --forward-prob 0.5 --paired-end)
Assembly: mm10
Supplementary files format and content: xls excel file with the transcript expression data of all four libraries

source_name: GV oocyte

extract_protocol:
The oocytes were recovered from the ovaries by follicle puncture and cumulus oocyte complexes were transferred to minimal essential medium (MEM) supplemented with 3mg/ml bovine serum albumin (Sigma Aldrich, St. Louis, MO) and milrinone (Sigma; 1 μg/ml) to prevent meiotic resumption. Surrounding cumulus cells were removed by gentle pipetting followed by several rinses in fresh medium. Oocytes were cultured for specified periods of time and maintained at 37°C in MEM/BSA plus milrinone under 5% CO2, 5%O2 and balanced N2.
For RNA-seq, oocytes are denuded in Tyrode’s solution (Sigma) and transferred to microcentrifuge tubes containing 3 μl of lysis buffer. Isolation of mRNA was conducted using oligo(dT)

value: GV oocyte


title: F123 GAM library f123_1NP_GAM171130_F03_1_S22_R1_001


title: Postnatal day 20 female oocyte, Classified as SN, Rep1


title: patient13_1y

description:
Library name: sample_70
Column name in counts.csv: sample_70


title: DMSO_pPolii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_DMSO_pPolii_2

value: Blood


title: Postnatal day 20 female oocyte, Classified as NSN, Rep2


title: patient13_day100

description:
Library name: sample_69
Column name in counts.csv: sample_69


title: F123 GAM library f123_1NP_GAM171130_F10_1_S78_R1_001


title: F123 GAM library f123_1NP_GAM171130_F01_1_S6_R1_001


title: DMSO_Polii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_DMSO_Polii_1

value: primary


title: totalRNAseq for mESC F123 Replicate2

data_processing:
RNAseq data from F123 was processed for standard and allele-specific gene expression analysis. The quality of the paired-end RNA sequencing reads was verified using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). No reads needed to be trimmed or removed due to quality concerns. The paired-end reads derived from RNA sequencing were mapped to the most recent mouse reference genome assembly mm10 (GRCm38.p6) using STAR (version 2.7.2c) (Dobin et al., 2013) under consideration of the current mm10 annotation (downloaded from ensemble: ftp://ftp.ensembl.org/pub/current_gtf/mus_musculus /Mus_musculus.GRCm38.98.gtf.gz) and available information of genomic variants in the mm10 F123 genome (described in SNP calling in F123 hybrid). Following recommendations about best practices for data processing in allelic expression analysis (Castel et al., 2015), duplicate reads were removed from the data using Picard MarkDuplicates (version 2.21.1: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.3.0/picard_sam_markdupl icates_MarkDuplicates.php). Default options were used with the exception of REMOVE_DUPLICATES = TRUE. To quantify the overall expression of genes, mapped reads overlapping exons were assigned to the respective genes and summarized as gene specific count values using HTSeq-count (Anders et al., 2015). The use of HTSeq-counts to generate gene level read count values is recommended by the gold standard tool used for differential gene expression analysis DESeq2 (Love et al., 2014). Options were set to count reads overlapping exons of genes, accounting for the paired end nature of reads, only considering primary alignments and the default minimal alignment quality of 10. The same annotation file was used as described before in the read mapping step.
Subsequently TPM values were calculated by normalizing count values for gene length and library size. To differentiate between the expression of genes located on the two parental alleles, reads overlapping heterozygous genomic variants were counted in an allele-specific manner. Reads overlapping those heterozygous variants located within exons of genes were counted using GATK ASEReadCounter (The Genome Analysis Toolkit (GATK) version 4.1.3.0: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.3.0/org_broadinstitute_he llbender_tools_walkers_rnaseq_ASEReadCounter.php). Subsequently only genomic variants within regions of high mappability and with a minimum total coverage of 20 reads were considered to reduce the risk of introduced biases. In case multiple genomic variants were present within the same gene, the counts were aggregated over the gene in an allele specific manner using the available haplotype information described above in the read mapping step. Aggregated counts were tested for significant allele specific expression differences (binomialtest vs 0.5) and the false discovery rate was controlled for by correcting resulting p-values for multiple testing using the Benjamini & Hochberg method.  Genes were defined as differentially expressed by an adjusted p-value <= 0.05, and a fold change (log2) >= 1 between reads mapping to CAST and S129.
Assembly: mm10 (M24)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Mouse F123 ESCs (a male, hybrid cell line, derived from a cross between S129/Jae and Cast mice) (Gribnau et al., 2003) were cultured in a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol , 1000 U / ml LIF). Before harvesting, mESCs were passaged onto feeder free 0.1% gelatin coated plates for at least 2 passages to remove feeder cells. As feeder-removal results in reduced levels of LIF in the culture, the LIF concentration in the media was doubled when the cells were in feeder-free culture conditions. Cells were harvested after ~ 48 h at 70 – 80 % confluency.

extract_protocol:
Total RNA was extracted from F123 mESCs using TRIzol Reagent (Invitrogen, Cat# 15596026) following manufacturer's instructions. Total RNA was analyzed on the Bioanalyzer using the Agilent RNA 6000 Nano Kit to ensure intact, non-degraded RNA presence and was subsequently treated with TURBO DNase I (Ambion, Cat# AM1907).
Total RNA-seq libraries were generated from 1 μg of DNase-treated RNA using the TruSeq Stranded total RNA library preparation kit (Illumina, Cat# 15031048) according to the manufacturer's instructions. Samples were pooled and sequenced on the NextSeq500, paired end 75 bp, following the manufacturer’s instructions.


title: F123 GAM library f123_1NP_GAM171130_F02_1_S14_R1_001


title: patient13_day0

description:
Library name: sample_68
Column name in counts.csv: sample_68


title: DMSO_Polii_2

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_DMSO_Polii_2

value: PBMC-derived macrophages


title: TNFa_IFNg_YKL_24h_6h_B2_rep4

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D12

data_processing:
Read quality filtering and adapter trimming were performed with fastP. Filtered reads were mapped to the mouse genome (mm10) or human genome (hg38) with the STAR aligner (2.7.0) and exonic reads were counted against GENCODE release 27 annotation with featureCount  sing a customised pipeline available at https://gitlab.com/hssgenomics/pipelines/RNAseq.
Differential gene expression analysis was performed with edgeR(3.38.4, ) using quasi-likelihood framework. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. P values were adjusted to correct for multiple testing using the Benhamini-Hochberg FDR procedure.
Assembly: mm10 or hg38
Supplementary files format and content: edgeR_DEGs_*.xlsx excel file with the results of differential analysis and datanormalization/transformation

growth_protocol:
1.YKL, LPS Mouse  time course experiment: Bone marrow derived Macrophages from tibiae and femora were flushed and incubated for 5 days in DMEM (Corning, 1 g/L glucose) supplemented with 20% FBS and 20% L-Cell conditioned media. Adherent cells were then scraped, seeded into 150 mm or 6-well plates in DMEM -20% FBS and treated the following day
2. TNF, IFNg polarized human macrophages YKL time course experiment: Deidentified human buffy coats were purchased from New York Blood Center. PBMC were isolated by gradient centrifugation of buffy coats with Lymphoprep (STEMCELL Technologies, 07851). Human monocytes were purified from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec, 130-050-201) as recommended by the manufacturer. Purified human monocytes were seeded into 150 mm plates (1.5 x 107 cells/ plate) or 6-well plates (2x106 cells/well) and cultured for 5 days in DMEM supplemented with 20% heat-inactivated FBS, penicillin/streptomycin, L-glutamine, with 20 ng/ml human macrophage colony-stimulating factor (hM-CSF) added fresh every other day.
3. YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients: Synovial tissue was obtained from patients consented into the HSS FLARE study (IRB no. 2014–233). De-identified 3x3 mm synovial biopsy specimens were collected from patients undergoing synovectomy and cryopreserved in Cryostor CS10 (Sigma-Aldrich). Cryopreserved synovial tissues were digested with Liberase TL (100 μg/ml, Roche) and DNAase I (100 μg/ml, NEB) for 15 min, single cells were separated using 70-μm cell strainers and resuspended in RBC lysis buffer for 3’ before plating in RPMI 1640 - 10% FBS - 1% glutamine in 96-well plates at 2 x 105 viable cells/well.

extract_protocol:
Total RNA was isolated from cells with RNeasy Plus micro kit (Qiagen)
The integrity of total RNA samples was evaluated with BioAnalyzer 2100 system (Agilent). Sequencing compatible libraries are prepared with NEBNext Ultra II RNA Kits (NEB) and NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs (NEB) following instructions from manufacturer. In brief, total RNA was poly(A)-enriched, fragmented, and reverse transcribed to cDNA. cDNA were ligated with adaptors and indexes. Sequencing compatible libraries were then quality-controlled with BioAnalyzer 2100 system (Agilent) and sequenced

treatment_protocol:
1.YKL, LPS Mouse  time course experiment: Mouse bone marrow derived macrophages were pretreated with YKL-5-124 for (250 nM, 6h), followed by treatment with LPS (10 ng/ml) for 1, 6 and 12 hours
2. TNF, IFNg polarized human macrophages: human macrophages were cultured in TNF+IFNγ for 24 hours(ab259410; 20 ng/ml and ab259377; 5 ng/ml, respectively), YKL-5-124  (250nm) added for the last 3 or 6 h,
3. YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients: Synovial cell suspensions were prepared from deidentified synovial tissue samples collected from RA patients, placed in culture and treated  YKL-5-124 (250 nm) for 3 or 6 hours

value: Differentiated macrophages

value: unknown

value: Male


title: Postnatal day 20 female oocyte, Classified as NSN, Rep1


title: patient6_day0

description:
Library name: sample_66
Column name in counts.csv: sample_66


title: F123 GAM library f123_1NP_GAM171130_E10_1_S77_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: WT_MEF_biol_rep_2

description:
Library name: Sample_2
column name in raw counts: WT-2_SR44-1_B6-1


title: TNFa_IFNg_YKL_24h_3h_B2_rep4

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D11


title: patient12_1y

description:
Library name: sample_65
Column name in counts.csv: sample_65

value: whole blood


title: F123 GAM library f123_1NP_GAM171130_E08_1_S61_R1_001


title: TNF-IFN_Polii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_TNF-IFN_Polii_1

value: 2 mkg, Bethyl, A304-405A


title: patient2_day0

description:
Library name: sample_71
Column name in counts.csv: sample_71

value: placebo sugar pills


title: totalRNAseq for mESC F123 Replicate1


title: TNFa_IFNg_24h_B2_rep4

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D10


title: D1

city: Beijing

first: Shao

state: Beijing

address: Haidian district

institute: Tsinghua University

description:
Library name: D1
FFPE Spatial transcriptome sequencing

data_processing:
10X Genomics Spaceranger. Spots with less than 200 UMIs were filtered out in quality control procedure.
ST data was then processed by the R package Seurat. SCTransform function was used to normalize the counts and RunPCA function was used to perform dimensionality reduction with principal component analysis (PCA). Top 30 principal components were selected for all samples.
Then, FindNeighbors function was adopted to perform the unsupervised shared-nearest-neighbor (SNN)–based clustering and FindClusters function was used to determine the spatial clusters with the resolution parameter set as 1.
Finally, RunUMAP function was utilized to construct a two-demensional UMAP embedding, and FindMarkers function was utilized to identify the differentially expressed genes for each cluster.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data in h5 format.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-resolution image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format.
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Pre-cancerours gastric

extract_protocol:
Samples were prepared using 10x Genomics Visium V4 Slide FFPE v2 chemistry, the Visium Human Transcriptome Probe Set v2.0
Pre-processing analysis Libraries were sequenced and aligned using the Visium SpaceRanger pipeline, where reads were mapped to the human reference genome (GRCh38, release 93).

value: Pre-cancerours gastric


title: F123 GAM library f123_1NP_GAM171130_E04_1_S29_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: DMSO_pPolii_1

description:
Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized  YKL-treated macrophages
Rogatsky-XC-12816_2022_07_18_DMSO_pPolii_1

value: 2 mkg, Abcam, Ab5131


title: patient12_day100

description:
Library name: sample_64
Column name in counts.csv: sample_64


title: patient6_1y

description:
Library name: sample_67
Column name in counts.csv: sample_67


title: vehicle_B2_rep4

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D09

value: vehicle


title: A1

description:
Library name: A1
FFPE Spatial transcriptome sequencing


title: patient12_day0

description:
Library name: sample_63
Column name in counts.csv: sample_63


title: F123 GAM library f123_1NP_GAM171130_E11_1_S85_R1_001


title: TNFa_IFNg_YKL_24h_6h_B1_rep3

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D08

value: Female


title: plasma, CON4

city: Xining

first: Xuefeng

last: Shi

address: NO2 Gonghe Road，Chengdong District

institute: Qinghai provincial people‘s hospital

data_processing:
illumina casava1.7 software used for basecalling
sequenced read were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence, then mapped mm8 whole genome using bowtie v0.12.2 with parameters
Assembly: mm8
Supplementary files format and content: tab-delimited text files included raw counts for each sample
Supplementary files format and content: tab-delimited text files included TPM values for each sample

source_name: plasma

extract_protocol:
4 mL venous blood was drawn in the morning, anti-coagulated with ethylene diamine tetraacetic acid (EDTA), and centrifuged at 1600 g and 4°C to collect the plasma. After centrifugation again, the plasma was stored at -80°C
RNA libraries were prepared for sequencing using standard Illunina protocols

value: plasma

tag: disease

value: Healthy


title: F123 GAM library f123_1NP_GAM171130_E03_1_S21_R1_001


title: F123 GAM library f123_1NP_GAM171130_E02_1_S13_R1_001


title: TNFa_IFNg_YKL_24h_3h_B1_rep3

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D07

value: Blood

value: primary


title: patient36_1y

description:
Library name: sample_62
Column name in counts.csv: sample_62


title: patient36_day100

description:
Library name: sample_61
Column name in counts.csv: sample_61


title: TNFa_IFNg_24h_B3_rep3

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D06

value: Differentiated macrophages


title: patient36_day0

description:
Library name: sample_60
Column name in counts.csv: sample_60


title: plasma, CON3


title: plasma, CON1


title: F123 GAM library f123_1NP_GAM171130_E01_1_S5_R1_001


title: vehicle_B1_rep3

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D05

value: unknown


title: F123 GAM library f123_1NP_GAM171130_D10_1_S76_R1_001


title: plasma, CON2


title: TNFa_IFNg_YKL_24h_6h_B1_rep2

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D04


title: F123 GAM library f123_1NP_GAM171130_D09_1_S68_R1_001


title: plasma, OSHAS5

value: OSAHS


title: patient35_day100

description:
Library name: sample_58
Column name in counts.csv: sample_58


title: patient35_1y

description:
Library name: sample_59
Column name in counts.csv: sample_59


title: TNFa_IFNg_YKL_24h_3h_B1_rep2

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D03


title: plasma, OSHAS4


title: F123 GAM library f123_1NP_GAM171130_D08_1_S60_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip

value: mouse embryonic stem cells


title: patient35_day0

description:
Library name: sample_57
Column name in counts.csv: sample_57


title: plasma, OSHAS3


title: TNFa_IFNg_24h_B1_rep2

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D02


title: patient8_1y

description:
Library name: sample_56
Column name in counts.csv: sample_56


title: F123 GAM library f123_1NP_GAM171130_D07_1_S52_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM171130_D11_1_S84_R1_001

value: male


title: vehicle_B1_rep2

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_D01


title: F123 GAM library f123_1NP_GAM171130_D06_1_S44_R1_001


title: plasma, OSHAS2


title: patient8_day100

description:
Library name: sample_55
Column name in counts.csv: sample_55

value: whole blood


title: F123 GAM library f123_1NP_GAM171130_D04_1_S28_R1_001


title: SNU638 cell, IP-YTHDF1, IFN-γ, biol rep 2

city: Seoul

first: Dongjun

last: Jang

address: 103 Daehak-ro (Yeongeon-dong), Jongno-gu

country: South Korea

institute: Seoul National University

data_processing:
Trimmed sequence reads were mapped to GRCh38 using STAR (v. 2.7.3a)
Read count extraction and normalization were performed using CLAM
Assembly: GRCh38
Supplementary files format and content: Tab-separated csv files includes annotated peaks for RIP sample

source_name: Stomach

growth_protocol: SNU638 cells were maintained in RPMI supplemented with 10 % fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5 % CO2 at 37C

extract_protocol:
RNA bound to YTHDF1 was harvested using Magna RIP RNA-Binding Protein Immunoprecipitation kit  (Merck).
RNA libraries for RNA-seq were prepared using SMARTer Stranded RNA library (Ribo-Zero) following manufacturer’s protocols

treatment_protocol: SNU638 cells were overexpressed YTHDF1 and preincubated in serum free medium for 24 hour and treated with 10 ng/ml IFN-γ for 24 h

value: Stomach

value: Gastric cancer cell

value: IFN-γ


title: plasma, OSHAS1


title: TNFa_IFNg_YKL_24h_6h_B2_rep1

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_C12

value: Male


title: patient8_day0

description:
Library name: sample_54
Column name in counts.csv: sample_54

value: placebo sugar pills


title: TNFa_IFNg_YKL_24h_3h_B2_rep1

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_C11


title: patient27_1y

description:
Library name: sample_53
Column name in counts.csv: sample_53


title: F123 GAM library f123_1NP_GAM171130_D03_1_S20_R1_001


title: patient27_day100

description:
Library name: sample_52
Column name in counts.csv: sample_52


title: SNU638 cell, Input, IFN-γ, biol rep 2

value: Input


title: F123 GAM library f123_1NP_GAM171130_D02_1_S12_R1_001


title: vehicle_B2_rep1

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_C09

value: vehicle


title: SNU638 cell, IP-YTHDF1, IFN-γ, biol rep 1


title: F123 GAM library f123_1NP_GAM171130_D01_1_S4_R1_001


title: patient27_day0

description:
Library name: sample_51
Column name in counts.csv: sample_51


title: SNU638 cell, Input, IFN-γ, biol rep 1


title: patient26_1y

description:
Library name: sample_50
Column name in counts.csv: sample_50


title: TNFa_IFNg_24h_B2_rep1

description:
TNF, IFNg polarized human macrophages YKL time course experiment
Sample_DD-10584_2021_05_26_C10


title: F123 GAM library f123_1NP_GAM171130_C11_1_S83_R1_001


title: Kang-PKCzsh-TGFb3

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th Ave NE

institute: Hormel Institute

data_processing:
Illumina Real time Analysis and CASAVA software 1.8.2 were used for basecalling.
Raw reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control checks on raw sequence data for each sample were performed with FastQC.  Read mapping was performed via Bowtie (v2.2.4.0) using the Human genome (hg19) as reference
Raw reads for each gene generated from the HiSeq2500 sequencer were subjected to statistical analysis using the edgeR package and cuffdiff2 package based on two selection criteria (fold change ≥ 2 & FDR < 0.05, and fold change ≥ 1.5 & FDR < 0.01).  The overlap of these four criteria was used to identify genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver hepatic stellate cells

growth_protocol: Cells obtained from ScienCell were cultured with DMEM supplemented with 10% FBS, streptomycin and penicillin.

extract_protocol:
RNA samples were isolated from the cells by using RNeasy Plus Mini kit (Qiagen, 74134) and gDNA Eliminator Columns were used to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing by using standard Illumina protocols

treatment_protocol: Cells were first subjected to serum-starvation for overnight and were incubated with TGFbeta1 (5 ng/ml) for 24 hours

value: Liver hepatic stellate cells

value: Cell expressing PKCz shRNA + TGFbeta

tag: time


title: patient26_day100

description:
Library name: sample_49
Column name in counts.csv: sample_49


title: patient26_day0

description:
Library name: sample_48
Column name in counts.csv: sample_48


title: Kang-PKCzsh-TGFb2


title: Kang-PKCzsh-TGFb1


title: F123 GAM library f123_1NP_GAM171130_C08_1_S59_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: patient25_1y

description:
Library name: sample_47
Column name in counts.csv: sample_47


title: Kang-PKCzsh-3

value: Cell expressing PKCz shRNA


title: F123 GAM library f123_1NP_GAM171130_C07_1_S51_R1_001


title: F123 GAM library f123_1NP_GAM171130_C06_1_S43_R1_001


title: Kang-PKCzsh-2


title: Kang-PKCzsh-1


title: patient24_day100

description:
Library name: sample_43
Column name in counts.csv: sample_43


title: F123 GAM library f123_1NP_GAM171130_C10_1_S75_R1_001


title: Kang-NT-TGFb2

value: Cell expressing control shRNA + TGFbeta


title: Kang-NT2

value: Cell expressing control shRNA


title: patient23_1y

description:
Library name: sample_41
Column name in counts.csv: sample_41


title: patient23_day0

description:
Library name: sample_39
Column name in counts.csv: sample_39


title: Kang-NT-TGFb3


title: F123 GAM library f123_1NP_GAM171130_C03_1_S19_R1_001


title: F123 GAM library f123_1NP_GAM171130_C04_1_S27_R1_001


title: Kang-NT1


title: F123 GAM library f123_1NP_GAM171130_C05_1_S35_R1_001


title: patient4_1y

description:
Library name: sample_38
Column name in counts.csv: sample_38


title: patient24_day0

description:
Library name: sample_42
Column name in counts.csv: sample_42


title: Kang-NT3


title: patient24_1y

description:
Library name: sample_44
Column name in counts.csv: sample_44


title: patient4_day100

description:
Library name: sample_37
Column name in counts.csv: sample_37


title: F123 GAM library f123_1NP_GAM171130_B10_1_S74_R1_001


title: GM170, liquid culture, 4.5hrs, 37 degrees celcius, rep4

city: Dundee

first: Sarah

last: Coulthurst

address: Dow Street

country: United Kingdom

institute: University of Dundee, School of Life Sciences

description: 75bp read length

data_processing:
Data was analysed using the RNA-seq analysis pipeline multi-bacpipe (github.com/apredeus/multi-bacpipe). Basic read quality control was performed with FastQC v0.11.8. 75bp Illumina reads were aligned to 1043 (GCA_946406265) using STAR v2.6.0c43 using “--alignIntronMin 20 --alignIntronMax 19 --outFilterMultimapNmax 20” options. 1051 is near-identical to 1043 (separated by 3 SNPs), and possess the same plasmids.
Assembly: GCA_946406265
Supplementary files format and content: Tab-delimited text file with transcript counts per million for each locus tag in GCA_946406265

organism: Serratia marcescens

source_name: Bacterial cell

growth_protocol: Cells grown in 25ml LB to an OD600 of 2.5 (~4.5 hours) at 37 degrees celcius with shaking, normalised to an OD600 of

extract_protocol:
Cultures were mixed with 10 ml ice-cold stop solution (19% ethanol, 1% acidic phenol pH 4.3) and incubated on ice for 30 min. Cells were then recovered by centrifugation, resuspended in 1 mL TRIzol and transferred into a 2 mL phase-lock tube, and 400 μL chloroform was added and immediately mixed for 10 s. After incubation for 2 min at room temperature, the suspension was separated by centrifugation for 15 min at 20,000 g. The upper phase containing the RNA (∼500 μL) was transferred into a 1.5 mL microcentrifuge tube, 450 μL isopropanol was added, and the suspension was mixed by inverting and then incubated at room temperature for 30 min. The precipitated RNA was recovered by centrifugation for 30 min at 20,000 g and washed in 350 μL 70% ethanol. Following a further centrifugation step (10 min, 20,000 g), the pellet was air-dried, resuspended in RNase-free water and stored at -80°C.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high fidelity DNA polymerase.  cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.

value: Bacterial cell

tag: protocol

value: 37 degrees celcius


title: Kang-NT-TGFb1


title: patient25_day100

description:
Library name: sample_46
Column name in counts.csv: sample_46


title: F123 GAM library f123_1NP_GAM171130_C02_1_S11_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM171130_B11_1_S82_R1_001

value: male


title: F123 GAM library f123_1NP_GAM171130_C09_1_S67_R1_001


title: GM170, liquid culture, 4.5hrs, 37 degrees celcius, rep3

description: 75bp read length


title: patient23_day100

description:
Library name: sample_40
Column name in counts.csv: sample_40

value: whole blood


title: F123 GAM library f123_1NP_GAM171130_B09_1_S66_R1_001


title: F123 GAM library f123_1NP_GAM171130_B08_1_S58_R1_001


title: patient25_day0

description:
Library name: sample_45
Column name in counts.csv: sample_45


title: patient4_day0

description:
Library name: sample_36
Column name in counts.csv: sample_36


title: F123 GAM library f123_1NP_GAM171130_C01_1_S3_R1_001


title: F123 GAM library f123_1NP_GAM171130_B07_1_S50_R1_001


title: patient7_1y

description:
Library name: sample_35
Column name in counts.csv: sample_35


title: GM170, liquid culture, 4.5hrs, 37 degrees celcius, rep2

description: 75bp read length


title: patient7_day100

description:
Library name: sample_34
Column name in counts.csv: sample_34


title: F123 GAM library f123_1NP_GAM171130_B06_1_S42_R1_001


title: GM162, liquid culture, 4.5hrs, 37 degrees celcius, rep4

description: 75bp read length


title: patient7_day0

description:
Library name: sample_33
Column name in counts.csv: sample_33


title: GM170, liquid culture, 4.5hrs, 37 degrees celcius, rep1

description: 75bp read length


title: patient5_1y

description:
Library name: sample_32
Column name in counts.csv: sample_32


title: GM162, liquid culture, 4.5hrs, 37 degrees celcius, rep3

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_B02_1_S10_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: patient5_day100

description:
Library name: sample_31
Column name in counts.csv: sample_31


title: F123 GAM library f123_1NP_GAM171130_B01_1_S2_R1_001


title: patient5_day0

description:
Library name: sample_30
Column name in counts.csv: sample_30


title: GM162, liquid culture, 4.5hrs, 37 degrees celcius, rep2

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A11_1_S81_R1_001


title: patient34_day0

description:
Library name: sample_27
Column name in counts.csv: sample_27


title: patient34_day100

description:
Library name: sample_28
Column name in counts.csv: sample_28


title: GM161, liquid culture, 4.5hrs, 37 degrees celcius, rep3

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A10_1_S73_R1_001


title: GM161, liquid culture, 4.5hrs, 37 degrees celcius, rep1

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A09_1_S65_R1_001


title: patient33_1y

description:
Library name: sample_26
Column name in counts.csv: sample_26


title: patient33_day0

description:
Library name: sample_25
Column name in counts.csv: sample_25


title: F123 GAM library f123_1NP_GAM171130_A08_1_S57_R1_001


title: 1051, liquid culture, 4.5hrs, 37 degrees celcius, rep4

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_B05_1_S34_R1_001


title: 1051, liquid culture, 4.5hrs, 37 degrees celcius, rep3

description: 75bp read length


title: GM162, liquid culture, 4.5hrs, 37 degrees celcius, rep1

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_B04_1_S26_R1_001


title: F123 GAM library f123_1NP_GAM171130_A06_1_S41_R1_001


title: F123 GAM library f123_1NP_GAM171130_B03_1_S18_R1_001


title: patient20_day100

description:
Library name: sample_23
Column name in counts.csv: sample_23


title: patient20_1y

description:
Library name: sample_24
Column name in counts.csv: sample_24


title: GM161, liquid culture, 4.5hrs, 37 degrees celcius, rep2

description: 75bp read length


title: patient34_1y

description:
Library name: sample_29
Column name in counts.csv: sample_29


title: GM161, liquid culture, 4.5hrs, 37 degrees celcius, rep4

description: 75bp read length


title: patient20_day0

description:
Library name: sample_22
Column name in counts.csv: sample_22


title: 1043, liquid culture, 4.5hrs, 37 degrees celcius, rep4

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A05_1_S33_R1_001


title: 1051, liquid culture, 4.5hrs, 37 degrees celcius, rep1

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A04_1_S25_R1_001


title: patient22_1y

description:
Library name: sample_21
Column name in counts.csv: sample_21


title: patient22_day100

description:
Library name: sample_20
Column name in counts.csv: sample_20


title: 1043, liquid culture, 4.5hrs, 37 degrees celcius, rep3

description: 75bp read length


title: patient22_day0

description:
Library name: sample_19
Column name in counts.csv: sample_19


title: 1043, liquid culture, 4.5hrs, 37 degrees celcius, rep2

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A03_1_S17_R1_001


title: F123 GAM library f123_1NP_GAM171130_A02_1_S9_R1_001


title: 1043, liquid culture, 4.5hrs, 37 degrees celcius, rep1

description: 75bp read length


title: F123 GAM library f123_1NP_GAM171130_A01_1_S1_R1_001


title: 1051, liquid culture, 4.5hrs, 37 degrees celcius, rep2

description: 75bp read length


title: patient11_day100

description:
Library name: sample_17
Column name in counts.csv: sample_17


title: F123 GAM library f123_1NP_GAM171130_A07_1_S49_R1_001


title: patient11_1y

description:
Library name: sample_18
Column name in counts.csv: sample_18


title: Liver, AAOT treated female NOG-TKm30 mice [NOG_AAOT]

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.38.
Trimmed reads were mapped to the transcript in the human  reference sequence mm10 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Liver

extract_protocol:
RNeasy Mini Kit was performed according to the manufacturer's instructions.
The sequencing libraries were prepared from 200 ng of total RNA with MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) according to the manufacturer's instructions.

treatment_protocol: Female 22-week-old C57BL mice were treated with 0 or 0.3% acetoaceto-o-toluidide (AAOT) for 4 weeks.

value: Liver

tag: strain background

value: female

value: AAOT

value: 4 weeks


title: F123 GAM library f123_1NP_GAM171024_H05_1_S40_R1_001


title: Liver, control female NOG-TKm30 mice [NOG_C]

value: Control


title: patient11_day0

description:
Library name: sample_16
Column name in counts.csv: sample_16

value: placebo sugar pills


title: F123 GAM library f123_1NP_GAM171024_E01_1_S5_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: patient9_1y

description:
Library name: sample_15
Column name in counts.csv: sample_15


title: F123 GAM library f123_1NP_GAM171024_D01_1_S4_R1_001


title: patient9_day100

description:
Library name: sample_14
Column name in counts.csv: sample_14


title: patient9_day0

description:
Library name: sample_13
Column name in counts.csv: sample_13


title: F123 GAM library f123_1NP_GAM171024_C01_1_S3_R1_001


title: F123 GAM library f123_1NP_GAM171024_B01_1_S2_R1_001


title: Pt25_Baseline

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner

data_processing: Raw CEL files were imported in Transcriptome Analysis Console software version 4.0.2 and pre-processed using the gene-level signal space transformation – robust multiarray average (SST-RMA) method.

label: Biotin

source_name: Pre-treatment HER2-positive breast cancer tumor core biopsy

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

extract_protocol: Total RNA from FFPE tissue sections was extracted using Qiazol (Qiagen).

treatment_protocol: Neo-adjuvant chemotherapy (anthracycline-taxane) plus trastuzumab (T). All patients received chemotherapy and T administered at 3-week intervals for six cycles.

tag: patient

tag: timepoint

value: Baseline

value: increase


title: Pt21_Baseline


title: F123 GAM library f123_1NP_GAM171024_A01_1_S1_R1_001

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.

tag: cell line

tag: cell type


title: patient32_day0

description:
Library name: sample_10
Column name in counts.csv: sample_10


title: F123 GAM library f123_0NP_GAM190122_H12_2_S192_R1_001

tag: genotype

tag: Sex


title: F123 GAM library f123_1NP_GAM171024_F01_1_S6_R1_001


title: patient32_day100

description:
Library name: sample_11
Column name in counts.csv: sample_11

tag: tissue


title: Pt2_Post

source_name: Post-neodjuvant therapy HER2-positive breast cancer tumor surgical sample

value: Post

value: decrease


title: Pt28_Baseline


title: Pt28_Post


title: patient31_1y

description:
Library name: sample_9
Column name in counts.csv: sample_9

tag: treatment


title: patient31_day100

description:
Library name: sample_8
Column name in counts.csv: sample_8


title: Pt26_Baseline


title: patient31_day0

description:
Library name: sample_7
Column name in counts.csv: sample_7


title: F123 GAM library f123_0NP_GAM180914_B09_1_S66_R1_001


title: F123 GAM library f123_0NP_GAM180812_H05_1_S40_R1_001


title: Pt22_Baseline


title: Pt27_Post


title: F123 GAM library f123_0NP_GAM180812_B06_2_S138_R1_001


title: patient21_1y

description:
Library name: sample_6
Column name in counts.csv: sample_6


title: patient32_1y

description:
Library name: sample_12
Column name in counts.csv: sample_12


title: naïve ESC in PXGL, Erlotinib, Rep2

first: Chunsheng

last: Han

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
The sequencing reads were mapped to the human genome (UCSC hg19) with TopHat (v2.1.1).
The mRNA expression levels were calculated by Cufflinks (v2.0.1).
The differentially expressed genes were identified with the Cuffdiff package.
Assembly: UCSC hg19
Supplementary files format and content: *.xlsx: Excel files include FPKM values for each Sample.

source_name: embryonic stem cells

extract_protocol:
RNAs were isolated using Trizol.
RNA libraries for RNA-seq were prepared using the KAPA Hyper Prep Kits (KK8504) following manufacturer's protocols.

value: embryonic stem cells

tag: condition

value: PXGL

value: Erlotinib, 1uM


title: F123 GAM library f123_0NP_GAM180716_H12_1_S96_R1_001

value: mouse embryonic stem cells


title: naïve ESC in PXGL, Erlotinib, Rep1


title: Pt23_Baseline


title: patient21_day100

description:
Library name: sample_5
Column name in counts.csv: sample_5


title: F123 GAM library f123_0NP_GAM190122_A12_1_S89_R1_001

value: Hybrid F1 S129/Jae and Cast


title: Pt26_Post


title: naïve ESC in PXGL, Afatinib, Rep1

value: Afatinib, 1uM


title: Pt22_Post


title: F123 GAM library f123_0NP_GAM180716_H03_2_S120_R1_001

value: male


title: F123 GAM library f123_0NP_GAM180716_B12_2_S186_R1_001


title: patient10_1y

description:
Library name: sample_3
Column name in counts.csv: sample_3

value: whole blood


title: naïve ESC in PXGL, Afatinib, Rep2


title: F123 GAM library f123_0NP_GAM180410_G06_1_S47_R1_001


title: Pt2_Baseline


title: naïve ESC in PXGL, control, Rep1


title: patient10_day0

description:
Library name: sample_1
Column name in counts.csv: sample_1


title: naïve ESC in PXGL, control, Rep2


title: patient10_day100

description:
Library name: sample_2
Column name in counts.csv: sample_2


title: hEPSC in XF-LCDM, Erlotinib, Rep2

value: XF-LCDM


title: Pt27_Baseline


title: Pt21_Post


title: Pt23_Post


title: mRNA #8 6h 24950 R4

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

description:
GBEP004P
mRNAseq

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution.  Alignments of raw reads to SK1 genome. mRNA seq reads were processed similarly except not assigned to one genomic position and counts were rather distribute over the entire read.
Assembly: SK1 genome (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary files format and content: RPKM values

organism: Saccharomyces cerevisiae

growth_protocol: treatment: cells were transferred to sporulation media to induce sporulation then collected 3h or 6h post transfer

extract_protocol:
Cells were mixermilled with frozen buffer (20mM Tris pH8, 140mM KCl, 1.5mM MgCl2, 100ug/ml cycloheximide, 1% Trition X-100), buffer was thawed, spun at 3Kg  for 5 minutes, then supernatatant was spun at 20Kg for 10 minutes.
As described in Powers and Brar, 2021, using linker ligation, circularization
size selection of 28-31 nt for ribosome footprints, 50nt for mRNA, dephosphorylation, linker ligation, RT, circularization, PCR

treatment_protocol: Cells were pretreated for 1 minute with 100uM cyclohexamide

value: dbp1 delete (Cas9)

value: meiosis


title: F123 GAM library f123_0NP_GAM180410_B07_2_S146_R1_001

first: Alexander

address: Hannoversche Str., 28

institute: Max-Delbrueck Center for Molecular Medicine


title: patient21_day0

description:
Library name: sample_4
Column name in counts.csv: sample_4

data_processing:
The reads were mapped to the human genome (GRCh38.p10) using HISAT2 v2.1.0 and counted with featureCounts from Subread v1.6.3, using gene coordinates from Ensembl 88.
Assembly: GRCh38.p10 and Ensembl 88
Supplementary files format and content: Csv file "counts.csv" includes gene counts for each sample

extract_protocol:
Total RNA was isolated from the blood using the Preserved Blood RNA Purification Kit I (Norgen Biotek, Thorold, Canada) according to the manufacturer’s instructions. DNAse treatment was included as recommended.
RNA was prepared for sequencing using TruSeq RNA library prep kits (Illumina) and sequenced with 2×75 bp paired-end configuration on the HiSeq3000 platform (Illumina)


title: F123 GAM library f123_0NP_GAM180410_C10_1_S75_R1_001


title: hEPSC in XF-LCDM, Erlotinib, Rep1


title: mRNA #7 3h 24950 R4

description:
GBEP004O
mRNAseq


title: F123 GAM library f123_0NP_GAM180410_B06_2_S138_R1_001


title: Pt24_Post


title: hEPSC in XF-LCDM, Afatinib, Rep2


title: Pt24_Baseline


title: mRNA #6 6h 24955 R4

description:
GBEP004N
mRNAseq

value: WT


title: F123 GAM library f123_0NP_GAM180410_A07_2_S145_R1_001


title: hEPSC in XF-LCDM, Afatinib, Rep1


title: mRNA #5 3h 24955 R4

description:
GBEP004M
mRNAseq


title: F123 GAM library f123_0NP_GAM180123_B06_2_S138_R1_001


title: hEPSC in XF-LCDM, control, Rep2

value: Control


title: Pt3_Baseline

value: Baseline


title: F123 GAM library f123_0NP_GAM180207_H05_1_S40_R1_001


title: Pt3_Post

value: increase


title: hEPSC in XF-LCDM, control, Rep1


title: F123 GAM library f123_0NP_GAM180123_A12_2_S185_R1_001


title: mRNA #3 3h 24950 R2

description:
GBEP004K
mRNAseq


title: Pt25_Post

value: Post


title: H1-ESC in mTeSR, Erlotinib, Rep2

value: mTeSR


title: mRNA #2 6h 24955 R3

description:
GBEP004J
mRNAseq


title: H1-ESC in mTeSR, Erlotinib, Rep1

value: embryonic stem cells


title: mRNA #1 3h 24955 R3

description:
GBEP004I
mRNAseq


title: Pt5_Post


title: H1-ESC in mTeSR, Afatinib, Rep2


title: F123 GAM library f123_0NP_GAM180116_H06_2_S144_R1_001


title: FP #8 6h 24950 R4

description:
GBEP004H
ribosome footprints

molecule: other


title: F123 GAM library f123_0NP_GAM180115_H12_1_S96_R1_001


title: Pt1_Post


title: F123 GAM library f123_0NP_GAM171221_H12_1_S96_R1_001


title: FP #7 3h 24950 R4

description:
GBEP004G
ribosome footprints


title: FP #6 6h 24955 R4

description:
GBEP004F
ribosome footprints


title: H1-ESC in mTeSR, control, Rep2


title: Pt5_Baseline


title: Pt4_Post

value: decrease


title: Pt1_Baseline


title: H1-ESC in mTeSR, control, Rep1


title: Pt4_Baseline


title: Pt9_Baseline


title: F123 GAM library f123_0NP_GAM171221_H06_1_S48_R1_001


title: FP #5 3h 24955 R4

description:
GBEP004E
ribosome footprints


title: mRNA #4 6h 24950 R2

description:
GBEP004L
mRNAseq


title: F123 GAM library f123_0NP_GAM171221_H04_2_S128_R1_001


title: PBMCs from Donor N at the ART timepoint

first: Rasmi

address: 503 Robert Grant Avenue

institute: Walter Reed Army Institute of Research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing: Generate FASTQ files using Cell Ranger mkfastq

extract_protocol:
Total PBMC were washed, resuspended in PBS plus 0.5% FBS, and processed for scRNA-seq.
PBMC suspensions were prepared using the Chromium NextGEM Single Cell 5’ v1.1 Kit and the Chromium Controller (both 10x Genomics, CA) per manufacturer’s instructions.

value: Blood

value: PBMC

value: ART


title: FP #3 3h 24950 R2

description:
GBEP004D
ribosome footprints


title: PBMCs from Donor M at the ART timepoint

description: 10x Genomics


title: FP #4 6h 24950 R2

description:
GBEP004C
ribosome footprints


title: F123 GAM library f123_0NP_GAM171214_H02_1_S16_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_0NP_GAM171221_H02_2_S112_R1_001

value: male


title: Pt9_Post


title: H1-ESC in mTeSR, Afatinib, Rep1

value: Afatinib, 1uM


title: PBMCs from Donor L at the ART timepoint

description: 10x Genomics


title: FP #2 6h 24955 R3

description:
GBEP004B
ribosome footprints


title: PBMCs from Donor K at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171221_H06_2_S144_R1_001


title: FP #1 3h 24955 R3

description:
GBEP004A
ribosome footprints


title: Pt10_Post


title: Pt8_Post


title: F123 GAM library f123_0NP_GAM171211_H12_2_S192_R1_001


title: PBMCs from Donor J at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171211_H12_1_S96_R1_001


title: 2xdbp1 r2 fp

description:
GBEP008L
ribosome footprints

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint or mRNA reads were assigned to one genomic position based on a-site analysis of fragment length distribution.  Alignments of raw reads to SK1 genome. mRNA seq reads were processed similarly except not assigned to one genomic position and counts were rather distribute over the entire read.
Assembly: SK1 genome (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary files format and content: RPKM values

growth_protocol: treatment: cells were grown in YEPD with aeration at 30C and harvested at OD 0.6

value: four copies of DBP1 under DED1 regulatory regions


title: ded1 r2 fp

description:
GBEP008M
ribosome footprints

value: DED1 under DED1 regulatory regions


title: PBMCs from Donor I at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171211_H06_1_S48_R1_001


title: F123 GAM library f123_0NP_GAM171211_H06_2_S144_R1_001


title: PBMCs from Donor H at the ART timepoint

description: 10x Genomics


title: Pt8_Baseline


title: Pt32_Post


title: PBMCs from Donor G at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171130_H12_1_S96_R1_001


title: dbp1 r1 fp

description:
GBEP008K
ribosome footprints

value: DBP1 under DED1 regulatory regions


title: ded1 r1 fp

description:
GBEP008J
ribosome footprints


title: F123 GAM library f123_0NP_GAM171130_H11_1_S88_R1_001


title: PBMCs from Donor F at the ART timepoint

description: 10x Genomics


title: Pt10_Baseline


title: F123 GAM library f123_0NP_GAM171130_H06_1_S48_R1_001


title: dbp1 r2 fp

description:
GBEP008N
ribosome footprints


title: 2xdbp1 r1 fp

description:
GBEP008I
ribosome footprints


title: PBMCs from Donor E at the ART timepoint

description: 10x Genomics


title: Pt6_Baseline


title: dbp1 r2 mrna

description:
GBEP008F
mRNAseq


title: PBMCs from Donor C at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171130_G12_1_S95_R1_001


title: Pt32_Baseline


title: PBMCs from Donor D at the ART timepoint

description: 10x Genomics


title: Pt7_Post


title: 2xdbp1 r2 mrna

description:
GBEP008D
mRNAseq


title: PBMCs from Donor B at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171120_H09_1_S72_R1_001


title: ded1 r2 mrna

description:
GBEP008E
mRNAseq


title: Pt31_Baseline


title: F123 GAM library f123_0NP_GAM171120_H04_1_S32_R1_001


title: PBMCs from Donor A at the ART timepoint

description: 10x Genomics


title: F123 GAM library f123_0NP_GAM171120_H12_1_S96_R1_001


title: dbp1 r1 mrna

description:
GBEP008C
mRNAseq


title: Pt7_Baseline


title: ded1 r1 mrna

description:
GBEP008B
mRNAseq


title: F123 GAM library f123_0NP_GAM171120_H02_1_S16_R1_001