title: shSLC25A1, Day 2, 30

first: Michael

middle: S

last: Chimenti

address: 431 Newton Road

department: Iowa Institute of Human Genetics

data_processing:
Barcoded samples were pooled and sequenced using an Illumina NovaSeq 6000 in the Iowa Institute of Human Genetics (IIHG) Genomics Core Facility. Paired-end reads were demultiplexed and converted from the native Illumina BCL format to FASTQ format using a custom python workflow wrapper to Illumina’s ‘bcl2fastq’ conversion utility.  FASTQ data were processed with nf-core/rnaseq (v3.12), a best-practices pipeline available at the open-source ‘nf-core’ project (https://nf-co.re/, Nextflow version 22.10). Reads from the samples were aligned against the mouse reference genome ‘GRCh38’ using the STAR aligner and quantified with ‘salmon’. Samtools was used in conjunction with Qualimap and MultiQC to inspect alignment results. Length-normalized gene-level counts from the STAR/salmon pipeline were used for differential gene expression analysis with DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-separated counts

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer's protocols.

value: mucociiliary differentiation

tag: knockdown

tag: treatment

value: Day 2


title: F123 GAM library f123_1NP_GAM180223_B04_1_S26_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: F123 GAM library f123_1NP_GAM180223_B05_2_S130_R1_001


title: Airway BCs of healthy control3

city: Shanghai

first: Tao

last: Ren

address: No. 600, Yi Shan Road

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

library_source: transcriptomic single cell

data_processing:
The sequencing platform is novaseq 6000. After the data is off the machine, RTA (real time analysis) is used to convert it into the original BCL file, and the version is v3.4.4; It is split by bcl2fastq (btq) software and converted into FQ, version v2.19. Fastp software is used for quality control, version 0.19.7, involving the parameter fastp-G-Q5-U50-N 15-L150.We applied BD Rhapsody Analysis pipeline (Version:1.8 https://hub.docker.com/r/bdgenomics/rhapsody) with default parameter to align reads and generate feature-barcode matrices. The reads were mapped to hg38 genome (GENCODE version 29) utilizing STAR mapping with customized parameter from BD Rhapsody Analysis pipeline. Seurat R package (version: 3.1.5) was used for cell normalization and regression according to the UMI counts of each cell, feature filtration and mitochondrial percentage, which in turn obtained the scaled data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: human bronchial epithelia

growth_protocol: Airway basal cells were isolated from the fifth-generation bronchi by fiberoptic bronchoscopy, cultured on a lawn of irradiated 3T3-J2 feeder as previously described (Rheinwald JG. and Green H., 1975). BCs with robust self-renewal properties were selectively expanded as colonies through cell passaging at 37°C in a 7.5% CO2 atmosphere.Distal airway basal cells were isolated from the margin of the excised lung tissue by mincing and enzymatic digestion, cultured on a lawn of irradiated 3T3-J2 feeder as previously described (Rheinwald JG. and Green H., 1975). Primary BCs were expanded as colonies at 37°C in a 7.5% CO2 atmosphere.Fibroblast were isolated from the margin of the excised lung tissue by mincing and enzymatic digestion, cultured in fibroblast medium. Primary fibroblast were expanded at 37°C in a 5% CO2 atmosphere.

extract_protocol:
BCs and  fibroblasts were resuspended and followed by single-cell capture and barcoding according to BD Rhapsody workflow.
RNA libraries were prepared for sequencing using BD Rhapsody Analysis pipeline (Version: 1.8) protocols.

tag: tissue

value: human bronchial epithelia

value: Airway basal cells

value: healthy


title: F123 GAM library f123_1NP_GAM180223_B03_2_S114_R1_001


title: shSLC25A1, Day 2, 28

city: Iowa City

state: IA

country: USA

institute: University of Iowa

library_source: transcriptomic

source_name: Airway basal cells


title: shSLC25A1, Day 2, 27


title: BMM_Pol2_YKL_3

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:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_YKL_3

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: Bone Marrow

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: Bone Marrow

value: primary

value: Bone Marrow derived macrophages

value: C57BL/6 LysMcre/cre

tag: age

tag: batch

tag: antibodies

value: 2 mkg, Bethyl, A304-405A


title: shSLC25A1, Day 2, 29


title: F123 GAM library f123_1NP_GAM180223_B02_1_S10_R1_001


title: F123 GAM library f123_1NP_GAM180223_B03_1_S18_R1_001


title: BMM_Pol2_YKL_1

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_YKL_1


title: F123 GAM library f123_1NP_GAM180223_B02_2_S106_R1_001


title: F123 GAM library f123_1NP_GAM180223_B01_1_S2_R1_001


title: BMM_Pol2_LPS_YKL_3

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_LPS_YKL_3


title: F123 GAM library f123_1NP_GAM180223_B01_2_S98_R1_001


title: CART_rep3

city: Memphis

first: Yogesh

last: Dhungana

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Gene expression was quantified as fragments per kilobase of transcript per million (FPKM) mapped reads using RSEM v.1.2.28PP with the GRCm38.p6 and annotation file (Gencode v.30)
Assembly: mm10
Supplementary files format and content: normalized count matrix

molecule: total RNA

source_name: CD19 CAR T cells

extract_protocol:
For in vivo comparison of CAR-T cells and tumors, mice were engrafted with CR or GPR65 KO tumors and treated with CAR-T cells 7 days later. Spleens were harvested 4 days after CAR-T treatment and RFP+ tumor cells and Thy1.1+ CAR-T cells were isolated by FACS.
For total RNA-seq, library was constructed from RNA using Illumina TrueSeq stranded mRNA library prep kit and sequenced using the HiSeq or NovaSeq platforms (2 × 101-bp paired-end reads)

value: CD19 CAR T cells


title: BMM_Pol2_LPS_YKL_1

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_LPS_YKL_1


title: F123 GAM library f123_1NP_GAM180223_A11_2_S177_R1_001


title: F123 GAM library f123_1NP_GAM180223_A12_2_S185_R1_001


title: shSLC25A1, Day 2, 26


title: F123 GAM library f123_1NP_GAM180223_A09_2_S161_R1_001


title: BMM_Pol2_LPS_3

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_LPS_3


title: shControl, Day 2, 25

value: shControl


title: F123 GAM library f123_1NP_GAM180223_A10_2_S169_R1_001


title: BMM_Pol2_DMSO_3

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_DMSO_3


title: BMM_Pol2_DMSO_1

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_DMSO_1


title: F123 GAM library f123_1NP_GAM180223_A09_1_S65_R1_001


title: F123 GAM library f123_1NP_GAM180223_A07_2_S145_R1_001


title: BMM_Pol2_LPS_1

description:
Pol2 chipseq in mouse macrophages treated with LPS, YKS or both
Rogatsky-DD-14439_2023_06_13_Pol2_LPS_1


title: F123 GAM library f123_1NP_GAM180223_A08_2_S153_R1_001


title: shControl, Day 2, 24


title: shControl, Day 2, 22


title: F123 GAM library f123_1NP_GAM180223_A06_2_S137_R1_001


title: F123 GAM library f123_1NP_GAM180223_A07_1_S49_R1_001


title: F123 GAM library f123_1NP_GAM180223_A03_1_S17_R1_001


title: F123 GAM library f123_1NP_GAM180223_A05_1_S33_R1_001


title: F123 GAM library f123_1NP_GAM180223_A02_2_S105_R1_001


title: NELF_BMM_YKL_3

description:
NELF-E ChIPseq in YKL treated mouse macrophages
Rogatsky-XC-11769_2022_01_12_NELF_Seq_mouse_BMM_YKL_3

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


title: shSLC25A1, Day 1, 20

value: Day 1


title: F123 GAM library f123_1NP_GAM180223_A03_2_S113_R1_001


title: F123 GAM library f123_1NP_GAM180223_A01_2_S97_R1_001


title: NELF_BMM_YKL_1

description:
NELF-E ChIPseq in YKL treated mouse macrophages
Rogatsky-XC-11769_2022_01_12_NELF_Seq_mouse_BMM_YKL_1


title: shSLC25A1, Day 1, 19

value: mucociiliary differentiation


title: F123 GAM library f123_1NP_GAM180223_A01_1_S1_R1_001


title: F123 GAM library f123_1NP_GAM180207_H11_1_S88_R1_001


title: NELF_BMM_DMSO_3

description:
NELF-E ChIPseq in YKL treated mouse macrophages
Rogatsky-XC-11769_2022_01_12_NELF_Seq_mouse_BMM_DMSO_3


title: shSLC25A1, Day 1, 18


title: F123 GAM library f123_1NP_GAM180207_H09_1_S72_R1_001


title: shControl, Day 2, 23

value: Day 2


title: F123 GAM library f123_1NP_GAM180207_H08_1_S64_R1_001

value: mouse embryonic stem cells


title: NELF_BMM_DMSO_1

description:
NELF-E ChIPseq in YKL treated mouse macrophages
Rogatsky-XC-11769_2022_01_12_NELF_Seq_mouse_BMM_DMSO_1


title: shSLC25A1, Day 1, 17


title: F123 GAM library f123_1NP_GAM180207_H07_1_S56_R1_001

value: Hybrid F1 S129/Jae and Cast


title: shControl, Day 2, 21


title: shSLC25A1, Day 1, 16


title: WT_PBS_3

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12766_2022_07_15_WT_PBS_3_BMM

value: male


title: shControl, Day 1, 15


title: input_WT

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_input_BMM

value: 2 mkg rabbit IgG (Thermo Fisher Scientific)


title: NELF_BMM_YKL_2

description:
NELF-E ChIPseq in YKL treated mouse macrophages
Rogatsky-XC-11769_2022_01_12_NELF_Seq_mouse_BMM_YKL_2


title: F123 GAM library f123_1NP_GAM180207_H02_1_S16_R1_001


title: WT_PBS_2

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_PBS_2_BMM


title: F123 GAM library f123_1NP_GAM180207_G11_1_S87_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: shControl, Day 1, 14

value: Airway basal cells


title: F123 GAM library f123_1NP_GAM180207_H01_1_S8_R1_001


title: shControl, Day 1, 13


title: F123 GAM library f123_1NP_GAM180207_G10_1_S79_R1_001


title: WT_PBS_1

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_PBS_1_BMM


title: F123 GAM library f123_1NP_GAM180207_G08_1_S63_R1_001


title: shControl, Day 1, 12


title: F123 GAM library f123_1NP_GAM180207_H10_1_S80_R1_001


title: F123 GAM library f123_1NP_GAM180207_G07_1_S55_R1_001


title: shControl, Day 1, 11


title: WT_60m_LPS_2

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_60m_LPS_2_BMM


title: F123 GAM library f123_1NP_GAM180207_G05_1_S39_R1_001


title: F123 GAM library f123_1NP_GAM180207_G04_1_S31_R1_001


title: WT_60m_LPS_1

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_60m_LPS_1_BMM


title: F123 GAM library f123_1NP_GAM180207_H03_1_S24_R1_001


title: F123 GAM library f123_1NP_GAM180207_H04_1_S32_R1_001


title: F123 GAM library f123_1NP_GAM180207_H06_1_S48_R1_001


title: shSLC25A1, Day 0, 10

value: Day 0


title: F123 GAM library f123_1NP_GAM180207_G01_1_S7_R1_001


title: F123 GAM library f123_1NP_GAM180207_G03_1_S23_R1_001


title: WT_30m_LPS_3

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12766_2022_07_15_WT_30m_LPS_3_BMM

value: Bone Marrow


title: F123 GAM library f123_1NP_GAM180207_G02_1_S15_R1_001


title: WT_30m_LPS_2

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_30m_LPS_2_BMM

value: primary


title: shSLC25A1, Day 0, 8


title: F123 GAM library f123_1NP_GAM180207_F11_1_S86_R1_001


title: shSLC25A1, Day 0, 9


title: F123 GAM library f123_1NP_GAM180207_G09_1_S71_R1_001


title: F123 GAM library f123_1NP_GAM180207_F10_1_S78_R1_001


title: F123 GAM library f123_1NP_GAM180207_F09_1_S70_R1_001


title: WT_30m_LPS_1

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_WT_30m_LPS_1

value: Bone Marrow derived macrophages


title: shSLC25A1, Day 0, 7


title: WT_60m_LPS_3

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12766_2022_07_15_WT_60m_LPS_3_BMM

value: C57BL/6 LysMcre/cre


title: F123 GAM library f123_1NP_GAM180207_F08_1_S62_R1_001


title: shSLC25A1, Day 0, 6


title: input_KO

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_input_BMM

value: C57BL/6 LysMcre/cre-Nelfbfl/fl

value: 2mkg, rabbit IgG (Thermo Fisher Scientific)


title: F123 GAM library f123_1NP_GAM180207_G06_1_S47_R1_001


title: F123 GAM library f123_1NP_GAM180207_F06_1_S46_R1_001


title: F123 GAM library f123_1NP_GAM180207_F05_1_S38_R1_001


title: shControl, Day 0, 5

value: shControl


title: KO_PBS_2

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_PBS_2_BMM

value: 2 mkg, Bethyl, A304-405A


title: F123 GAM library f123_1NP_GAM180207_F07_1_S54_R1_001


title: KO_PBS_3

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12766_2022_07_15_KO_PBS_3_BMM


title: F123 GAM library f123_1NP_GAM180207_F03_1_S22_R1_001


title: F123 GAM library f123_1NP_GAM180207_F02_1_S14_R1_001


title: shControl, Day 0, 3


title: F123 GAM library f123_1NP_GAM180207_F01_1_S6_R1_001


title: F123 GAM library f123_1NP_GAM180207_E10_1_S77_R1_001


title: shControl, Day 0, 4


title: KO_60m_LPS_2

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_60m_LPS_2_BMM


title: F123 GAM library f123_1NP_GAM180207_E09_1_S69_R1_001


title: KO_PBS_1

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_PBS_1_BMM


title: F123 GAM library f123_1NP_GAM180207_E11_1_S85_R1_001


title: shControl, Day 0, 1


title: F123 GAM library f123_1NP_GAM180207_E07_1_S53_R1_001


title: shControl, Day 0, 2


title: F123 GAM library f123_1NP_GAM180207_E06_1_S45_R1_001


title: KO_60m_LPS_1

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_60m_LPS_1_BMM


title: KO_60m_LPS_3

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12766_2022_07_15_KO_60m_LPS_3_BMM


title: F123 GAM library f123_1NP_GAM180207_E04_1_S29_R1_001


title: F123 GAM library f123_1NP_GAM180207_E08_1_S61_R1_001


title: COiMg_biol rep 2

city: NEW YORK

first: Alice

last: Buonfiglioli

state: NY

address: 1468 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Demultiplexing
Assembly: GRCh38
Supplementary files format and content: h5 files containing the cellbender-processed counts for each barcode.

source_name: cerebral organoids

growth_protocol: cerebral organoids mantained in Maturation Media (Stem Cell Technologies) in humified atmosphere with 5% CO2 at 37C.

extract_protocol:
mechanical dissociation of the freshly collected tissue, cell isolation by a series of centrifuges
single cell library preparation was done using 10x Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits (10x Genomics).

value: cerebral organoids

tag: condition

value: COiMg

value: unstimulated


title: F123 GAM library f123_1NP_GAM180207_E03_1_S21_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180207_F04_1_S30_R1_001

value: Hybrid F1 S129/Jae and Cast


title: KO_30m_LPS_2

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_30m_LPS_2_BMM

value: male


title: F123 GAM library f123_1NP_GAM180207_E01_1_S5_R1_001


title: F123 GAM library f123_1NP_GAM180207_E02_1_S13_R1_001


title: COiMg_biol rep 1


title: F123 GAM library f123_1NP_GAM180207_D11_1_S84_R1_001


title: KO_30m_LPS_1

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12631_2022_06_24_KO_30m_LPS_1_BMM


title: F123 GAM library f123_1NP_GAM180207_D10_1_S76_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_GAM180207_D09_1_S68_R1_001


title: YKL_LPS_12h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C8

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: 12 weeks


title: CO_biol rep 1

value: CO


title: F123 GAM library f123_1NP_GAM180207_D08_1_S60_R1_001


title: YKL_LPS_6h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C7


title: Human hypothalamus Sample q65KC_C1_a

city: Cambridge

first: Georgina

last: Dowsett

address: Box 289

country: United Kingdom

institute: Institute of Metabolic Science

data_processing:
Fastq data was aligned to the Human GRCh38 genome using Spaceranger version 2.0.1. The final matrix is stored in HDF5
Assembly: GRCh38
Supplementary files format and content: The gene expression data matrices are stored in standard HDF5 format
Library strategy: Spatial Transcriptomics

source_name: Hypothalamus

extract_protocol:
FFPE samples were sectioned using a microtome in an RNase free environment at 5μm and stored at room temp prior to performing spatial transcriptomics.
10X Genomics Visium CytAssist Spatial Transcriptomics (version 2) reagents and protocol for FFPE tissues was used to create the libraries

value: Hypothalamus


title: F123 GAM library f123_1NP_GAM180207_D07_1_S52_R1_001


title: F123 GAM library f123_1NP_GAM180207_D06_1_S44_R1_001


title: F123 GAM library f123_1NP_GAM180207_D05_1_S36_R1_001


title: Human hypothalamus Sample IbV8d_b1_b


title: YKL_LPS_1h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C6

value: Bone Marrow


title: F123 GAM library f123_1NP_GAM180207_D04_1_S28_R1_001


title: KO_30m_LPS_3

description:
Pol II chipSeq in WT and NELF-cKO  LPS-treated macrophages
Rogatsky-XC-12766_2022_07_15_KO_30m_LPS_3_BMM

value: primary


title: Human hypothalamus Sample bT5r4_b8


title: F123 GAM library f123_1NP_GAM180207_D03_1_S20_R1_001


title: F123 GAM library f123_1NP_GAM180207_D02_1_S12_R1_001


title: YKL_0h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C5

value: Bone Marrow derived macrophages


title: Human hypothalamus Sample JpLuT_a7


title: F123 GAM library f123_1NP_GAM180207_D01_1_S4_R1_001


title: F123 GAM library f123_1NP_GAM180207_C11_1_S83_R1_001


title: CO_biol rep 2


title: Human hypothalamus Sample OgTiF_b6


title: LPS_6h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C3


title: F123 GAM library f123_1NP_GAM180207_C09_1_S67_R1_001


title: Human hypothalamus Sample JpLuT_a5


title: F123 GAM library f123_1NP_GAM180207_C10_1_S75_R1_001


title: LPS_1h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C2


title: F123 GAM library f123_1NP_GAM180207_C08_1_S59_R1_001


title: F123 GAM library f123_1NP_GAM180207_C07_1_S51_R1_001


title: F123 GAM library f123_1NP_GAM180207_C05_1_S35_R1_001


title: Human hypothalamus Sample oYtkk_b4


title: F123 GAM library f123_1NP_GAM180207_C06_1_S43_R1_001


title: Human hypothalamus Sample hp9Yr_a3


title: F123 GAM library f123_1NP_GAM180207_C04_1_S27_R1_001


title: DMSO_0h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C1


title: F123 GAM library f123_1NP_GAM180207_C03_1_S19_R1_001


title: YKL_LPS_12h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B9


title: YKL_LPS_6h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B8


title: F123 GAM library f123_1NP_GAM180207_C02_1_S11_R1_001


title: F123 GAM library f123_1NP_GAM180207_C01_1_S3_R1_001


title: YKL_LPS_1h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B6


title: LPS_12h_Rep3

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_C4


title: KT-186

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Illumina DRAGEN BCL, then fastq files were analysed with salmon to get counts data. The counts were imported to DESeq2.
Assembly: GRCh38
Supplementary files format and content: DESeq2 raw counts

source_name: blood

growth_protocol: total blood drawn into TEMPUS tubes

extract_protocol:
TEMPUR S tubes and TEMPUS spin extraction kit
whole transcriptome library preparartion with ribominus depletion for rRNA

value: blood

value: female

tag: dgn

value: HC

tag: subdgn


title: Human hypothalamus Sample oYtKK_b2


title: F123 GAM library f123_1NP_GAM180207_B10_1_S74_R1_001


title: YKL_0h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B5


title: F123 GAM library f123_1NP_GAM180207_B09_1_S66_R1_001


title: KT-180


title: KT-166


title: F123 GAM library f123_1NP_GAM180207_B05_1_S34_R1_001


title: F123 GAM library f123_1NP_GAM180207_B08_1_S58_R1_001


title: LPS_12h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B4


title: KT-161


title: F123 GAM library f123_1NP_GAM180207_B06_1_S42_R1_001


title: LPS_6h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B3


title: F123 GAM library f123_1NP_GAM180207_B04_1_S26_R1_001


title: F123 GAM library f123_1NP_GAM180207_B03_1_S18_R1_001


title: F123 GAM library f123_1NP_GAM180207_B01_1_S2_R1_001


title: LPS_1h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B2


title: F123 GAM library f123_1NP_GAM180207_A11_1_S81_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: KT-144


title: DMSO_0h_Rep2

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_B1


title: F123 GAM library f123_1NP_GAM180207_B07_1_S50_R1_001


title: YKL_LPS_12h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A8


title: F123 GAM library f123_1NP_GAM180207_A09_1_S65_R1_001


title: KT-143


title: F123 GAM library f123_1NP_GAM180207_A07_1_S49_R1_001


title: YKL_LPS_6h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A7


title: F123 GAM library f123_1NP_GAM180207_A06_1_S41_R1_001


title: KT-132


title: jejunum_low_feed_efficiency_RNA_rep2

city: Wuhan

first: yi

last: huang

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
TrimGalore was first used to remove adapters and quality control with default parameters. The cleaned reads were then aligned to the pig susScr11 reference genome using STAR. Gene expression levels were quantified using RSEM to calculate TPM values.
Adapter sequences were trimmed from the raw ATAC-seq reads using TrimGalore. The trimmed reads were then aligned to the pig susScr11 reference genome using Bowtie2. SAMtools and Picard were used to filter the BAM files, removing reads with low mapping quality, unmapped reads, singletons, secondary alignments, and PCR duplicates. Subsequently, BEDTools was used to remove reads mapped to the mitochondrial genome and convert the filtered BAM file into a BEDPE format, which was then extracted as tagAlign. MACS2 was used to call peaks, generating narrowPeak files.
Assembly: susScr11
Supplementary files format and content: bigwig

organism: Sus scrofa

source_name: Jejunum

extract_protocol:
Total RNA was extracted from jejunal tissues using TRIzol reagent.Jejunal tissue samples were ground into fine powder in liquid nitrogen.  Approximately 0.02g of tissue was used for ATAC-seq library preparation.
RNA integrity was assessed by measuring the RNA Integrity Number (RIN), which was required to be more than 7. Subsequently, mRNA was purified using the VAHTS mRNA Capture Beads (Vazyme N401) kit. A strand-specific RNA-seq library was constructed using the Vazyme NR605 kit, which involved the following steps: first-strand cDNA synthesis, second-strand cDNA synthesis, adapter ligation, PCR enrichment, and purification using magnetic beads. The constructed strand-specific sequencing library was then sequenced on an Illumina NovaSeq 6000 platform.  The tissue was suspended in 1mL of pre-cooled DPBS and mixed by pipetting. 1mL of lysis buffer (50mM HEPES, pH 7.5, 140mM NaCl, 1mM EDTA, pH 8.0, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) was added and mixed by pipetting. The mixture was incubated on ice for 10 minutes with gentle inversion. After centrifugation at 1000×g for 5 minutes at 4°C, the supernatant was discarded. The cell pellet was resuspended in 1mL of DPBS and filtered through a 70μm cell strainer into a new tube. Trypan blue was added at a ratio of 1:4 to the cell suspension and mixed. Cells were counted using an inverted microscope. 50,000 cells were collected and centrifuged at 500×g for 10 minutes at 4°C, the supernatant was removed and the cell pellet was resuspended in 50μl of Transposition mixture (25μl 2×TD buffer, 16.5μl PBS, 0.5μl 1% Digitonin, 0.5μl 10% Tween-20, 5μl H2O, 2.5μl Tn5 enzyme). The mixture was gently mixed and incubated at 37°C, 1000 rpm for 1 hour in a thermomixer. After incubation, DNA was purified using the DNA Clean & Concentrator-5 Kit (TD413-50) from Zymo Research. For library amplification, the following reaction was performed: 10μl 5×TAB, 1μl TAE, 2.5μl each of Index 1 and Index 2, 14μl nuclease-free ddH2O, and 20μl DNA fragments. The PCR conditions were as follows: 72°C for 3min, 98°C for 30s, followed by 9 cycles of 98°C for 10s, 60°C for 30s, and 72°C for 30s, with a final extension at 72°C for 5min. The amplified DNA fragments were purified using KAPA Pure Beads (Roche) to obtain fragments of 150-800bp for sequencing. Sequencing was then performed on an Illumina NovaSeq 6000 platform.

value: Jejunum

value: low feed


title: KT-160


title: F123 GAM library f123_1NP_GAM180207_A05_1_S33_R1_001


title: KT-121


title: F123 GAM library f123_1NP_GAM180207_B02_1_S10_R1_001


title: LPS_12h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A4


title: F123 GAM library f123_1NP_GAM180207_A04_1_S25_R1_001


title: KT-108


title: jejunum_high_feed_efficiency_RNA_rep2

value: high feed


title: KT-149


title: F123 GAM library f123_1NP_GAM180207_A08_1_S57_R1_001


title: KT-107


title: F123 GAM library f123_1NP_GAM180207_A10_1_S73_R1_001


title: jejunum_high_feed_efficiency_RNA_rep1


title: YKL_0h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A5


title: KT-104


title: LPS_6h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A3


title: jejunum_low_feed_efficiency_ATAC_rep2


title: F123 GAM library f123_1NP_GAM180207_A02_1_S9_R1_001


title: LPS_1h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A2


title: jejunum_low_feed_efficiency_ATAC_rep1


title: DMSO_0h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A1


title: KT-103


title: YKL_LPS_1h_Rep1

description:
YKL, LPS Mouse  time course experiment
Sample_Rogatsky.DD.10074_2021_02_26_A6


title: jejunum_low_feed_efficiency_RNA_rep1


title: jejunum_high_feed_efficiency_ATAC_rep2


title: F123 GAM library f123_1NP_GAM180123_H12_2_S192_R1_001


title: male_wd_6

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Quality of reads were analyzed using FastQC
Reads were trimmed of adapters and quality trimmed using Cutadapt with the following options: -a AGATCGGAAGAGCACACGTC -A AGATCGGAAGAGCGTCGTGT --nextseq-trim=20 --minimum-length 50
Genome indices were generated using the GRCm39 mouse genome downloaded from GENCODE (Release M27) using STAR sequence aligner with the following options: --sjdbOverhang 99.
Reads were aligned using STAR sequence aligner with the following options: --readFilesCommand zcat –outSAMtype BAM SortedByCoordinate --outSAMunmapped Within.
Reads were counted using HTSeq assigning reads to genes using the following options: -s no -r pos -f bam.
DESeq2 R package was used to perform differential gene expression analysis using the design ~Batch + Diet for comparison of MatOb compared to control controlling for litter and different dates of collection within each sex group.
Assembly: GRCm39
Supplementary files format and content: txt file containing space delimited counts for each gene from each library

source_name: Bone marrow

growth_protocol: Animals were housed in a temperature-controlled, 12-hour light-dark cycled animal care facility with free access to water and food.

extract_protocol:
Bone marrow was harvested by crushing from femurs, tibiae, and hips and lineage depletion was performed using the EasySepTM Mouse Hematopoietic Progenitor Cell Isolation kit (STEMCELL Technologies). LSK cells from P21 offspring were collected by FACS directly into RLT Plus lysis buffer and RNA was harvested (Qiagen RNeasy Micro Plus Kit).
mRNA-seq libraries were prepared using samples with RIN > 8.0 with NEBNext Ultra Low Input/Single Cell RNA sequencing library preparation kit.

treatment_protocol: Four to five-week-old C57BL/6J female mice acclimatized to the animal facility for >72 hours prior to randomization. Female dams were randomly assigned to regular chow (2018SX; Inotiv, IL) as a control, or Western diet (TD.88137; Inotiv, IL) to induce maternal obesity. The female mice received the same diet for four weeks prior to mating, and through pregnancy as well as during lactating period.

value: Bone marrow

value: LSK

tag: maternal diet

value: western diet


title: KT-96


title: KT-97


title: male_wd_5


title: jejunum_high_feed_efficiency_ATAC_rep1


title: Pig oocyte, scRNA-Seq, in-vivo, cell AC

city: Murcia

first: Francisco

last: Huertas

address: C/ Campus Universitario de Espinardo Nº7 (Edificio CEEIM)

country: Spain

institute: Marbyt - Smart Solutions for Biotechnology

data_processing:
Demultiplexed reads were trimmed using TrimGalore! for removing Nextera XT adapters.
Trimmed sequence reads were mapped to Sscrofa11.1 using STARsolo.
Read count and post-processing were performed with Seurat.
Assembly: Sscrofa11.1
Supplementary files format and content: STAR processed files (barcodes.tsv, genes.tsv and matrix.mtx). Information about gene reads by sample

source_name: Oocyte

extract_protocol:
Matured oocytes were individually lysed and flash-frozen in 5 μL of RLT Plus buffer (Qiagen) at −80°C until further use. Both DNA and RNA from lysate were separated using the G&T-seq and Smartseq2 protocol (Angermueller et al., 2016). Magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were employed to capture polyadenylated mRNA from cell lysates
Single-cell RNA-seq libraries were prepared from 100 to 400 pg of cDNA using the Nextera XT Kit (Illumina), per the manufacturer's instructions but with one-fifth volumes. All 96 single-cell RNA-seq libraries were pooled together and sequenced on the Illumina NextSeq platform to an average depth of 4.2 million reads, using paired-end 75 bp read-length settings

treatment_protocol: In vitro versus in vivo matured porcine oocytes

tag: breed

value: Landrace-Large-White

value: Oocyte

value: WT

value: in-vivo


title: F123 GAM library f123_1NP_GAM180123_H11_2_S184_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: Pig oocyte, scRNA-Seq, in-vivo, cell AB


title: male_wd_4


title: F123 GAM library f123_1NP_GAM180207_A03_1_S17_R1_001


title: Pig oocyte, scRNA-Seq, in-vivo, cell AA


title: male_wd_3


title: KT-79


title: Pig oocyte, scRNA-Seq, in-vivo, cell Z


title: male_wd_2


title: KT-75


title: F123 GAM library f123_1NP_GAM180207_A01_1_S1_R1_001


title: F123 GAM library f123_1NP_GAM180123_H08_2_S160_R1_001


title: F123 GAM library f123_1NP_GAM180123_H07_2_S152_R1_001


title: male_wd_1


title: Pig oocyte, scRNA-Seq, in-vivo, cell X


title: KT-99


title: F123 GAM library f123_1NP_GAM180123_H06_2_S144_R1_001


title: KT-70


title: Pig oocyte, scRNA-Seq, in-vivo, cell V


title: male_control_6

value: control


title: KT-68

value: blood


title: F123 GAM library f123_1NP_GAM180123_H10_2_S176_R1_001


title: F123 GAM library f123_1NP_GAM180123_H05_2_S136_R1_001


title: Pig oocyte, scRNA-Seq, in-vivo, cell U


title: male_control_5


title: F123 GAM library f123_1NP_GAM180123_H04_2_S128_R1_001


title: Pig oocyte, scRNA-Seq, in-vivo, cell T


title: KT-65

value: female


title: male_control_4


title: F123 GAM library f123_1NP_GAM180123_H09_2_S168_R1_001


title: KT-62

value: HC


title: F123 GAM library f123_1NP_GAM180123_H03_2_S120_R1_001


title: KT-92


title: male_control_3


title: Pig oocyte, scRNA-Seq, in-vivo, cell S


title: KT-60


title: F123 GAM library f123_1NP_GAM180123_H02_2_S112_R1_001


title: KT-56


title: Pig oocyte, scRNA-Seq, in-vivo, cell R


title: F123 GAM library f123_1NP_GAM180123_H01_2_S104_R1_001


title: F123 GAM library f123_1NP_GAM180123_G12_2_S191_R1_001


title: male_control_1


title: Pig oocyte, scRNA-Seq, in-vivo, cell Q


title: Pig oocyte, scRNA-Seq, in-vivo, cell O


title: KT-52


title: female_wd_5


title: Pig oocyte, scRNA-Seq, in-vivo, cell N


title: female_wd_6


title: F123 GAM library f123_1NP_GAM180123_G11_2_S183_R1_001


title: KT-49


title: F123 GAM library f123_1NP_GAM180123_G10_2_S175_R1_001


title: KT-47


title: F123 GAM library f123_1NP_GAM180123_G09_2_S167_R1_001


title: female_wd_3


title: Pig oocyte, scRNA-Seq, in-vivo, cell M


title: Pig oocyte, scRNA-Seq, in-vivo, cell L


title: KT-43


title: male_control_2


title: KT-57


title: female_wd_2


title: female_wd_4


title: Pig oocyte, scRNA-Seq, in-vivo, cell K


title: F123 GAM library f123_1NP_GAM180123_G07_2_S151_R1_001


title: KT-25


title: female_wd_1


title: Pig oocyte, scRNA-Seq, in-vivo, cell J


title: F123 GAM library f123_1NP_GAM180123_G06_2_S143_R1_001


title: KT-19


title: Pig oocyte, scRNA-Seq, in-vivo, cell C


title: F123 GAM library f123_1NP_GAM180123_G05_2_S135_R1_001


title: KT-20


title: female_control_5


title: female_control_6


title: Pig oocyte, scRNA-Seq, in-vivo, cell B


title: KT-18


title: female_control_4


title: F123 GAM library f123_1NP_GAM180123_G04_2_S127_R1_001


title: Pig oocyte, scRNA-Seq, in-vivo, cell A


title: F123 GAM library f123_1NP_GAM180123_G03_2_S119_R1_001


title: KT-17


title: F123 GAM library f123_1NP_GAM180123_G08_2_S159_R1_001


title: female_control_3


title: Pig oocyte, scRNA-Seq, in-vitro, cell 26

value: in-vitro


title: F123 GAM library f123_1NP_GAM180123_G02_2_S111_R1_001


title: Pig oocyte, scRNA-Seq, in-vitro, cell 25


title: F123 GAM library f123_1NP_GAM180123_G01_2_S103_R1_001


title: KT-10


title: female_control_1


title: KT-15


title: Pig oocyte, scRNA-Seq, in-vitro, cell 24


title: F123 GAM library f123_1NP_GAM180123_F12_2_S190_R1_001


title: LP4

city: San Antonio

first: Venkatesh

last: Kumaresan

state: TX

address: 3.230, BSE Building, One UTSA circle

department: Molecular Microbiology and Immunology

institute: The University of Texas at San Antonio

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger v7.1.0
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Bone marrow derived macrophages

extract_protocol:
Bone marrow cells were collected from the C3H/HeN mice, pooled, and centrifuged at 500xg for 5 minutes at 4°C. Supernatant was discarded. Cell pellet was resuspended in 4 mL of 0.14M Ammonium Chloride solution to lyse RBC. After 5 minutes incubation at RT, RBC lysis was stopped by adding 8 mL of fresh R10. Centrifuged at 500xg for 5 minutes at 4°C. Supernatant was discarded. Cells were resuspended in 40 mL of R10+15%LCCM and passed through 70 µM cell strainer. 10 mL of cell suspension was plated in each petri dish and incubated at 37°C. After 4 days, 70% media was replaced with fresh R10 media and incubated at 37°C. After 8 days of initial plating, the culture media was removed and washed with 10 mL of cold PBS twice and 2 mL of Accutase™ Cell Dissociation Reagent (Stem cell) was added, incubated at 37°C. After 20 minutes, plates were tapped well to detach the cells completely from the plate. BMDM cell suspension was supplemented with 4 mL of fresh R10 media and centrifuged at 500xg for 5 minutes. Supernatant was discarded. The cells were resuspended at 1x106 cells/mL concentration in fresh R10 media without Pen/Strep. In a non-treated 6-well plate, 1x106 BMDM were plated in each well. After overnight incubation, the cells were infected with 1 mL of BbLP (1 µg/mL) resuspended in R10 media. PBS treated BMDM was maintained as control. After 1 or 4 hpi, Cells were removed by accutase, washed with cold PBS and the viability of the cells were checked using Trypan Blue and counted using a hemocytometer. After viability check, the cells were used for RNA isolation.
10x Genomics single cell libraries were generated by the University of Texas at San Antonio (UTSA) Genomics Core. Cell suspensions were loaded into 10x Genomics microfluidics chips and onto the 10x Chromium to capture single cells in Gel Beads-in-emulsion (GEMs) reactions. 5000 cells/sample were targeted for capture in GEMs preceding library prep following manufacture’s recommendations for the 3’ Gene Expression v3 kit.

value: Bone marrow derived macrophages

tag: strain

value: 6-8 weeks

value: Female

value: Purified Borrelial lipoproteins for 4 hrs


title: Pig oocyte, scRNA-Seq, in-vitro, cell 22


title: KT-9


title: F123 GAM library f123_1NP_GAM180123_F11_2_S182_R1_001


title: LP1

description: 10x Genomics

value: Purified Borrelial lipoproteins for 1 hr


title: Pig oocyte, scRNA-Seq, in-vitro, cell 21

value: Landrace-Large-White


title: KT-6


title: F123 GAM library f123_1NP_GAM180123_F10_2_S174_R1_001


title: Pig oocyte, scRNA-Seq, in-vitro, cell 19

value: Oocyte


title: F123 GAM library f123_1NP_GAM180123_F09_2_S166_R1_001


title: Aged pulp cell, scRNAseq

city: ChangChun

first: Zhengwen

last: An

state: JiLin

address: HeGuang Road 763

department: Department of Oral Biology

institute: Jilin University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger (7.0.1). (https://www.10xgenomics.com)
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Incisor Pulp

extract_protocol:
Mouse mandibles were carefully dissected from 15 C57BL/6 mice aged 8-12 months, which representative of the early stages of aging, using precise dissection under a stereomicroscope. The surrounding bones and soft tissues were carefully removed with scalpels and fine-point tweezers. The incisor pulp, with minimal inclusion of dental epithelium, was isolated, fragmented, and immersed in cold PBS. Subsequently, these fragments were digested in α-MEM (Gibco) containing collagenase at 37°C for 30-45 mins
The single cell suspension was quantified and loaded into the 10X Chromium system, targeting approximately10,000 cells for barcoding in preparation for scRNA-seq using a Single Cell 5′ Library Kit (10X Genomics). Cells were successfully barcoded and their transcriptomes were sequenced using the  Illumina Novaseq System (Illumina, San Diego, CA).

value: Incisor Pulp

value: Dental pulp cell

value: WT


title: KT-4


title: Pig oocyte, scRNA-Seq, in-vitro, cell 20


title: UI

description: 10x Genomics

value: Untreated


title: AF

city: Beijing

first: Hua

last: Jin

address: Yong an Road 95

institute: Beijing Friendship Hospital

data_processing:
Basecalls were performed using Novaseq 6000 platform PE150.
After the library construction, Qubit 2.0 was used for preliminary quantification, and then Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, qPCR was used to accurately quantify the effective concentration of the library to ensure the quality of the library.
When the number of N in single-ended paired reads was greater than 3, or the base ratio with quality value＜5 was >=20%, the paired reads were removed. And when removing the adapter sequence, the adapter sequence must >= 8bp.
bigWig files were generated using Vaztme cloud CUT_Tag_tool.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: spleen and lymph node

extract_protocol:
FOXO1 antibody (Cat 2880T, CST) and Hyperactive Universal CUT & Tag Assay Kit (TD903-01, Vazyme) were used to extract binding site of FOXO1 according to the manufacturer’s instructions.
TruePrep Index Kit V2 (TD202, Vazyme) was used to amplify the cDNA libraries according to the manufacturer’s instructions.

value: spleen and lymph node

tag: chip antibody

value: FOXO1 antibody (Cat 2880T, CST)

value: T cell

value: Wild type


title: Pig oocyte, scRNA-Seq, in-vitro, cell 17


title: F123 GAM library f123_1NP_GAM180123_F08_2_S158_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: ALS-63

value: blood

value: MND

value: PBP


title: ALS-62

value: female

value: ALS


title: F123 GAM library f123_1NP_GAM180123_F07_2_S150_R1_001


title: female_control_2

value: Bone marrow

value: LSK

value: control


title: KT-16

value: HC


title: Pig oocyte, scRNA-Seq, in-vitro, cell 16

value: Landrace-Large-White

value: Oocyte

value: WT

value: in-vitro


title: AG

value: spleen and lymph node

value: Rabbit IgG

value: T cell

value: Wild type


title: ALS-61

value: blood

value: male


title: F123 GAM library f123_1NP_GAM180123_F06_2_S142_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: Pig oocyte, scRNA-Seq, in-vitro, cell 14


title: F123 GAM library f123_1NP_GAM180123_F05_2_S134_R1_001


title: RA-2

data_processing:
HISAT2 2.1.0 --dta –t –p 4
RNA samples were purified, fragmented, reverse transcribed, end-repaired. After sequenced adapters were added, the target fragments were recovered by magnetic bead screening, and PCR amplification was performed to complete the entire library preparation work.
After the library construction was completed, use Agilent2100 to detect the insert size of the library.
If insert size met the expectation, Bio-RAD CFX 96 fluorescent quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN were used to perform q-PCR to accurately quantify the effective concentration of the library (the effective concentration of the library was > 10nM) to ensure the quality of the library.
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
CD4+T cell converted DNT cells were treated with or without 400µM ATPgs for 6 hours. Or DNT cells were stimulated with or without 400µM adenosine for 6 hours. In addition, 250nM A2aR inhibitor stimulated DNT were treated with or without 400µM adenosine for 6 hours. Trizol reagent was used for collecting total RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: Pig oocyte, scRNA-Seq, in-vitro, cell 13


title: ALS-60

value: female

value: MND

value: PBP


title: ALS-59

value: ALS


title: ALS-58


title: Pig oocyte, scRNA-Seq, in-vitro, cell 9


title: RA-1


title: F123 GAM library f123_1NP_GAM180123_F03_2_S118_R1_001


title: F123 GAM library f123_1NP_GAM180123_F04_2_S126_R1_001


title: Pig oocyte, scRNA-Seq, in-vitro, cell 8


title: F123 GAM library f123_1NP_GAM180123_F02_2_S110_R1_001


title: ALS-57


title: R-2

value: anti-CD3/CD28 antibody+A2aR inhibitor


title: Pig oocyte, scRNA-Seq, in-vitro, cell 7

value: Landrace-Large-White


title: ALS-56


title: Pig oocyte, scRNA-Seq, in-vitro, cell 6

value: Oocyte


title: F123 GAM library f123_1NP_GAM180123_E12_2_S189_R1_001


title: F123 GAM library f123_1NP_GAM180123_F01_2_S102_R1_001


title: ADO-3

value: anti-CD3/CD28 antibody+adenosine


title: ALS-55


title: Pig oocyte, scRNA-Seq, in-vitro, cell 5

value: WT

value: in-vitro


title: RA-3

value: spleen and lymph node


title: ALS-54


title: F123 GAM library f123_1NP_GAM180123_E11_2_S181_R1_001


title: ADO-2

value: T cell


title: ALS-53


title: ADO-1

value: Wild type


title: Pig oocyte, scRNA-Seq, in-vitro, cell 4


title: Pig oocyte, scRNA-Seq, in-vitro, cell 3


title: ALS-52

value: blood

value: PMA


title: DNT-3

value: anti-CD3/CD28 antibody


title: F123 GAM library f123_1NP_GAM180123_E07_2_S149_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: DNT-1


title: R-3


title: Pig oocyte, scRNA-Seq, in-vitro, cell 1


title: F123 GAM library f123_1NP_GAM180123_E09_2_S165_R1_001


title: R-1


title: Pig oocyte, scRNA-Seq, in-vitro, cell 2


title: Hormone induced prostate tissue 3

city: GuiYang

first: XiaoHu

last: Tang

address: No. 83 Zhongshan East Road

institute: Guizhou Provincial People's Hospital

data_processing:
illumina HiSeg novaseq 6000 used for basecalling
Sequenced reads were filtered for Seqtk, and get clean Reads that can be used for data analysis, using the bowtie2 (version: 2-2.0.5), the Genome mapping was performed on post-pretreatment reads, which was more suitable for the sequencing data of the prokaryotic transcriptome. The comparison result generated by Mapping is the BAM file
Fragments Per Kilobase of exon model per Million mapped reads.We first apply HTSeq in TopHat than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
Supplementary files format and content: Excel file includes FPKM and  count values for each Sample

organism: Rattus norvegicus

source_name: prostate

growth_protocol: All the rats were kept in a standard laboratory environment (12/12 hours of light/dark cycle, 22±2 °C with 55±5% relative humidity), and allowed to consume standard laboratory pellets and water ad libitum.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.
The cDNA fragments afterwards through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Rats in the test group were subcutaneously implanted with 4 pellets (every pellet containing 25 mg testosterone and 2.5 mg estradiol) for 4 weeks and the control group only underwent skin incision and stapling.

value: BPH

value: prostate

value: induction of testosterone and estradiol


title: ALS-46

value: female

value: MND

value: PLS


title: ALS-45

value: ALS


title: WTATPgs-3

value: anti-CD3/CD28 antibody+ATPgs


title: F123 GAM library f123_1NP_GAM180123_E05_2_S133_R1_001


title: Hormone induced prostate tissue 1


title: F123 GAM library f123_1NP_GAM180123_E06_2_S141_R1_001


title: WTATPgs-2

value: spleen and lymph node


title: Hormone induced prostate tissue 2


title: ALS-44


title: F123 GAM library f123_1NP_GAM180123_E04_2_S125_R1_001


title: WTATPgs-1

value: T cell


title: F123 GAM library f123_1NP_GAM180123_E03_2_S117_R1_001


title: ALS-43


title: F123 GAM library f123_1NP_GAM180123_E10_2_S173_R1_001


title: Control prostate tissue 3

value: no induction of testosterone and estradiol


title: WT-3

value: Wild type


title: ALS-51

value: blood


title: F123 GAM library f123_1NP_GAM180123_E08_2_S157_R1_001


title: ALS-49


title: DNT-2

value: anti-CD3/CD28 antibody


title: ALS-42


title: F123 GAM library f123_1NP_GAM180123_E02_2_S109_R1_001

value: mouse embryonic stem cells


title: WT-2


title: WT-1


title: ALS-41

value: PMA


title: Control prostate tissue 1


title: a711r7

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Reads were aligned to the Ciona genome using STAR (version 2.7.10a) with the ‘--quantMode GeneCounts’ option to quantify reads per gene (Dobin et al., 2013). Exon annotation was taken from the KH.KH.Gene2013.gff3 file reprocessed for compatibility with STAR gene/exon format. ReadsPerGene files were merged to a single gene by cell type raw count matrix.
Assembly: Ciona robusta sequences and annotation were taken from the GHOST database (http://ghost.zool.kyoto-u.ac.jp/download_kh.html)
Supplementary files format and content: raw_counts.txt : STAR reads per gene quantification matrix for all cells (Dobin et al., 2013)

organism: Ciona robusta

extract_protocol:
Embryos were dissected on a 1.5% agarose-coated dish with a fine glass ‘hair’ smeared with cellular debris. A single isolated cell was transferred in 0.5μl of seawater into a 0.2ml PCR tube containing 9μl RNase-free water. After visual inspection of the presence of the cell under stereomicroscope, 1μl of 10x Reaction buffer (SMARTer Ultra Low Input RNA Kit, Takara Bio) was added and the tube was vortexed immediately and stored at -80°C before being processed for library preparation.
Indexed Illumina libraries were prepared using Nextera XT kits (Illumina) from cDNAs generated with SMARTer Ultra low input RNA kit (Takara Bio) according to manufacturers’ instructions. Sequencing was conducted in the UCA GenomiX genomics platform (Sophia Antipolis, France) using Illumina NextSeq500 system. For each library, single end 75bp reads were obtained with sequencing depth of around 8 million reads.

tag: developmental stage

value: 64-cell stage

tag: lineage

value: a

tag: replicate

value: embryo7/right side


title: a711r8

tag: cell type

value: embryo8/right side


title: ALS-39

value: female


title: F123 GAM library f123_1NP_GAM180123_D12_2_S188_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: genotype

value: Hybrid F1 S129/Jae and Cast

value: male


title: C8CART_host

data_processing:
The Cell Ranger (v.6.0.0) Single-Cell software suite (10X Genomics) was implemented to process raw sequencing data from the Illumina NovaSeq 6000 run
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: cell ranger count matrix for single cells in each sample

source_name: spleen

extract_protocol:
B6 mice were injected with CR or GPR65 KO tumor cells (i.v.) followed by treatment 7 days later with 10x106 activated CAR-T cells or mock PBS injection (retro-orbital). Spleens were harvested from untreated mice at day 7 and from CAR-T treated mice at day 11 after tumor engraftment. Processed spleens were stained and sorted to isolate CR or GPR65 KO tumor cells (RFP+), and the host immune cell compartment (RFP–Thy1.1–CD45.2+)
6000 cells were targeted from each sample using the 10X Chromium Next GEM Single Cell 5’ Reagent kits v2 (Dual Index). Cells were partitioned into droplets and barcoded using the Chromium Controller using Chip K. Reverse transcription, cDNA amplification, TCR amplification, fragmentation, adapter and sample index ligation were all done following the 10X CG000331 Rev C protocol. cDNA and libraries were quantified using the High Sense DNA chip on the Agilent Bioanalyzer. Libraries were pooled and sequenced on the NovaSeq 6000 using paired end reads as recommended by 10X genomics

tag: agent

value: 7-8 weeks

tag: tissue

value: spleen


title: C8GPR65KOCART_host

tag: age


title: ALS-35

tag: Sex

value: MND

value: ALS


title: F123 GAM library f123_1NP_GAM180123_D11_2_S180_R1_001


title: a711r6

value: embryo6/right side


title: F123 GAM library f123_1NP_GAM180123_D10_2_S172_R1_001


title: ALS-34


title: F123 GAM library f123_1NP_GAM180123_D09_2_S164_R1_001


title: ALS-32


title: a711r5

value: embryo5/right side


title: F123 GAM library f123_1NP_GAM180123_D08_2_S156_R1_001


title: C8GPR65KOuntreated


title: a711r3

value: embryo3/right side


title: ALS-33

value: blood


title: C8CART_tumor_CART


title: ALS-28


title: C8untreated

value: untreated


title: F123 GAM library f123_1NP_GAM180123_D07_2_S148_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180123_E01_2_S101_R1_001


title: Control prostate tissue 2

tag: condition

value: BPH

value: prostate

tag: treatment

value: no induction of testosterone and estradiol


title: a711r4

value: 64-cell stage

value: a

value: embryo4/right side


title: a710r8

value: embryo8/right side


title: ALS-26

value: female

tag: dgn

tag: subdgn


title: ALS-25


title: F123 GAM library f123_1NP_GAM180123_D06_2_S140_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: Bone marrow, HFD, 12m, rep1

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v6.1.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 40%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

extract_protocol:
Bone marrow was flushed and kept in MACS Tissue Storage Solution (Miltenyi Biotec). Samples were sieved through 40-μm cell strainers and centrifuged at 300 g for 5 min. Pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) for lysing red blood cells. Brain tissues were surgically removed and minced into small pieces (approximately 1 mm ) on ice and digested by 200 U/ml Papine (Diamond) and Cysteine-HCL (Sigma).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone marrow

value: bone marrow cells

value: wild type

value: 12-month HFD


title: F123 GAM library f123_1NP_GAM180123_D05_2_S132_R1_001

institute: Max-Delbrueck Center for Molecular Medicine


title: F123 GAM library f123_1NP_GAM180123_D04_2_S124_R1_001


title: Brain, HFD, 12m, rep1

description: 10x Genomics

source_name: Whole brain

value: Whole brain

value: brain cells


title: ALS-24

value: blood

value: MND

value: ALS


title: C8GPR65KOCART_tumor_CART

value: 7-8 weeks

value: spleen


title: Brain, CD, 12m, rep1

description: 10x Genomics

value: 12-month CD


title: a710r5

value: 64-cell stage

value: a

value: embryo5/right side


title: ALS-23

value: female

value: PMA


title: a710r4

value: embryo4/right side


title: F123 GAM library f123_1NP_GAM180123_D03_2_S116_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: Bone marrow, CD, 12m, rep1

description: 10x Genomics

value: Bone marrow

value: bone marrow cells

value: wild type


title: ALS-22

value: blood

value: MND


title: Brain, HFD, 7m, rep1

description: 10x Genomics

value: Whole brain

value: brain cells

value: 7-month HFD


title: F123 GAM library f123_1NP_GAM180123_D01_2_S100_R1_001


title: ALS-20

value: ALS


title: F123 GAM library f123_1NP_GAM180123_D02_2_S108_R1_001


title: a710r2

value: 64-cell stage

value: a

value: embryo2/right side


title: a710r3

value: embryo3/right side


title: F123 GAM library f123_1NP_GAM180123_C12_2_S187_R1_001


title: Bone marrow, HFD, 7m, rep1

description: 10x Genomics


title: ALS-19

value: female


title: Brain, CD, 7m, rep1

description: 10x Genomics

value: 7-month CD


title: a710r7

value: embryo7/right side


title: F123 GAM library f123_1NP_GAM180123_C11_2_S179_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: a710r1

value: embryo1/right side


title: ALS-18

value: blood


title: ALS-16

value: MND


title: aN31

value: 6-row neural plate stage

value: embryo3/left column2


title: F123 GAM library f123_1NP_GAM180123_C10_2_S171_R1_001


title: ALS-15


title: F123 GAM library f123_1NP_GAM180123_C09_2_S163_R1_001


title: olfactory epithelium, androstenone treatment, biol rep 4

city: Chengdu

first: Pei-Dong

last: Yang

address: 211 Gongping street

institute: Sichuan Agricultural University

description: Androstenone-treatment group-4

data_processing:
We applied fastp(version 0.23.1) for base quality filtering on raw data to obtain clean data
Read alignment and quantification on clean data using Kallisto(version 0.48.0)
Assembly: Sus_scrofa.Sscrofa11.1.cdna.all.fa
Supplementary files format and content: table-delimited text file includes raw counts for each Sample
Supplementary files format and content: table-delimited text file includes TPM values for each Sample

source_name: olfactory epithelium

extract_protocol:
RNA was extracted using Trizol (Invitrogen, USA, 15596018CN) according to the manufacturer's instructions
RNA-seq libraries were prepared following the NEBNext® UltraTM RNA Library Prep Kit (NEB, USA, 7530)

value: olfactory epithelium

value: androstenone treatment


title: AN24

value: A

value: embryo2*/right column2


title: a710r6

value: 64-cell stage

value: a

value: embryo6/right side


title: olfactory epithelium, androstenone treatment, biol rep 3

description: Androstenone-treatment group-3


title: F123 GAM library f123_1NP_GAM180123_C08_2_S155_R1_001

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28


title: ALS-12

value: PMA


title: aN_22

value: embryo2/left column1


title: olfactory epithelium, androstenone treatment, biol rep 2

description: Androstenone-treatment group-2


title: AN23

value: embryo2*/right column1


title: AN22

value: embryo2*/left column1


title: olfactory epithelium, androstenone treatment, biol rep 1

description: Androstenone-treatment group-1


title: F123 GAM library f123_1NP_GAM180123_C07_2_S147_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: ALS-11

value: blood

value: MND

value: ALS


title: olfactory epithelium, no solution treatment, biol rep 4

description: Control group-4

value: olfactory epithelium

value: no solution treatment


title: F123 GAM library f123_1NP_GAM180123_C06_2_S139_R1_001


title: AN21

value: 6-row neural plate stage

value: A

value: embryo2*/left column2


title: Bone marrow, CD, 7m, rep1

city: Shanghai

description: 10x Genomics

value: Bone marrow

value: bone marrow cells

value: wild type

value: 7-month CD


title: ALS-5


title: aN_21

value: a

value: embryo2/left column2


title: olfactory epithelium, no solution treatment, biol rep 3

description: Control group-3


title: ALS-7

value: female


title: ALS-2


title: F123 GAM library f123_1NP_GAM180123_C04_2_S123_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: olfactory epithelium, no solution treatment, biol rep 2

description: Control group-2


title: aN13

value: embryo1/right column1


title: aN_12

value: embryo1/left column1


title: ALS-1

value: blood

value: male

value: MND

value: ALS


title: F123 GAM library f123_1NP_GAM180123_C02_2_S107_R1_001


title: F123 GAM library f123_1NP_GAM180123_C03_2_S115_R1_001


title: PAO1WT3_run1

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

description:
BacWT3
bacteria_only_samples_run1.txt

data_processing:
reads were mapped to the human genome (hg19) using STAR mapping software
Unmapped reads were written into a new FastQ-file
Unmapped reads were then mapped against the PAO1 genome (NCBI: txid208964)
Gene counts were again assigned using FeatureCounts
Assembly: PAO1 genome (NCBI: txid208964)
Supplementary files format and content: tab delimited file with raw counts

organism: Pseudomonas aeruginosa

source_name: bacteria-only sample

extract_protocol:
RNA was isolated from the cultures using the MasterPure Complete DNA and RNA Purification Kit (Immunosource, Belgium) following manufacturer instructions. To remove all the gDNA, two additional rounds of DNase treatment were performed using TURBO DNase (ThermoFisher Scientific) following manufacturer’s protocol. RNA was subsequently isolated again using the MasterPure RNA isolation kit and the RNA was dissolved in MQ and stored at -80 °C until further use.
Truseq RNA stranded ribo-zero

value: bacterial cell

value: WT

value: bacteria only culture


title: olfactory epithelium, no solution treatment, biol rep 1

description: Control group-1

value: olfactory epithelium

value: no solution treatment


title: AN12

value: 6-row neural plate stage

value: A

value: embryo1*/left column1


title: F123 GAM library f123_1NP_GAM180123_C01_2_S99_R1_001


title: PAO1WT2_run1

description:
BacWT2
bacteria_only_samples_run1.txt


title: K27me3_siNC

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
Novagene used Illumina Novaseq 6000 platform for ChIP-seq
The clean reads were align to the reference genome sequnence using Bowtie2
Peak calling using Macs2 with default parameters
DiffBind (version 1.34.0) software was used for differential peak calculation, q value <= 0.05 was the threshold. The bigwig files were generated with Deeptools (version 3.4.3).
Assembly: NCBI, Homo_sapiens , GCF_000001405.39_GRCh38.p13
Supplementary files format and content: The bigwig files were generated with Deeptools (version 3.4.3).
Library strategy: CUT&Tag

growth_protocol: Cardiomyocyte AC16 cells were cultured in DMEM/F12 . DMEM/F12 supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Utilizing the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (TD903), we performed CUT&Tag experiments as follows: AC16 cells were harvested at room temperature and incubated with ConA Beads for 10 minutes. They were then incubated with anti-MLF1 (ABclonal, A13329), anti-SUZ12 antibody (CST, 3737S, 1:50), anti-EP300 (CST, #57625), anti-H3K27ac (CST, #4353S), or anti-H3K27me3 (CST, #9733) antibodies overnight at 4°C. On the next day, the samples were incubated with a secondary antibody at room temperature for 1h, followed by incubation with pA/G-Tnp for 1h.  After DNA purification with the MinElute kit, and the PCR was performed to amplify the library for 12 cycles and libraries were purified with the MinElute kit.
Amplified ChIP-seq libraries were sequenced on the Illumina Novaseq 6000 platform.

treatment_protocol: Medium without FBS was replaced before transfection. Negative control siRNA , Mlf1 siRNA, and SUZ12 siRNA were transfected into AC16 cells at ~70% confluence using jetPRIME® (Polyplus-transfection, NY, USA). After 12 h of transfection, fresh complete medium was replaced.

value: siRNA  Control


title: aN_11

value: a

value: embryo1/left column2


title: F123 GAM library f123_1NP_GAM180123_B12_2_S186_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: AN11

value: embryo1*/left column2


title: PAO1WT1_run1

description:
BacWT1
bacteria_only_samples_run1.txt


title: K27ac_siSUZ12


title: F123 GAM library f123_1NP_GAM180123_B11_2_S178_R1_001

value: male


title: PAO1QS3_run1

description:
BacQS3
bacteria_only_samples_run1.txt


title: F123 GAM library f123_1NP_GAM180123_C05_2_S131_R1_001


title: PAO1QS2_run1

description:
BacQS2
bacteria_only_samples_run1.txt


title: AM31

value: embryo3*/left column2


title: K27ac_siMLF1


title: K27ac_siNC


title: AM24

value: embryo2*/right column2


title: F123 GAM library f123_1NP_GAM180123_B10_2_S170_R1_001


title: K27me3_siSUZ12


title: F123 GAM library f123_1NP_GAM180123_B09_2_S162_R1_001


title: F123 GAM library f123_1NP_GAM180123_B08_2_S154_R1_001


title: AM22

value: embryo2*/left column1


title: PAO1QS1_run1

description:
BacQS1
bacteria_only_samples_run1.txt

value: bacterial cell


title: AM23

value: embryo2*/right column1


title: EP300_siSUZ12


title: K27me3_siMLF1


title: PAO1Pqs2_run1

description:
BacPqs2
bacteria_only_samples_run1.txt

value: bacteria only culture


title: AM21

value: embryo2*/left column2


title: EP300_siNC


title: F123 GAM library f123_1NP_GAM180123_B07_2_S146_R1_001


title: AM11

value: 6-row neural plate stage


title: MLF1_siSUZ12

value: MLF1 (ABclonal, A13329)


title: PAO1Pqs1_run1

description:
BacPqs1
bacteria_only_samples_run1.txt


title: PAO1WT3_run2

description:
bac3
bacteria_only_samples_run2.txt

value: WT


title: F123 GAM library f123_1NP_GAM180123_B04_2_S122_R1_001


title: aE31

value: embryo3/left column2


title: MLF1_siMLF1


title: PAO1WT2_run2

description:
bac2
bacteria_only_samples_run2.txt


title: MLF1_siNC

value: siRNA  Control


title: F123 GAM library f123_1NP_GAM180123_B02_2_S106_R1_001


title: PAO1WT1_run2

description:
bac1
bacteria_only_samples_run2.txt


title: aE22

value: a

value: embryo2/left column1


title: PAO1Pqs3_run1

description:
BacPqs3
bacteria_only_samples_run1.txt


title: Healthy lymph node [RNA-seq]

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description: Lymphnode

data_processing:
Data quality was controlled using FastQC followed by the removal of low-quality reads and adapter trimming with Atropos, sequences were aligned (GRCh38) using STAR, and post-alignment quality control was performed with MultiQC. Salmon was used for transcript quantification of protein-coding genes, expressed in variance stabilizing transformation (VST) counts. XY genes and low-expressed genes (with a mean count < 5) were filtered out of the processed data.
Assembly: GRCh38
Supplementary files format and content: Tab delimited *.txt with processed and filtered variance stabilizing transformation (VST) counts
Supplementary files format and content: Tab delimited *.txt with raw counts

source_name: Lymph node sample

growth_protocol: No growth; biobanked frozen samples.

extract_protocol:
The RNA was extracted using the AllPrep kit (Qiagen).
Pair ended 150 bp RNA sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit with RiboZero Gold treatment, and sequencing was performed using the Illumina NovaSeq 6000 system (Illumina, CA, USA).

value: Lymph node sample

tag: tissue type

value: Control

tag: cimp subgroup

value: CIMP low

tag: disease

value: Healthy


title: aE21

tag: developmental stage

value: embryo2/left column2


title: Sorted CD34+ from healthy blood donor [RNA-seq]

source_name: Peripheral blood sample

value: Peripheral blood sample


title: aE13

tag: lineage

value: embryo1/right column1


title: F123 GAM library f123_1NP_GAM180123_B01_2_S98_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: EP300_siMLF1

tag: chip antibody


title: F123 GAM library f123_1NP_GAM180123_A11_2_S177_R1_001

tag: cell type


title: Sorted CD3+ from healthy blood donor [RNA-seq]


title: mESC, primed pluripotency, WT, IGG, rep3

city: San Francisco

first: Harold

last: Marin

state: CA

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

institute: University of California San Francisco

description: Library name: WT_epi_IGG_3

data_processing:
Raw sequencing reads were mapped to the “soft masked” mm39 mouse genome using Bowtie2 version 2.3.5.1: -X 2000 -N 1 --local --dovetail.
SAMtools version 1.10 was used to keep properly paired, primary alignments and filter out unassembled contigs, read duplicates, and reads mapped to mitochondria.
RPKM signal coverage in 1kb and 10kb bins were calculated using the deepTools2 (version 3.4.3) function bamCoverage using the GENCODE M30 primary annotation file and the output was saved as bigwig files. Blacklist regions in the mm39 genome were obtained from a published dataset (PMID: 37067481) and excluded from the RPKM calculation.
Scale factors were calculated from the S. cerevisiae spike-in control to quantitatively compare RPKM signal between samples. Raw sequencing reads were mapped to the sacCer3 genome assembly. As was done for mm39, Bowtie2 and SAMtools were used for alignment and post-alignment processing, respectively. The SAMtools function flagstat was used to find the number of properly paired reads in sacCer3 alignments. These were used to calculate a scale factor that was defined by dividing an arbitrary constant number (7,000 for H3K9me3 CUT&RUN; 8,000 for LAP2B and IGG CUT&RUN) by the number of properly paired reads (Zheng Y et al (2020). Protocol.io). Using with the deepTools2 function bamCoverage, the scale factors for each library were used to generate 1kb- and 10kb-binned bigWig files containing spike-in normalized RPKM signal coverage tracks.
For transposable elements, spike-in controlled LAP2B RPKM signal coverage in 10kb bins were calculated with the deepTools2 function bamCoverage using a custom annotation file from the Hammell lab and including Blacklist regions where many transposable elements reside. For calculating modified z-scores of RPKM signal, RPKM values for each transposable element were first averaged across replicates of wildtype naive mESCs. Then, the median RPKM and median absolute deviation were calculated for all transposable elements. A modified z-score for each transposable element was calculated using the following formula: 0.6745 * (individual TE RPKM – median RPKM score) / (median absolute deviation RPKM).
Assembly: mm39
Supplementary files format and content: bigWig, RPKM values per 10kb bins.
Supplementary files format and content: bigWig, spike-in normalized RPKM values per 1kb bins.
Supplementary files format and content: bigWig, spike-in normalized RPKM values per 10kb bins.
Supplementary files format and content: csv file includes spike-in normalized signal from either LMNB1, LAP2B, or IGG CUT&RUN in gene bodies
Supplementary files format and content: csv file includes spike-in normalized signal from either LMNB1, LAP2B, or IGG CUT&RUN in transposable elements
Supplementary files format and content: csv file includes modified z-scores for LAP2B CUT&RUN signal in transposable elements in wildtype naive mESCs
Library strategy: CUT&Run

source_name: EpiLC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 2.11 x 104 cells/cm2 on dishes pre-coated with either Geltrex (Gibco™ A1413202) or Cultrex (Bio-Techne 3445-005-01). mESCs were replenished with fresh 2i + LIF medium after 24 hours then collected at 48 hours for CUT&RUN. EpiLCs were differentiated by seeding 2.11 x 104 cells/cm2 mESCs into either Geltrex or Cultrex coated dishes containing N2B27 media supplemented with 20 ng/mL FGF (Peprotech 100-18B) and 12 ng/mL Activin A (Peprotech 120-14E). EpiLCs were replenished with fresh differentiation medium after 24 hours then collected at 48 hours for CUT&RUN.

extract_protocol:
CUT&RUN was performed as described in Skene et al. 2018. Live cells were harvested with accutase and washed once with PBS prior to starting the procedure. Three replicates containing 200,000 mESCs or EpiLCs each were used per condition, except for H3K9me3 CUT&RUN which only included two replicates of wildtype naïve mESCs. LAP2B antibody (Invitrogen PA5-52519, 1:100), H3K9me3 antibody (abcam 8898, 1:1000 dilution), and Lamin B1 antibody (sc56144, 1:500) were diluted in antibody buffer and incubated at 4°C overnight. Rabbit anti-mouse secondary antibody (abcam ab6709, 1:100 dilution) was used for as an IGG negative control in parallel with the LAP2B CUT&RUN. pA-MNase (batch #6 143µg/mL) generously gifted from the Hennikoff lab was used for the cleavage reaction. The 2X STOP buffer included genomic DNA from Saccharomyces cerevisiae such that each sample received 0.3pg of spike-in DNA as a spike-in control. The chromatin release step was carried out at 37°C for 1 hour. DNA was isolated by phenol-chloroform extraction. Purified DNA was resuspended with 40uL of 1mM Trish-HCl pH 8.0 and 0.1mM EDTA.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep with Sample Purification Beads (NEB E7103S) following the manufacturer’s protocol with 5ng of starting DNA input. Libraries were amplified using 8 cycles on the thermocycler. Each library was uniquely indexed with NEBNext Multiplex Oligos for Illumina (NEB E6440S), then pooled together in equimolar amounts. Library size was analyzed with the Agilent Bioanalyzer 2100 using the High sensitivity DNA kit.

tag: cell line

value: EpiLC

value: wildtype


title: F123 GAM library f123_1NP_GAM180123_B05_2_S130_R1_001

tag: genotype


title: T-ALL Sample 332 [RNA-seq]

description:
TALL332
taken at diagnosis

source_name: T-ALL bone marrow/peripheral blood sample

value: Tumor

value: CIMP high

value: Pediatric T-cell acute lymphoblastic leukemia


title: F123 GAM library f123_1NP_GAM180123_A10_2_S169_R1_001


title: mESC, primed pluripotency, WT, IGG, rep2

description: Library name: WT_epi_IGG_2


title: A62r6

value: 32-cell stage

value: A

tag: replicate

value: embryo6/right side


title: F123 GAM library f123_1NP_GAM180123_B03_2_S114_R1_001


title: F123 GAM library f123_1NP_GAM180123_A09_2_S161_R1_001


title: T-ALL Sample 331 [RNA-seq]

description:
TALL331
taken at diagnosis

tag: tissue

value: T-ALL bone marrow/peripheral blood sample


title: F123 GAM library f123_1NP_GAM180123_A08_2_S153_R1_001


title: A62r4

value: embryo4/right side


title: mESC, primed pluripotency, WT, IGG, rep1

description: Library name: WT_epi_IGG_1


title: T-ALL Sample 325 [RNA-seq]

description:
TALL325
taken at diagnosis


title: T-ALL Sample 329 [RNA-seq]

description:
TALL329
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180123_A07_2_S145_R1_001


title: A62l5

value: embryo5/left side


title: mESC, naive pluripotency, WT, IGG, rep1

description: Library name: WT_naive_IGG_1

source_name: mESC

value: mESC


title: A61r6


title: F123 GAM library f123_1NP_GAM180123_A06_2_S137_R1_001


title: mESC, naive pluripotency, WT, H3K9me3, rep2

description: Library name: WT_naive_H3K9me3_2


title: T-ALL Sample 324 [RNA-seq]

description:
TALL324
taken at diagnosis


title: mESC, naive pluripotency, WT, IGG, rep3

description: Library name: WT_naive_IGG_3


title: F123 GAM library f123_1NP_GAM180123_A05_2_S129_R1_001


title: T-ALL Sample 318 [RNA-seq]

description:
TALL318
taken at diagnosis

value: CIMP low


title: aE11

value: 6-row neural plate stage

value: a

value: embryo1/left column2


title: A61r4


title: mESC, naive pluripotency, WT, H3K9me3, rep1

description: Library name: WT_naive_H3K9me3_1


title: aE12

value: embryo1/left column1


title: T-ALL Sample 317 [RNA-seq]

description:
TALL317
taken at diagnosis


title: F123 GAM library f123_1NP_GAM180123_A04_2_S121_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: A61l5


title: mESC, naive pluripotency, QKO, LAP2B, rep3

description: Library name: QKO_naive_LAP2B_3

value: Lamins and LBR quadruple knockout


title: mESC, primed pluripotency, QKO, LAP2B, rep3

description: Library name: QKO_epi_LAP2B_3

value: EpiLC


title: T-ALL Sample 316 [RNA-seq]

description:
TALL316
taken at diagnosis

value: Tumor

value: Pediatric T-cell acute lymphoblastic leukemia


title: A87r7

value: 112-cell stage

value: A

value: embryo7/right side


title: F123 GAM library f123_1NP_GAM180123_A02_2_S105_R1_001


title: mESC, primed pluripotency, TKO, LAP2B, rep3

description: Library name: TKO_epi_LAP2B_3

value: Lamins triple knockout