title: ZBTB18KO_4

first: xiaocui

last: luo

address: Haidian District

institute: Tsinghua university

description:
Library name: ZBTB18KO_4
18_GCMP_4

data_processing:
RNA-seq reads were trimmed from 3'end until the final base had a quality score >20, using trim_galore (v0.6.6), discarding reads left with <20 bp
Trimmed reads were mapped to the mouse genome (mm10) through STAR v2.2.0 with default settings.
Read count extraction was performed using STAR v2.2.0
FeatureCounts software was used to collect reads located in the coding sequence (CDS) of each gene. CDS counts normalized to mappable reads were used for measuring gene expression.
Assembly: mm10
Assembly: Supplementary files format and content: tab-delimited text file includes normalized CDS counts for each sample
Supplementary files format and content: 18_GCMPvsM_GCMP.csv files includes Raw counts

source_name: spleen

extract_protocol:
4 mice were used for cell-sorting in each experiment. Splenocyte single cell suspensions were generated by crushing spleens in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA). Cells were filtered through 70 uM nylon mesh and washed at 1700 RPM, 4 ⁰C, 5 minutes. Pellets were resuspended in RT ACK lysis buffer and incubated RT for 3 minutes, followed by addition of 5-10 volumes of MACS buffer and washing at 1700 RPM, 4 ⁰C, 5 minutes. Single-cell suspension of splenocytes was stained in MACS buffer containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations on ice for 25 min. Cells were washed again with 5-10 volumes of MACS, and resuspended in MACS for analysis on BD Aria II. Approximately 200 cells of desired type were sorted into 6 μl lysis buffer (0.2% Triton X-100 and 2 U/μl of RNase inhibitor).
Lysates were mixed with 3 μl of anchored oligo-dT primer (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 μl of dNTP mix (10 mM, Fermentas), denatured at 72 °C for 3 min and immediately placed on ice afterwards. The first-strand reaction mix containing 1 μl SuperScript II reverse transcriptase (Invitrogen), 0.5 μl RNAse inhibitor (Clontech), 4 μl Superscript II First-Strand Buffer (Invitrogen), 1 μl DTT (100 mM, Invitrogen), 4 μl betaine (5 M, Sigma), 0.12 μl MgCl2 (1 M, Sigma), 0.2 μl TSO (100 μM) and 0.58 μl nuclease-free water, were added to each sample. Reverse transcription reaction was carried out by incubating at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). Finally, the reverse transcriptase was inactivated by incubation at 70 °C for 15 min. PCR mix containing 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl IS PCR primers (10 μM) and 1.1 μl nuclease-free water were added to each sample. The reaction was incubated at 98 °C for 3 min, then cycled 17 times (98 °C 20 s, 67 °C 15 s, 72 °C 6 min), with a final extension at 72 °C for 5 min. cDNAs were purified by Vazyme DNA clean beads following manufacturer's instructions. 1 ng of cDNA were used for the tagmentation reaction using Tn5 (Vazyme). The tagmentation reaction (20 μl) was incubated at 55 °C for 10 min and stopped by addition of 2 μl 0.2%SDS and incubated at 70 °C for 20 min. A second amplification was performed using Q5 polymerase (NEB) as follows: 72 °C 3 min, 98 °C 30 s, then 12 cycles of (98 °C 15 s, 60 °C 30 s, 72 °C 3 min), final extension at 72 °C 5 min. Libraries were purified using Vazyme DNA clean beads

treatment_protocol: Mice were immunized intraperitoneally with 100 μg NP-KLH (conjugate ratios20, Biosearch Technologies) mixed with 1 μg lipopolysaccharide (LPS, Sigma) in alum (Thermo Scientific). Single-cell suspension of splenocytes was stained in MACS buffer (PBS supplemented with 1% FBS and 5 mM EDTA) containing Fc blocker (supernatant from 2.4G2 cell culture) for 20 min on ice before surface staining with primary antibodies in appropriate concentrations. GC B cells were enriched from pooled splenocytes of 3 to 4 Cd79acre/+Zbtb18fl/fl or Cd79acre/+ mice with anti-mouse GL7 (clone GL7, eBioscience) 28 days after NP-KLH immunization. Memory precursor cells (GL7+FAS+CD38+IgD-CD19+) were then sorted into 4 replicates of ~200 cells per PCR tube containing the lysis buffer. Samples were reverse transcribed with SuperScript™ II Reverse Transcriptase (Catalog:18064022, Invitrogen) and the complement DNA library was constructed with TruePrep DNA Library Prep Kit for Illumina (Catalog:TD501, Vazyme), following the Smart-seq2 protocol. Amplified products were purified with VAHTS DNA Clean Beads (Vazyme) and quantified using Qubit and 2100 Bioanalyzer (Agilent). Quantitative RT-PCR was used for quality control. All libraries were sequenced on a HiSeq X Ten sequencer (Illumina).

value: spleen

value: memory B cell precursor in germinal center

value: NP-KLH/LPS/Alum 14dpi


title: ZBTB18KO_3

status: Public on Mar 01 2025

type: SRA

city: Beijing

country: China

description:
Library name: ZBTB18KO_3
18_GCMP_3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: ZBTB18KO_2

description:
Library name: ZBTB18KO_2
18_GCMP_2


title: HEK293T cells, Control, rep1

city: City

first: Lianhao

last: Song

state: Guangzhou

address: Jinsui road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Library name: Ctrl 1

data_processing:
The raw RNA-seq data were preprocessed and subjected to quality control using fastp.
Bowtie2 was used to construct the reference index and perform local alignment, effectively filtering out reads that mapped to the rRNA sequences.
STAR was employed to build the reference index and perform the alignment, followed by RSEM for quantification of gene expression from the resulting alignment data.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text flie includes raw counts for each sample

organism: Homo sapiens

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine (FBS) and antibiotics in humidified atmosphere with 5% C02 at 37℃

extract_protocol:
Total RNA was isolated using the EZ-press RNA Purification Kit (EZBioscience). 2 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA), following the manufacturer's instructions

treatment_protocol: RNA was transfected using Lipofectamine MessengerMax (Invitrogen) at 500 ng per well for 24-well plates

tag: cell line

value: Human Embryonic Kidney Cells

value: RNA transfection

tag: batch


title: HEK293T cells, Control, rep2

description: Library name: Ctrl 2


title: ZBTB18KO_1

description:
Library name: ZBTB18KO_1
18_GCMP_1


title: HEK293T cells, RNA produced by Linear transfection, rep3

description: Library name: Linear 3


title: HEK293T cells, Control, rep3

description: Library name: Ctrl 3


title: HEK293T cells, RNA produced by Linear transfection, rep2

description: Library name: Linear 2


title: HEK293T cells, RNA produced by Linear transfection, rep1

description: Library name: Linear 1


title: HEK293T cells, RNA produced by SCAP transfection, rep3

description: Library name: SCAP 3


title: WT_3

description:
Library name: WT_3
M_GCMP_3


title: WT_4

description:
Library name: WT_4
M_GCMP_4


title: WT_1

description:
Library name: WT_1
M_GCMP_1


title: WT_2

description:
Library name: WT_2
M_GCMP_2


title: HEK293T cells, RNA produced by SCAP transfection, rep1

description: Library name: SCAP 1


title: HEK293T cells, RNA produced by SCAP transfection, rep2

description: Library name: SCAP 2


title: ConA96h_2

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

country: USA

institute: NIAAA

description: Library name: ConA96h_2

library_source: transcriptomic single cell

data_processing:
The FASTQ data files were aligned to the 10x Genomics mouse reference sequence (refdata-gex-mm10-2020-A) using 10X Genomics CellRanger on the NIH HPC Biowulf cluster (http://hpc.nih.gov). Seurat package was used to further analyze the single cell RNA seq data
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: .h5

source_name: Liver

extract_protocol:
Naïve mice and mice treated with ConA for 72 or 96 hours were anesthetized, and their livers were perfused and digested using a 0.075% collagenase solution (Worthington, Lakewood, NJ). Liver samples were homogenized, filtered through 70 μm cell strainers, and centrifuged at 400g through a Percoll density gradient (40% and 70%).
The cells were loaded in the lanes using 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 with a single capture lane per sample targeting recovery of 8,000 cells. All subsequent steps of library preparation and quality control were performed according to the 10X Genomics Chromium Single Cell 3' Reagent Kits User Guide.

value: Liver


title: HEK293T cells, RNA produced by AnaPIE transfection, rep2

description: Library name: AnaPIE 2


title: HEK293T cells, RNA produced by AnaPIE transfection, rep1

description: Library name: AnaPIE 1


title: ConA72h_1

description: Library name: ConA72h_1


title: OVCAR3, UAB,2

city: RICHMOND

first: Hengbin

last: Wang

state: VA

address: 401 college st

institute: Virginia Commonwealth University

data_processing:
Raw FASTQ sequences were quality-controlled using FastQC. Samples were aligned to the GRCh38/hg38 human primary assembly genome (version release 108) using STAR aligner (version 2.7.9a.). The SourceForge Subread package was used to generate raw counts, with reads counted over exons using the ENSEMBL gtf file for Homo sapiens, GRCm38 assembly (version release 108)
Assembly: GRCh38/hg38
Supplementary files format and content: Combined raw count

source_name: Cell line

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen™, #15596018) and purified with the Direct-zol™ RNA Microprep kit (Zymo, #R1051).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: OVCAR3 treated with 2000 ng/ml doxycycline for 6days before harvest

value: Cell line

value: ovarian cancer cell

value: UAB peptide expression

value: 2000ng dox 6 days


title: ConA96h_1

description: Library name: ConA96h_1


title: Control_2

description: Library name: Control_2


title: Control_3

description: Library name: Control_3


title: Control_1

description: Library name: Control_1


title: OVCAR3, control,1

value: scramble control


title: ConA72h_2

description: Library name: ConA72h_2


title: TMEM41B-KO, Naive T cell, scRNA-seq

first: Gang

last: Jin

address: Zhongguancun North street

department: Institute for Immunology

institute: Tsinghua University

description: Library name: Sample2

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform, targeting approximately 13,000 cells per sample.
CeleScope (v1.9.0) pipeline was used for scRNA-seq data alignment and quantification.
The generated data files including aligned and filtered reads, barcodes and unique molecular identifiers were processed by Seurat (v4.3.0)
Cell-level quality control was performed by filtering cells based on the following criteria: (1) gene numbers between 500 and 5000, (2) total UMI counts between 1000 and 20000, and (3) mitochondrial gene percentage less than 10%.
After filtering, the top 2,000 variable genes were selected for principal component analysis (PCA).
The first 1-10 principal components (PCs), as determined by the JackStraw method, were used for Uniform Manifold Approximation and Projection (UMAP) and clustering analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen and peripheral lymphonode

extract_protocol:
Lymphocytes from CD4CreTMEM41Bfl/fl mice (KO) and wild-type (WT) littermates were stained with markers for TCRb, CD44, CD62L, and CD25. TCRb was used to identify both CD4 and CD8 T cells, and CD44 and CD62L were used to isolate naive T cells (CD44-CD62L+), while CD25 was used to exclude regulatory T cells. The TCRb+CD44-CD62L+CD25- naive T cells (sorted as the 20% lowest CD44-) from WT or KO mice were sorted for single-cell RNA sequencing (scRNA-seq) analysis. Then naive T cells from WT or KO mice were directly loaded onto a microfluidic chip, and libraries were prepared using the Singleron GEXSCOPETM Single Cell RNA-seq Kit (Singleron Biotechnologies), following the manufacturer’s protocol.
The sample was processed for scRNA-seq library preparation according to manufacturer’s protocol.

value: Spleen and peripheral lymphonode

value: naive T cell


title: HEK293T cells, RNA produced by AnaPIE transfection, rep3

description: Library name: AnaPIE 3


title: Control, Naive T cell, scRNA-seq

description: Library name: Sample1


title: HUVEC, 50μl/ml XBJ for 30 min before LPS, rep2

city: 青岛市

first: Jiayin

last: Cui

state: 山东省

address: 市南区鱼山路5号

department: 医药学院

institute: 中国海洋大学

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq.Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate theexpression pattern of genes in different groups and samples. The radar map of top 30 genes wasdrew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HUVEC

growth_protocol: Isolated HUVEC were resuspended using endothelial cell medium (1001, ScienCell, CA, USA) containing 5% fetal bovine serum supplemented with streptomycin and penicillin and cultured in incubator at 37°C with 5% CO2.

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

treatment_protocol: CT group: no treatment. LPS group: treated with 1μg/ml LPS for 4 hours. XBJ+LPS group: pretreated with 50μl/ml XBJ for 30 minutes, then stimulated with LPS for 4 hours.

value: HUVEC

value: Primary human umbilical vein endothelial cells

value: 50μl/ml XBJ for 30 min before LPS


title: OVCAR3, UAB,1


title: HUVEC, 50μl/ml XBJ for 30 min before LPS, rep3


title: hCOs, hypoxia-48h

city: shanghai

first: quanlong

last: jiang

institute: PICB

description: Library name: hypoxia-48h

data_processing:
Raw sequencing reads were evaluated using quality metrics and analyzed with Cell Ranger software (v3.1.0). Cells deemed low quality—characterized by fewer than 200 unique detected genes, fewer than 500 UMIs, or mitochondrial content exceeding 15%—were filtered out. Additionally, genes expressed in fewer than 100 cells were removed. Subsequently, the UMIs were normalized and logarithmically transformed.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: hCOs

extract_protocol:
Hypoxic and normoxic hCOs were collected and dissociated into single-cell suspensions using papain (Sigma, 9001-73-4), resulting in a concentration of 2 × 10⁵ cells/mL in ice-cold D-PBS.
Single cells were barcoded, and mRNA was captured using the GEXSCOPE Single Cell RNA Library Kit (Singleron Biotechnologies, Nanjing, China), followed by cDNA library generation for scRNA-seq. The individual libraries were then diluted to 4 ng/mL and pooled for sequencing on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA) with 150-bp paired-end reads.

value: hCOs


title: HUVEC, 50μl/ml XBJ for 30 min before LPS, rep1


title: HUVEC, 1μg/ml LPS for 4h, rep3

value: 1μg/ml LPS for 4h


title: balb/c-nude mice skin tissue, uvb hCOL3A1, rep2

description: Library name: UVB-hCOL3A1.2

data_processing:
RNA-seq raw data were preprocessed and quality-controlled using fastp (v0.23.4).
Reads aligned to the rRNA reference sequence were aligned and filtered out by Bowtie2 (v2.5.4).
Mouse reference index was built and aligned using STAR (v2.7.11b), and gene expression was quantified via RSEM (v1.3.3).
Gene expression matrices were normalized and differentially expressed genes were identified by DESeq2 (v1.44.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text flie includes raw counts for each sample

source_name: Skin

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, USA)
Library clustering and sequencing were conducted as follows: index-coded sample clustering was performed using a cBot cluster generation system with the HiSeq PE Cluster Kit v4-cBot-HS (Illumina), in accordance with the manufacturer’s instructions. Following cluster generation, the libraries were sequenced on an Illumina platform, producing 150 bp paired-end reads.

value: Skin


title: balb/c-nude mice skin tissue, uvb hCOL3A1, rep1

description: Library name: UVB-hCOL3A1.1


title: HUVEC, 1μg/ml LPS for 4h, rep1


title: balb/c-nude mice skin tissue, uvb saline, rep2

description: Library name: UVB-Saline.2


title: HUVEC, control, rep3

value: control


title: balb/c-nude mice skin tissue, uvb saline, rep1

description: Library name: UVB-Saline.1


title: OVCAR3, control,2


title: HUVEC, control, rep2


title: balb/c-nude mice skin tissue, no uvb, rep3

description: Library name: NoUVB.3


title: balb/c-nude mice skin tissue, uvb hCOL3A1, rep3

description: Library name: UVB-hCOL3A1.3


title: balb/c-nude mice skin tissue, no uvb, rep2

description: Library name: NoUVB.2


title: balb/c-nude mice skin tissue, no uvb, rep1

description: Library name: NoUVB.1


title: balb/c-nude mice skin tissue, uvb saline, rep3

description: Library name: UVB-Saline.3


title: C3

city: Nanjing

first: Xinyi

last: Xia

state: Jiangsu

address: 138 XianLin Road, Nanjing, JiangSu, China

institute: Nanjing University of Chinese Medicine

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software
Assembly: hg38,mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PANC-1 subcutaneous tumor in nude mice

extract_protocol:
Tumor tissues were dissociated using 2mg/ml Collagenase II (Sigma, C2-28-100MG) for 1h in 37℃ water bath. Digestion was terminated by wash with 5ml DMEM twice. Cells were passed through 40μm cell strainer to get single cell suspension. Cell viability were confirmed using AO/PI reagent (Absin, abs9727-100T). Then, single cell suspension was washed and resuspended in DPBS containing 0.02%BSA for single cell RNA-seq library construction.
Construction of single cell RNA-seq library was performed using 10x Genomics Chromiun Single-Cell 3’ kit(V3) according to the manufacturer’s instructions. Briefly, cells were loaded onto the 10x Genomics single-cell-A chip for a target capture of 8000 cells. After droplet generation, sample were transferred into a PCR tube and performed reverse transcription and library construction.

value: PANC-1 subcutaneous tumor in nude mice

value: PDAC tumor cell line

value: Agrimoniin+Erlotinib treatment


title: HUVEC, control, rep1


title: D9

value: Erlotinib treatment


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 3.5 days, repeat2

city: Shanghai

first: Fei-Long

last: Meng

state: Shanghai

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

description:
Library name: ELOF1_Lib229
iABC_IL4.LPS.d3.5_WT_rep2

data_processing:
1. cutadapters; 2. remove rRNA reads using bowtie2; 3. align to mm10+dm6 genome; 4. count with featureCounts
Assembly: mm10
Assembly: dm6
Supplementary files format and content: raw counts output from featureCounts

source_name: Spleen

growth_protocol: See the paper methods.

extract_protocol:
Tiangen total RNA extraction kit, cat. no. DP430
NEB rRNA depletion kit and strand specific RNA prep kit (cat. no. E7770S, E7400L)

treatment_protocol: See the paper methods.

value: Spleen

value: B cell

value: wild-type

value: IL4, LPS


title: B3

value: Agrimoniin treatment


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 3.5 days, repeat3

description:
Library name: ELOF1_Lib230
iABC_IL4.LPS.d3.5_WT_rep3


title: HUVEC, 1μg/ml LPS for 4h, rep2


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 3.5 days, repeat1

description:
Library name: ELOF1_Lib228
iABC_IL4.LPS.d3.5_WT_rep1


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 2.5 days, repeat5

description:
Library name: ELOF1_Lib015
iABC_IL4.LPS.d2.5_WT_rep5


title: A4


title: APA-mut HepG2 cells, peroxide 4hr, replicate 2

city: Greenwood

first: Lela

last: Lackey

state: SC

address: 114 Gregor Mendel Circle

department: Genetics and Biochemistry

institute: Clemson University

data_processing:
Paired end reads were aligned to the human genome (GRCh38.p13) using STAR for gene expression analysis
Paired-end aligned reads were counted and normalized using edgeR for gene expression analysis
Reverse reads was aligned to the human genome (GRCh38.p13) using STAR for polyadenylation analaysis
Reverse aligned reads were analyzed using MAAPER for polyadenylation analysis
Assembly: GRCh38
Supplementary files format and content: tab delimited files with gene expression data for each sample

source_name: liver

growth_protocol: Cell lines were seeded in 10 cm2 plates and grown at 5% CO2 and 37 C. Cells were grown in Eagle’s Minimum Essential Media (EMEM) supplemented with 5% FBS (Thermo Scientific) and 0.5% Penicillin-Streptomycin (MilliporeSigma).

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher) according to manufacturer’s recommendations for adherent cell lines using Phaselock columns (Quantabio) prior to RNA purification with RNA clean up columns (NEB). Genomic DNA was removed using TURBO DNase (Fisher Scientific) according to the given protocol. RNA was quantified via NanoDrop (Thermo Scientific ND-8000) and quality checked by RNA Screentape on a Tapestation 4150 (Agilent).
RNA samples were prepared using the QuantSeq 3’ mRNA REV Library Prep Kit V2 (Lexogen), which captures polyadenylated RNA. Quality assurance for loading samples for sequencing was performed using a Qubit dsDNA High Sensitivity Assay (Thermo Scientific) on a Qubit 4 fluorometer (Thermo Scientific), and a High Sensitivity D1000 Screentape (Agilent) on a Tapestation 4150 (Agilent).
The Lexogen QuantSeq samples were sequenced on a NovaSeq 6000 (Illumina) using a 2x100 cycle cartridge. A custom sequence primer was used for Read 1 according to instructions from Lexogen and Illumina.

treatment_protocol: Cell lines were seeded into at 3.0 x 10^5 cells in 6-well plates. Cells were incubated for 24 hours then serum-starved using 1 mL serum-free EMEM for another 24 hours. After media starvation, the cells were treated in 1 mL serum-free media with 170mM ethanol diluted in PBS (EtOH, 3, and 24 hours. Fisher Scientific), 150 uM hydrogen peroxide diluted in PBS (H2O2, 4 hours. Fisher Scientific) or 20ng/mL interleukin-6 diluted in 0.1% of BSA at (IL-6, 4, and 24 hours. Fisher Scientific).

value: liver

value: hepatocellular carcinoma

value: APA-CRISPR

value: peroxide


title: APA-mut HepG2 cells, peroxide 4hr, replicate 3


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 2.5 days, repeat4

description:
Library name: ELOF1_Lib021
iABC_IL4.LPS.d2.5_WT_rep4


title: APA-mut HepG2 cells, peroxide 4hr, replicate 1


title: APA-mut HepG2 cells, peroxide control, replicate 3


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 2.5 days, repeat3

description:
Library name: ELOF1_Lib224
iABC_IL4.LPS.d2.5_WT_rep3


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 2.5 days, repeat2

description:
Library name: ELOF1_Lib223
iABC_IL4.LPS.d2.5_WT_rep2


title: RNA-seq of spleenic B cells: wild-type, IL4+LPS 2.5 days, repeat1

description:
Library name: ELOF1_Lib222
iABC_IL4.LPS.d2.5_WT_rep1


title: APA-mut HepG2 cells, peroxide control, replicate 2


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 3.5 days, repeat3

description:
Library name: ELOF1_Lib231
iABC_IL4.LPS.d3.5_Elof1.cKO_rep3


title: APA-mut HepG2 cells, ethanol 24hr, replicate 3

value: ethanol


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 3.5 days, repeat2

description:
Library name: ELOF1_Lib227
iABC_IL4.LPS.d3.5_Elof1.cKO_rep2


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 3.5 days, repeat1

description:
Library name: ELOF1_Lib226
iABC_IL4.LPS.d3.5_Elof1.cKO_rep1


title: APA-mut HepG2 cells, ethanol 24hr, replicate 2


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 2.5 days, repeat5

description:
Library name: ELOF1_Lib016
iABC_IL4.LPS.d2.5_Elof1.cKO_rep5


title: APA-mut HepG2 cells, peroxide control, replicate 1


title: APA-mut HepG2 cells, ethanol 3hr, replicate 3


title: APA-mut HepG2 cells, ethanol 24hr, replicate 1


title: APA-mut HepG2 cells, ethanol 3hr, replicate 2


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 2.5 days, repeat3

description:
Library name: ELOF1_Lib225
iABC_IL4.LPS.d2.5_Elof1.cKO_rep3


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 2.5 days, repeat2

description:
Library name: ELOF1_Lib221
iABC_IL4.LPS.d2.5_Elof1.cKO_rep2


title: APA-mut HepG2 cells, ethanol 3hr, replicate 1


title: APA-mut HepG2 cells, ethanol control, replicate 3


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 2.5 days, repeat1

description:
Library name: ELOF1_Lib220
iABC_IL4.LPS.d2.5_Elof1.cKO_rep1


title: APA-mut HepG2 cells, ethanol control, replicate 2


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 7 days, repeat2

description:
Library name: ELOF1_Lib217
CH12_CITd7_Vector_rep2

value: Elof1-KO +Vector

value: α-CD40, IL4, TGF-β


title: APA-mut HepG2 cells, ethanol control, replicate 1


title: APA-mut HepG2 cells, IL-6 24hr, replicate 2


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 7 days, repeat1

description:
Library name: ELOF1_Lib216
CH12_CITd7_Vector_rep1


title: APA-mut HepG2 cells, IL-6 24hr, replicate 1


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 3 days, repeat2

description:
Library name: ELOF1_Lib213
CH12_CITd3_Vector_rep2


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 3 days, repeat1

description:
Library name: ELOF1_Lib212
CH12_CITd3_Vector_rep1


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 1.5 days, repeat4

description:
Library name: ELOF1_Lib209
CH12_CITd1.5_Vector_rep4


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 1.5 days, repeat3

description:
Library name: ELOF1_Lib208
CH12_CITd1.5_Vector_rep3


title: APA-mut HepG2 cells, IL-6 4hr, replicate 2


title: APA-mut HepG2 cells, IL-6 4hr, replicate 1


title: RNA-seq of spleenic B cells: Elof1-cKO, IL4+LPS 2.5 days, repeat4

description:
Library name: ELOF1_Lib022
iABC_IL4.LPS.d2.5_Elof1.cKO_rep4


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 1.5 days, repeat2

description:
Library name: ELOF1_Lib019
CH12_CITd1.5_Vector_rep2


title: RNA-seq of CH12F3: Elof1-KO +Vector, CIT 1.5 days, repeat1

description:
Library name: ELOF1_Lib017
CH12_CITd1.5_Vector_rep1


title: APA-mut HepG2 cells, IL-6 control, replicate 3


title: APA-mut HepG2 cells, IL-6 4hr, replicate 3


title: APA-mut HepG2 cells, IL-6 control, replicate 2


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 7 days, repeat2

description:
Library name: ELOF1_Lib219
CH12_CITd7_ELOF1_rep2

value: Elof1-KO +ELOF1


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 7 days, repeat1

description:
Library name: ELOF1_Lib218
CH12_CITd7_ELOF1_rep1


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 3 days, repeat2

description:
Library name: ELOF1_Lib215
CH12_CITd3_ELOF1_rep2


title: APA-mut HepG2 cells, IL-6 control, replicate 1


title: HepG2 cells, peroxide 4hr, replicate 3

value: WT


title: HepG2 cells, peroxide 4hr, replicate 2


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 3 days, repeat1

description:
Library name: ELOF1_Lib214
CH12_CITd3_ELOF1_rep1


title: HepG2 cells, peroxide 4hr, replicate 1


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 1.5 days, repeat3

description:
Library name: ELOF1_Lib210
CH12_CITd1.5_ELOF1_rep3


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 1.5 days, repeat4

description:
Library name: ELOF1_Lib211
CH12_CITd1.5_ELOF1_rep4


title: HepG2 cells, peroxide control, replicate 3


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 1.5 days, repeat2

description:
Library name: ELOF1_Lib020
CH12_CITd1.5_ELOF1_rep2


title: HepG2 cells, peroxide control, replicate 2


title: RNA-seq of CH12F3: Elof1-KO +ELOF1, CIT 1.5 days, repeat1

description:
Library name: ELOF1_Lib018
CH12_CITd1.5_ELOF1_rep1


title: HepG2 cells, peroxide control, replicate 1


title: PRO-seq of CH12F3: +Vector NVP-2 60 min, repeat2

description: Library name: ELOF1_Lib177

data_processing:
Adapter sequences were trimed before alignment to mouse mm10 or mouse-human mixed (mm10-hg38) genome. The 16 bases at the 5’ end of the paired read which indicated the 3' end of the nascent RNA were used to generate bigwig files.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: PRO-Seq

molecule: nuclear RNA

extract_protocol:
Total nuclear RNA was extratcted from run-on reaction using TRIZol, then the bition NTP integrated nascent RNA was retrieved by C1 beads (thermofisher) and subjected to PRO-seq library prep.
A 3' adapter is first ligated to nascent RNA, 5' illumina adapter sequence is added in RT reaction using template switch. The full adapters are added by PCR.

value: Aicda-Elof1-KO Clone2, +3xHA, CIT day1.5, K562 cells were used as spike-in


title: HepG2 cells, ethanol 24hr, replicate 2


title: PRO-seq of CH12F3: +Vector NVP-2 30 min, repeat2

description: Library name: ELOF1_Lib176


title: HepG2 cells, ethanol 24hr, replicate 3


title: HepG2 cells, ethanol control, replicate 3


title: PRO-seq of CH12F3: +Vector NVP-2 0 min, repeat2

description: Library name: ELOF1_Lib175


title: HepG2 cells, ethanol 3hr, replicate 1


title: HepG2 cells, ethanol 3hr, replicate 3


title: HepG2 cells, ethanol 24hr, replicate 1


title: PRO-seq of CH12F3: +Vector NVP-2 30 min, repeat1

description: Library name: ELOF1_Lib170

value: Aicda-Elof1-KO Clone1, +3xHA, CIT day1.5, K562 cells were used as spike-in


title: PRO-seq of CH12F3: +ELOF1 NVP-2 30 min, repeat2

description: Library name: ELOF1_Lib173

value: Aicda-Elof1-KO Clone2, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in


title: HepG2 cells, ethanol 3hr, replicate 2


title: PRO-seq of CH12F3: +ELOF1 NVP-2 0 min, repeat2

description: Library name: ELOF1_Lib172


title: HepG2 cells, ethanol control, replicate 2


title: PRO-seq of CH12F3: +Vector NVP-2 0 min, repeat1

description: Library name: ELOF1_Lib169


title: HepG2 cells, ethanol control, replicate 1


title: PRO-seq of CH12F3: +ELOF1 NVP-2 60 min, repeat1

description: Library name: ELOF1_Lib168

value: Aicda-Elof1-KO Clone1, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in


title: PRO-seq of CH12F3: +ELOF1 NVP-2 60 min, repeat2

description: Library name: ELOF1_Lib174

value: B cell


title: HepG2 cells, IL-6 24hr, replicate 3


title: PRO-seq of CH12F3: +ELOF1 NVP-2 30 min, repeat1

description: Library name: ELOF1_Lib167


title: HepG2 cells, IL-6 24hr, replicate 2


title: HepG2 cells, IL-6 4hr, replicate 4


title: RPB1 S5-p ChIP-seq of CH12F3: +ELOF1 repeat1

description: Library name: ELOF1_Lib289

library_source: genomic

data_processing:
See the paper.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
Sonication and IP
ChIP-seq library was prepared using NEB Ultral II DNA prep kit. Other seq library was prepared using home-made protocol (refer to our paper).

value: Aicda-Elof1-KO Clone1, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S5-p (Abcam ab252852)


title: RPB1 S5-p ChIP-seq of CH12F3: +Vector repeat1

description: Library name: ELOF1_Lib288

value: Aicda-Elof1-KO Clone1, +3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S5-p (Abcam ab252852)


title: APA-mut HepG2 cells, IL-6 24hr, replicate 3


title: RPB1 S5-p ChIP-seq of CH12F3: +ELOF1 repeat2

description: Library name: ELOF1_Lib286

value: Aicda-Elof1-KO Clone2, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S5-p (Abcam ab252852)


title: HepG2 cells, IL-6 4hr, replicate 2

value: liver


title: RPB1 S5-p ChIP-seq of CH12F3: +Vector repeat2

description: Library name: ELOF1_Lib287

value: Aicda-Elof1-KO Clone2, +3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S5-p (Abcam ab252852)


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB wash out 20 min repeat2

description: Library name: ELOF1_Lib277

value: Aicda-Elof1-KO Clone2, +3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: HepG2 cells, IL-6 control, replicate 3

value: hepatocellular carcinoma


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB wash out 20 min repeat2

description: Library name: ELOF1_Lib276

value: Aicda-Elof1-KO Clone2, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: HepG2 cells, IL-6 control, replicate 1


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB 2.5 hours repeat2

description: Library name: ELOF1_Lib275


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB 2.5 hours repeat2

description: Library name: ELOF1_Lib274


title: HepG2 cells, IL-6 24hr, replicate 1


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB 20 min repeat2

description: Library name: ELOF1_Lib273


title: PRO-seq of CH12F3: +ELOF1 NVP-2 0 min, repeat1

description: Library name: ELOF1_Lib166


title: HepG2 cells, IL-6 4hr, replicate 3


title: PCW20

first: Qi

last: Dashi

address: 450 Tengyue Road

department: Center for Clinical Research and Translational Medicine, Yangpu Hospital

institute: Tongji University, Shanghai

description: 10x Genomics

data_processing:
Post-sequencing, the raw FASTQ files were processed using CellRanger v6.0.1, which included demultiplexing, alignment to the GRCh38 reference genome, and quantification of gene expression by counting Unique Molecular Identifiers (UMIs). Low-quality cells and doublets were filtered out, followed by normalization and scaling of the data for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: leptomeninges

extract_protocol:
Nuclei were extracted from tissue samples by mechanical dissociation and enzymatic digestion, followed by filtration to remove debris and intact cells. The nuclei were then isolated using a sucrose density gradient or a similar method to enrich for nuclei. Finally, the isolated nuclei were washed and counted to ensure the appropriate concentration for downstream single-cell RNA-seq applications.
Nuclei were isolated from tissue samples following the 10x Genomics Chromium protocol. Nuclei were encapsulated into Gel Beads in Emulsion (GEMs) for lysis and reverse transcription, generating barcoded cDNA. The cDNA was then amplified, fragmented, and prepared into sequencing libraries using the Chromium Next GEM Single Cell 3’ Kit v3.1, and sequenced on an Illumina NovaSeq 6000 platform.

value: leptomeninges

value: All resident cells in leptomeninges


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB 20 min repeat2

description: Library name: ELOF1_Lib272


title: HepG2 cells, IL-6 4hr, replicate 1


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB 0 min repeat2

description: Library name: ELOF1_Lib271


title: PCW19

description: 10x Genomics


title: HepG2 cells, IL-6 control, replicate 2


title: PCW21

description: 10x Genomics


title: PRO-seq of CH12F3: +Vector NVP-2 60 min, repeat1

description: Library name: ELOF1_Lib171


title: PCW13

description: 10x Genomics


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB 0 min repeat2

description: Library name: ELOF1_Lib270


title: RPB1 NTD ChIP-seq of RPB1-dTAG CH12F3: dTAG-13 3 hours repeat2

description: Library name: ELOF1_Lib269

value: Aicda-Elof1-KO RPB1-dTAG, CIT day1.5, K562 +ELOF1-GFP-3xHA cells were used as spike-in, anti-RPB1 NTD (CST 14958)


title: PCW14

description: 10x Genomics


title: PCW9.r2

description: 10x Genomics


title: PCW9.r1

description: 10x Genomics


title: ELOF1 ChIP-seq of RPB1-dTAG CH12F3: dTAG-13 3 hours repeat2

description: Library name: ELOF1_Lib268

value: Aicda-Elof1-KO RPB1-dTAG, CIT day1.5, K562 +ELOF1-GFP-3xHA cells were used as spike-in, anti-HA (CST 3724)


title: ELOF1 ChIP-seq of RPB1-dTAG CH12F3: untreat repeat2

description: Library name: ELOF1_Lib266


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB wash out 20 min repeat1

description: Library name: ELOF1_Lib164

value: Aicda-Elof1-KO Clone1, +ELOF1-3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB wash out 20 min repeat1

description: Library name: ELOF1_Lib165

value: Aicda-Elof1-KO Clone1, +3xHA, CIT day1.5, K562 cells were used as spike-in, anti-RPB1 S2-p (Abcam ab5095)


title: GBM tumorsphere, TMZ treated, replicate 1

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

data_processing:
The quality of the reads was assessed using fastQC (v.0.10.1), and the sequencing adapters were removed using trimmomatic (v.0.38).
Filtered reads were mapped to the human reference genome (GRCh38) using HISAT2.
Transcript assembly and quantification for RNA-Seq were performed using StringTie.
Read count normalization as TPM is performed with R.
Differentially expressed gene analysis was performed by a linear regression model using ballgown between each treatment and control group.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files containing TPM values for each sample

source_name: Cultured glioblastoma tumorsphere

growth_protocol: Human tissue samples were obtained from 75 patients with GBM at the Yonsei University Severance Hospital. From these samples, we established GBM TSs. For TS culture, cells were cultured in TS complete media composed of Dulbecco’s modified Eagle’s medium/F12 (Mediatech), 1x B27 (Invitrogen), 20 ng/mL basic fibroblast growth factor, and 20 ng/mL epidermal growth factor (Sigma-Aldrich).

extract_protocol:
RNA was extracted with Rneasy mini plus kit (Qiagen).
The samples of TSs for RNAseq were processed with Aglient SureSelect Human Alll Exon v6 + UTR kit to build sequence libraries under maufacturer's protocols.

treatment_protocol: PER (Sigma-Aldrich, St. Louis, MO, USA) and TMZ (Sigma-Aldrich) were dissolved in dimethyl sulfoxide (DMSO; Sigma-Aldrich) and treated to the cell cultures for 72 hours before RNA extraction process.

value: Cultured glioblastoma tumorsphere

value: TMZ (temozolomide)


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB 2.5 hours repeat1

description: Library name: ELOF1_Lib163

value: B cell


title: GBM tumorsphere, PER treated, replicate 3

value: PER (perphenazine)


title: PCW8

description: 10x Genomics


title: GBM tumorsphere, TMZ treated, replicate 2


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB 2.5 hours repeat1

description: Library name: ELOF1_Lib162


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB 20 min repeat1

description: Library name: ELOF1_Lib161


title: GBM tumorsphere, PER treated, replicate 2


title: GBM tumorsphere, PER treated, replicate 1


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB 20 min repeat1

description: Library name: ELOF1_Lib160


title: RPB1 NTD ChIP-seq of RPB1-dTAG CH12F3: untreat repeat2

description: Library name: ELOF1_Lib267


title: RPB1 S2-p ChIP-seq of CH12F3: +Vector DRB 0 min repeat1

description: Library name: ELOF1_Lib159


title: GBM tumorsphere, untreated control, replicate 2

value: untreated


title: RPB1 S2-p ChIP-seq of CH12F3: +ELOF1 DRB 0 min repeat1

description: Library name: ELOF1_Lib158


title: GBM tumorsphere, untreated control, replicate 1


title: RPB1 NTD ChIP-seq of RPB1-dTAG CH12F3: dTAG-13 3 hours repeat1

description: Library name: ELOF1_Lib138


title: RPB1 NTD ChIP-seq of RPB1-dTAG CH12F3: untreat repeat1

description: Library name: ELOF1_Lib137


title: GBM tumorsphere, PER+TMZ treated, replicate 3

value: PER+TMZ


title: GBM tumorsphere, PER+TMZ treated, replicate 2


title: GBM tumorsphere, TMZ treated, replicate 3


title: GBM tumorsphere, PER+TMZ treated, replicate 1


title: ELOF1 ChIP-seq of RPB1-dTAG CH12F3: dTAG-13 3 hours repeat1

description: Library name: ELOF1_Lib136


title: ELOF1 ChIP-seq of RPB1-dTAG CH12F3: untreat repeat1

description: Library name: ELOF1_Lib135


title: siCnot1_rep2

first: Xiang

last: Wu

address: 639 longmiandadao

institute: China Pharmaceutical University

data_processing:
To get high quality clean reads, reads were further filtered by fastp (https://github.com/OpenGene/fastp, version:fastp-0.19.4). We aligned reads of all samples to the mm10 reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, and then maps the reads to the reference genome. The genes were identified as significantly differentially expressed using DESeq2 package(1.40.2).The significantly differentially expressed genes were subjected to GO pathway enrichment and KEGG analysis using the DAVID website (https://david.ncifcrf.gov/). Gene Set Enrichment Analysis (GSEA) was performed on the 2C gene set using the enrichplot package(1.20.0).
Assembly: mm10
Supplementary files format and content: .txt files include gene expression

source_name: embryo

growth_protocol: The mouse embryonic cells were cultured on 0.2% gelatin-coated dishes in Knock-out DMEM, 15% KnockOut Serum Replacement, 1% non-essential amino acids, 1% Glutamax, 1% penicillin/streptomycin, 0.1 mM β-mercaptoethanol, and 1000 U/ml Recombinant Mouse leukemia inhibitory factor Protein.

extract_protocol:
Total RNA was extracted and purified using Trizol reagent(Invitrogen) following the manufacturer's procedure.
The RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA).An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform following the vendor’s recommended protocol.

value: embryo

value: mouse embryonic stem cell


title: H1299 sgM5 input rep2

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

data_processing:
For the paired-end sequencing, only the read1 in the raw FASTQ files were used for subsequent analyses. Cutadapt (v.2.8) was used to trim the adapters and low quality sequences with parameter (--match-readwildcards -a NNNNNNNNNNAGATCGGAAGAGCAC -q 20 -e 0.1 -O 6 -m 25 -M 35 --discard-untrimmed). Reads were aligned to human rRNA and tRNA sequences so as to remove rRNA and tRNA contamination using bowtie2 (v2.2.5) software. Then the clean reads were aligned to human genome (GRCh38) using hisat2 aligner (v2.2.1) with default parameters. The mapped reads were quantified using featureCounts (v2.0.1) with -t exon parameter by using GRCh38.106 gtf annotation file from ensembl database. Differential analysis of translation efficiency (TE) was calculated by Riborex (v2.4.0) and only genes with |log2FC| >= 1 and pvalue < 0.05 were considered as significant translation-regulated genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with gene counts

source_name: lung

growth_protocol: A549 and H1299 lung cancer cells were cultured in DMEM (BI, Cat#06-1055-57-1ACS) and RPMI 1640(BI, Cat#01-100-1ACS) supplemented with 10% FBS (Viva Cell, C04001-500) and 1% Penicillin-Streptomycin (Life,15140122) at 37℃ with 5% CO2.

extract_protocol:
Input RNA was extracted with TRIzol LS followed by chemical fragmentation. Ribo-seq samples were produced by RNase I digestion followed by RNA extraction using TRIzol LS.
40-60nt region for input and 30nt for ribo-seq were selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. The purified RNA was dephosporylated and added with 3’adapter. The 5’ adapter was added after reverse transcription. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: A549 with H1299 lung cancer cells are treated with fresh complete medium for 2 h

value: lung

value: Non-Small Cell Lung Cancer

value: METTL5 knockout

value: treated with CHX for 5min,normal culture


title: siNT_rep2


title: siCnot1_rep1


title: shYtdhf2_Mut


title: H1299 sgCtrl input

value: WT


title: H1299 sgM5 ribo-seq rep3


title: H1299 sgM5 input rep1


title: GBM tumorsphere, untreated control, replicate 3


title: H1299 sgM5 ribo-seq rep2


title: siNT_rep1


title: shYthdf2_WT


title: H1299 sgM5 ribo-seq rep1


title: shYthdf2_EV


title: H1299 sgCtrl ribo-seq


title: H1299 sgM5 input rep3


title: shscr_EV


title: A549 sgM5 input rep3


title: A375 cells, sgYAE1-2

city: Guangzhou

first: Xiaoling

state: Guangdong

address: No. 195, West Dongfeng Road

institute: Guangzhou Medical University

data_processing:
The quality of raw reads was assessed using the FANSe algorithms, and then the adapters were trimmed using Cutadatp (v4.8) and the low-quality reads were filtered out for percentage of N base larger than 10% and rRNA sequences.
Assembly: Clean reads were subsequently mapped to the human genome (HUMAN GENCODE 34 GRCh37) using START (v2.7.10b) software.
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

extract_protocol:
RNA was isolated using the RaPure Total RNA Micro Kit (Magen, R4012-03).
RNA purity was assessed using Nanodrop and its integrity is evaluated using Agilent 4200 TapeStation. 1 μg RNA per sample was used as input for the library preparation following standard protocols. Library preparations were sequenced on a NovaSeq 6000 platform (Chi-Biotech, Guangzhou, China) and 150 bp stand-specific paired-end reads were generated.

value: human melanoma cells

value: Yae2 knockout


title: HFD-STZ+DH_A3

city: HAJIPUR

first: NIVEDITA

last: SINGH

address: INDUSTRIAL AREA HAJIPUR

department: Pharmacology and Toxicology

country: India

institute: NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH HAJIPUR

description:
Library name: Sample 9: NHP001 A3
Column name in counts_raw.txt:  NHP001 A3

data_processing:
Prepared libraries were sequenced on Illumina Nextseq 2K to generate 40M, 2x150bp reads /sample. Up to 75% of the sequenced bases were of Q30 value >90. Sequenced data were processed to generate FASTQ files and proceeded with data analysis.
Paired-end raw sequence reads quality report is generated by using FastQC to estimate base quality and contamination by sequencing artefacts. Trim Galore is used to perform trimming of adapters and poor-quality sequences. Trimmed sequence reads are mapped to the reference transcriptome with STAR splice aware alignment tool. Rsubread R package is used to obtain feature specific expression counts. Low count features across samples are detected and removed with NOISeq R package. Expression counts normalization was performed with TMM method from NOISeq R package. Estimation of significant differential features was performed with NOISeq R package which simulates technical replicates for data without biological replicates. Enrichment of functional annotation was performed with R package gprofiler2.
The UCSC Genome Browser of mice version mm39, GRCm39 (GCA_000001635.9), Jun. 2020 was used as reference genome for identifying differential transcriptome.
Assembly: UCSC Genome Browser of mice version mm39, GRCm39 (GCA_000001635.9), Jun. 2020
Supplementary files format and content: count_raw.txt files are included for each sample

source_name: kidney

growth_protocol: Six week old mice were fed either an HFD (49.0% of total calories from fats, 24.20% from protein, and 29.23% from carbohydrate) or a normal calorie diet (NCD) (calories: fats 11.32%, proteins 22.48%, carbohydrates 63.0%). In addition, mice in the HFD group received two low doses of STZ (30 mg/kg, ip) on days 60th and 63rd of the dietary modification. Diabetes was confirmed on day 65 by elevated fasting blood glucose levels.

extract_protocol:
9 kidney tissues samples were extracted using RNeasy mini kit (Cat no: 74106) and quantified accordingly. Concentrations of RNA were measured with the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and Qubit 4 Fluorometer (Thermo Fisher Scientific – IN) while RNA quality was assessed with the Tapestation 4200™ (Agilent Technologies, Santa Clara, US).
For library preparation, 9 RNA samples were taken with an initial RNA input of 500ng. “KAPA mRNA Capture kit” were used for mRNA capture by oligo mag beads, followed by mRNA fragmentation using heat and magnesium. The KAPA RNA Hyper prep kit for Illumina sequencing contains all the buffers and enzymes required for the rapid construction of stranded mRNA-Seq libraries. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA where Uracil is added instead of Thymine and adds dAMP to the 3′ ends of the resulting dscDNA. In Adapter ligation, where dsDNA adapters with 3′ dTMP overhangs are ligated to library insert fragments followed by library amplification, to amplify library fragments carrying appropriate adapter sequences at both ends using high-fidelity, low-bias PCR. The strand marked with dUTP is not amplified, allowing strand-specific sequencing.

treatment_protocol: After confirming the hyperglycemic state, HFD-STZ-treated mice were administered dehydrozingerone (50 mg/kg, orally) for two weeks.

value: kidney

value: Dehydrogingerone


title: A549 sgM5 input rep2


title: HFD-STZ+DH_A2

description:
Library name: Sample 8: NHP001 A2
Column name in counts_raw.txt:  NHP001 A2


title: A375 cells, sgYAE1-1

value: Yae1 knockout


title: A549 sgM5 input rep1


title: A375 cells, sgAbce1-2

value: Abce2 knockout


title: HFD-STZ+Veh_A2

description:
Library name: Sample 5: HFD A2
Column name in counts_raw.txt: HFD A2


title: A549 sgM5 ribo-seq rep2


title: HFD-STZ+DH_A1

description:
Library name: Sample 7: NHP001 A1
Column name in counts_raw.txt:  NHP001 A1


title: A549 sgM5 ribo-seq rep3


title: A549 sgCtrl input


title: NCD+Veh_A1

description:
Library name: Sample 1: Control A1
Column name in counts_raw.txt: ControlA1


title: A375 cells, sgCon-2

value: wild type


title: HFD-STZ+Veh_A1

description:
Library name: Sample 4: HFD A1
Column name in counts_raw.txt: HFD A1


title: H2AZ_control_GO_untreated

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Library name: Sample9

data_processing:
*library strategy: CATCH-seq, CUT&RUN
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10, dm6
Supplementary files format and content: bigwig

source_name: ovary

extract_protocol:
After ZP of SN-type FGOs were removed by acid tyrodes’ solution, ZP-free oocytes were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80C until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21C or 37C for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021).
CUT&RUN libraries were prepared as previously described (Hayashi and Inoue 2023). The antibodies used were mouse anti-H2A (1/100, MBL D210-3), rabbit anti-H2A.X (1/100, Abcam 11175), and rabbit anti-TH2A antibody (1/100) (Shinagawa et al. 2014). Protein A-MNase was provided by the Steven Henikoff Lab (Skene and Henikoff 2017). For CATCH-seq, 3 uL of rabbit anti-H2A.Z (Active motif 39113, 200 oocytes/library), 500 ng of mouse anti-H2A (MBL D210-3, 200 oocytes/library), 1 uL of rabbit anti-H2A.X (Abcam ab11175, 200 oocytes/library), 500 ng of rabbit anti-TH2A antibody (a gift from Shunsuke Ishii, 200 oocytes/library) (Shinagawa et al. 2014), 0.25 uL of rabbit anti-H3K4me3 (Active Motif 39159, 40 oocytes/library), 500 ng of rabbit anti-H3K27me3 (Diagenode C15410069, 80 oocytes/library), or 1.0 µl of rabbit anti-H2AK119ub1 antibody (Cell Signaling Technology 8240, 500 oocytes/library) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. The quality of these antibodies was validated in previous studies [H2A.Z (Murphy et al. 2018), H2A (Inoue and Zhang 2014), H2A.X (Inoue and Zhang 2014), TH2A (Shinagawa et al. 2014), H3K4me3 (Kaya-Okur et al. 2020), H3K27me3 (Inoue et al. 2018), H2AK119ub1 (Mei et al. 2021)]. After immunoprecipitation at 4C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 13-15 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37C for 2 hrs followed by heat inactivation at 65C for 20 min and purified by 0.9x SPRIselect beads.

treatment_protocol: Growing oocytes (GO) were collected from ovaries of 10-11 day-old BDF1 females. They were incubated in α-MEM/5% FBS containing 100 µM 5, 6-Dichloro-1-β-D-Ribofuranosyl-1H-Benzimidazole (DRB, Cayman Chemical 53-85-0), 0.2% DMSO (the solvent of DRB), or 100 µg/mL α-amanitin (Fiji-film 010-22961). For each CATCH-seq library construction, 250-300 GOs were collected at 24 hrs culture under the inhibitors.

value: ovary

tag: developmental stage

value: 10d growing oocyte


title: A375 cells, sgAbce1-1

value: Abce1 knockout


title: NCD+Veh_A2

description:
Library name: Sample 2: Control A2
Column name in counts_raw.txt: ControlA2


title: Input_100Amanitin_GO

description: Library name: Sample12

value: amanitin-treated


title: A375 cells, sgCon-1


title: HFD-STZ+Veh_A3

description:
Library name: Sample 6: HFD A3
Column name in counts_raw.txt: HFD A3


title: Input_control_GO_untreated

description: Library name: Sample11

value: untreated


title: H2AZ_100Amanitin_GO

description: Library name: Sample10


title: TKPTS cell, pcDNA,rep2

city: Shenyang

first: Ling

last: Hou

email: 79594942@qq.com, houl@sj-hospital.org

address: No.36 Sanhao street

institute: China Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: TKPTS

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: TKPTS

value: renal proximal tubule cells


title: Input GO DRB-24h treated

description: Library name: Sample8

value: DRB-24h treated


title: NCD+Veh_A3

description:
Library name: Sample 3: Control A3
Column name in counts_raw.txt: ControlA3


title: A549 sgCtrl ribo-seq

value: lung

value: Non-Small Cell Lung Cancer

value: treated with CHX for 5min,normal culture


title: A549 sgM5 ribo-seq rep1

value: METTL5 knockout


title: R112H-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone F8_(10)

city: Prague

first: Viktor

last: Stranecky

state: Czech Republic

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Salmon output file and raw expression matrix

data_processing:
The raw FASTQ files were subjected to QC control and trimmed using Atropos (version1.128).
Gene-level abundances were estimated using Salmon (version 1.3)  with the Ensembl gene definition version 75 (hg19).
Normalization and differential expression analyses were performed within DESeq2 R package.
Assembly: hg19
Supplementary files format and content: raw.csw -  expression matrix - unnormalized data
Supplementary files format and content: *.sf files - gene-level expression for individual samples output from Salmon

source_name: cell line

growth_protocol: HEK293 cells stably producing p.394P AGAL-FLAG, classic FD causing variant p.112H AGAL-FLAG or WT AGAL-FLAG were seeded to T25 flasks (4*106 cells per flask) and grown for next 48 hours in selective culture media. Then cells were mechanically harvested by scrape into PBS1x, pelleted (by centrifugation - 800g / 8 mins) and immediately freezed on dry ice.

extract_protocol:
Cells were mechanically harvested, RNA was isolated using RNeasy Mini Kit (Qiagen), 0.5ug of total RNA was used for the constraction of sequencing libraries
RNA librarioes for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer´s protocols

treatment_protocol: no treatment

value: cell line

value: Human Embryonic Kidney 293 cell line

value: HEK cells stably producing eithe wt, or mut-AGAL

value: no treatment


title: Input GO DMSO-24h treated

description: Library name: Sample7

value: wild type

value: DMSO-24h treated


title: H2A.Z GO DRB-24h treated

description: Library name: Sample6

value: ovary

value: 10d growing oocyte


title: L394P-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone C8_(100)


title: H2A.Z GO DMSO-24h treated

description: Library name: Sample5


title: TKPTS cell, pcDNA,rep1

value: WT


title: TKPTS cell, pcDNA,rep3


title: RNA-seq FGO Mll2 KO rep2

data_processing:
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
About 20 FGOs per sample were pooled to generate each RNA-seq library. The zona pellucida was removed by brief incubation in acidic Tyrode's solution. All samples for RNA-seq were washed three times in 0.2% BSA/PBS before being transferred into a 0.2-ml tube with ~0.5μl carryover.
For RNA-seq, libraries were prepared as previously described (Inoue et al., Genes Dev. 2018). Briefly, cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA, 634890) according to the manufacture's instructions. Two hundreds picograms of cDNA were used for the library construction by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to the manufacture's instructions.

value: Full-grown oocyte

value: Mll2 knockout


title: RNA-seq FGO Mll2 KO rep1


title: RNA-seq FGO Mll2 WT rep2


title: TKPTS cell, HNF3α overexpression,rep3

value: TKPTS

value: renal proximal tubule cells

value: HNF3alpha overexpression


title: Input Mll2 WT FGO rep1

data_processing:
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10, dm6
Supplementary files format and content: bigwig


title: RNA-seq FGO Mll2 WT rep1


title: H2A.Z Mll2 KO FGO rep2


title: Input Mll2 KO FGO rep1


title: H2A.Z Mll2 KO FGO rep1


title: L394P-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone C4_(10)


title: H2A.Z Mll2 WT FGO rep2


title: TKPTS cell, HNF3α overexpression,rep2


title: DM3

city: Xiamen

first: Yijun

last: Lin

state: Fujian

address: NO.2999, Jinshan Road, Huli District, Xiamen, China

institute: Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University

data_processing:
CLC Genomics Workbench v 11.0.1
Reads were trimmed for adaptor sequence using CLC genomic benchwork with quality limit 0.05.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

source_name: Peritoneal macrophages

extract_protocol:
Mice were i.p. with 1.5mL of 3% thioglycollate.3 days later, mouse were sacrificed, peritoneally injected with 10mL PBS and the peritoneal exudate was collected 5 minutes later. The cells were collected by 800×g, 10 minutes centrifugal and for RNA isolation with TriZOL.
RNA libraries for RNA-seq were preparing with SMARTER mRNA-seq Library Pre Kit following manufacturer's protocols.

treatment_protocol: APOE-/- mice were rendered diabetes from 8 weeks of age by intraperitoneal injections of streptozotocin (STZ, 40 mg/kg) or citrate buffer (nondiabetic) on 5 consecutive days, then the mice were fed with western diet for 8 weeks.

value: Peritoneal macrophages

value: APOE-/-

value: streptozotocin (diabetes)


title: R112H-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone C9_(10)

value: cell line


title: Patient_GV

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

institute: Guangxi university

data_processing:
quality-controlled and filtered using SOAPnuke (v1.5.2)
mapping by TopHat (version 2.0.6)
annotation by Cufflinks (v2.2.1)
Functional annotation was performed using the Database for Annotation, Visualization, and Integrated Discovery (https://david.ncifcrf.gov/).
Statistical analyses were performed using R software (http://www.rproject.org).
Assembly: GRCh38
Supplementary files format and content: Raw fastq and FPKM files for each Sample

source_name: Ovary

extract_protocol:
RNA-Seq Library Preparation: Oocytes or embryos were collected from healthy control and patient (oocytes at the germinal vesicle (GV) stage and embryos at the 1-cell stage).
Then total RNA was extracted using the RNeasy micro kit (QIAGEN) following the manufacturer’s instructions after picking the cells into 350 mL of the lysis buffer supplied in the kit. Libraries were prepared using an NEBNext Ultra.

value: Ovary

value: Oocyte

value: Patient

value: no


title: H2A.Z Mll2 WT FGO rep1

value: wild type


title: R112H-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone D9_(100)

value: Human Embryonic Kidney 293 cell line

value: HEK cells stably producing eithe wt, or mut-AGAL

value: no treatment


title: DM2


title: Patient_1cell3

source_name: early embryo

value: early embryo


title: wt-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone B6_(100)


title: L394P-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone E8_(100)


title: wt-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone F4_(10)


title: DM4


title: DM1


title: Patient_1cell1


title: Quad_D8_DKO_rep4 [S36]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description: P14 cells d8 post LCMV Cl13 infection

library_source: other

data_processing:
FASTQ files were aligned using STAR 2.5.2a against the mm10 mouse reference genome
The aligned files were processed using PORT (https://github.com/itmat/Normalization) to normalize at the read level by resampling and to quantify gene counts
Differential gene expression was performed with R package Limma (version 3.50.0)
Limma-voom function was used to identify transcripts that were significantly differentially expressed between experimental groups using an adjusted p-value < 0.05 or otherwise specified
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for all samples

molecule: other

extract_protocol:
mRNA of sorted cells was extracted using RNeasy Plus Micro kit (QIAGEN) according to the manufacturer’s protocol
mRNA was converted into cDNA using the SMART-Seq V4 Ultra Low Input RNA Kit (Takara Bio) according to the manufacturer’s protocol

treatment_protocol: Mice were treated with LCMV clone 13 infection

value: Spleen

value: CD8 T cells

value: Lag3&PD1 knockdown

value: LCMV clone 13


title: Quad_D8_PD1KO_rep4 [S35]

description: P14 cells d8 post LCMV Cl13 infection

value: PD1 knockdown


title: Control_GV4

value: Control


title: NC-3

city: guangdong

first: chen

middle: feng

last: zhi

address: 深圳市光明区新湖街道中山大学医学园南721

institute: chen

data_processing:
During sequencing, the Raw Reads obtained may include reads with relatively low overall quality, sequencing adapters, and bases with low quality at the ends. These unqualified reads are likely to have a certain impact on the quality of the analysis. Therefore, it is necessary to filter them out to obtain clean Reads that can be used for data analysis. Seqtk  is used for filtering, with the following main steps:
1.Eliminate adapter sequences contained in reads;
2.Discard bases at the 3' end with a quality score (Q) lower than 20, which corresponds to a base error rate of less than 0.01, where Q=-10log(error_ratio);
3.Remove reads shorter than 25 bases;
4.Exclude reads of ribosomal RNA from the corresponding species.
The spliced mapping algorithm of Hisat2 (version: 2.0.4) was used to map preprocessed reads to the genome, allowing the mapping of reads that do not fully match by splitting them. This algorithm is particularly suitable for eukaryotic transcriptome sequencing data that contain intron intervals. Default parameters were employed.
In transcriptome sequencing, we estimate gene expression levels by mapping the number of reads to gene regions. However, the read count not only correlates with gene expression levels but also depends on the gene length and the sequencing data volume. To ensure comparability of gene expression levels between different genes and samples, reads are converted to FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for standardization . Initially, we utilize Stringtie (version: 1.3.0) to tally the fragment counts for each gene post alignment by Hisat2. Subsequently, normalization is performed using the TMM (trimmed mean of M values) approach, followed by FPKM value computation for each gene using a Perl script.
Supplementary files format and content: FPKM

extract_protocol:
To extract total RNA, we utilized the MJzol Animal RNA Isolation Kit (Majorivd) following the standard protocol provided by the manufacturer. Subsequently, we purified the RNA using the RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN). The integrity of the RNA was assessed with the Agilent 2100 Bioanalyzer/Agilent 4200 TapeStation (Agilent technologies), while the total quantity and purity of RNA were measured using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific).
Following RNA purification, the Total RNA is further processed for mRNA separation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3' end A-tailing, adapter ligation, and enrichment to complete the construction of the mRNA sequencing library.
Subsequently, the library concentration is determined using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and the fragment distribution is analyzed with the Agilent 4200 TapeStation (Agilent technologies).

value: human embryonic kidney cells

value: WT

value: medium containing 10μM nitidine chloride for 12 hours


title: TKPTS cell, HNF3α overexpression,rep1

value: TKPTS

value: renal proximal tubule cells

value: HNF3alpha overexpression


title: Quad_D8_Lag3KO_rep4 [S34]

description: P14 cells d8 post LCMV Cl13 infection

value: Lag3 knockdown


title: Ctrl4

value: Peritoneal macrophages

value: APOE-/-

value: citrate buffer (nondiabetic)


title: Ctrl2


title: wt-AGAL in pCR3.1 plasmid, C-term FLAG tagged, clone D4_(10)

value: cell line

value: Human Embryonic Kidney 293 cell line

value: HEK cells stably producing eithe wt, or mut-AGAL

value: no treatment


title: Ctrl1


title: Control_GV1

value: Ovary

value: Oocyte

value: no


title: DMSO-2

address: 深圳市光明区新湖街道中山大学医学园南721

value: human embryonic kidney cells

value: DMSO-containing medium for 12 hours


title: DMSO-3

address: 深圳市光明区新湖街道中山大学医学园南721

value: WT


title: Quad_D8_WT_rep4  [S33]

description: P14 cells d8 post LCMV Cl13 infection

value: Spleen

value: CD8 T cells

value: LCMV clone 13


title: Quad_D8_PD1KO_rep3 [S31]

description: P14 cells d8 post LCMV Cl13 infection

value: PD1 knockdown


title: Control_1cell10

value: early embryo

value: Control


title: mESC_RNAseq.shYthdf2_rep2

value: embryo

value: mouse embryonic stem cell


title: Quad_D8_Lag3KO_rep3 [S30]

description: P14 cells d8 post LCMV Cl13 infection

value: Lag3 knockdown


title: DMSO-1

address: 深圳市光明区新湖街道中山大学医学园南721


title: Control_1cell9


title: Patient_1cell2

value: Patient


title: Quad_D8_WT_rep3  [S29]

description: P14 cells d8 post LCMV Cl13 infection


title: Control_GV3


title: NC-2

address: 深圳市光明区新湖街道中山大学医学园南721

value: medium containing 10μM nitidine chloride for 12 hours


title: NC-1

address: 深圳市光明区新湖街道中山大学医学园南721


title: Ctrl3

value: Peritoneal macrophages

value: APOE-/-

value: citrate buffer (nondiabetic)


title: Quad_D8_DKO_rep3 [S32]

description: P14 cells d8 post LCMV Cl13 infection

value: Lag3&PD1 knockdown


title: Quad_D8_DKO_rep2 [S28]

description: P14 cells d8 post LCMV Cl13 infection


title: Control_1cell8

value: no


title: mESC_RNAseq.shScramble_rep2


title: mESC_RNAseq.shScramble_rep1


title: mESC_RNAseq.shYthdf2_rep1


title: 19577X114 PG10 C Bead

city: Salt Lake City

first: Matthew

middle: T

last: Rondina

state: Utah

department: Hematology

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
The output files were summarized using MultiQC to check for sample outliers and plot alignment statistics
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCh38
Supplementary files format and content: featureCount ouput files combined into a single tab-delimited raw count matrix

source_name: Blood

extract_protocol:
RNA from with Washed Platelets or Leukocyte-depletion using CD45 beads, or PALL-filtered platelets, were isolated using the standard TRIzol® protocol (ThermoFisher #15596018) with the addition of 20 µg glycogen (Sigma #10901393001) at the isopropanol precipitation step.  Following a 75% ethanol wash, RNA pellets were allowed to air dry. RNA pellets were next suspended in nuclease-free water. Any potential contaminating DNA was digested 25 minutes at 37°C using Turbo DNA Free Kit (ThermoFisher AM1907) and the final RNA was cleaned and eluted in 26 µl nuclease-free water using Zymo RNA Clean & Concentrate kit (Zymo R1017) following the product instructions.
Intact poly(A) RNA was purified from total RNA samples (150 ng) with oligo(dT) magnetic beads. RNA concentration was evaluated using a Nanodrop (ThermoFisher Scientific; Illkirch, France). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102) with PolyA Selection. The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were normalized to 5 nM and equal volumes were pooled in preparation for sequencing. RNA was sequenced by an Illumina NovaSeq sequencer using the NovaSeq 6000 using v1.5 reagents and S4 flow cell to produceKit 1 150x150 bp (paired end reads).

value: Blood

value: platelets

tag: isolation technique

value: Leukocyte-bead depletion Isolation


title: Control_GV2

value: Ovary

value: Oocyte


title: Quad_D8_Lag3KO_rep2 [S26]

description: P14 cells d8 post LCMV Cl13 infection

value: Spleen

value: CD8 T cells

value: LCMV clone 13


title: 19577X113 PG10 B Washed Plts

value: Washed Platelet Isolation


title: 19577X112 PG09 C Bead


title: Control_1cell7

value: early embryo

value: Control


title: 19577X111 PG09 B Washed Plts


title: Control_1cell5


title: mESC_RIPseq.Ythdf2IP_rep1_IP

data_processing:
To get high quality clean reads, reads were further filtered by fastp (https://github.com/OpenGene/fastp, version:fastp-0.19.4). We aligned reads of all samples to the mm10 reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, and then maps the reads to the reference genome.The DESeq2 package(1.40.2) was employed to identify peaks associated with Ythdf2 binding.
Assembly: mm10
Supplementary files format and content: .txt files include Ythdf2 binding counts

extract_protocol:
Total RNA was extracted and purified using Trizol reagent(Invitrogen) following the manufacturer's procedure.The RNA used in immunoprecipitation reactions with anti-YTHDF2 (abcam,ab220163) as IP.
The RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA).An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform following the vendor’s recommended protocol.

treatment_protocol: RIP-seq was performed in mESCs using anti-Ythdf2 antibody.

value: embryo

value: mouse embryonic stem cell


title: Ctrl5

value: Peritoneal macrophages

value: APOE-/-


title: Quad_D8_WT_rep2  [S25]

description: P14 cells d8 post LCMV Cl13 infection

value: WT


title: Control_1cell6

value: no


title: mESC_RIPseq.Ythdf2IP_rep2_IP


title: Quad_D8_PD1KO_rep2 [S27]

description: P14 cells d8 post LCMV Cl13 infection

value: PD1 knockdown


title: Control_1cell4


title: mESC_RIPseq.Ythdf2IP_input


title: Quad_D8_DKO_rep1 [S24]

description: P14 cells d8 post LCMV Cl13 infection

value: Lag3&PD1 knockdown


title: 19577X110 UD10 Bead

value: Blood

value: platelets

value: Leukocyte-bead depletion Isolation


title: 19577X107 UD09 Washed Plts


title: mESC_MeRIPseq.Dox_rep2_input

data_processing:
To get high quality clean reads, reads were further filtered by fastp (https://github.com/OpenGene/fastp, version:fastp-0.19.4). We aligned reads of all samples to the mm10 reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, and then maps the reads to the reference genome. the R package of Exomepeak(http://www.bioconductor.org/packages/2.13/bioc/html/exomePeak.html) was used to predict the site of m6A. And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Assembly: mm10
Supplementary files format and content: .bed files include methylation level

extract_protocol:
Total RNA was extracted and purified using Trizol reagent(Invitrogen) following the manufacturer's procedure. Poly(A) RNA was subsequently isolated from the total RNA using oligo dT beads (New England BioLabs, S1419S) to remove rRNA.The mRNA was then chemically fragmented into 150 nt fragments.Enrichment of m6A-modified mRNA was carried out using anti-m6A antibody (abcam, ab151230).
The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA).An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor’s recommended protocol.
MeRIP-seq

treatment_protocol: The mouse embryonic cells were treated with Dox or DMSO for 24 h


title: Pt13, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

first: Michael

last: Klichinsky

state: Pennsylvania

address: 3675 Market Street Ste. 401

institute: Carisma Therapeutics

description: Library name: Pt13_PD_Week4_Tumor

data_processing:
Data processing was performed by Adaptive Biotechnologies according to their pipeline
Assembly: MM10
Supplementary files format and content: tab-delimited text file with TCR sequences, counts, frequencies, and VDJ gene predictions
Library strategy: TCR-Seq

source_name: Tumor

extract_protocol:
Extraction performed by Adaptive Biotechnologies
Library construction performed by Adaptive Biotechnologies

value: Tumor

value: CT-0508 CAR Macrophages


title: mESC_MeRIPseq.Dox_rep1_input


title: Control_1cell2


title: 19577X106 C11 Filter

value: PALL-Filtration Isolation


title: Control_1cell3


title: Quad_D8_Lag3KO_rep1 [S22]

description: P14 cells d8 post LCMV Cl13 infection

value: Spleen

value: CD8 T cells

value: Lag3 knockdown

value: LCMV clone 13


title: Pt13, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt13_PD_Day8_Tumor


title: 19577X109 UD10 Washed Plts

value: Washed Platelet Isolation


title: Quad_D8_WT_rep1  [S21]

description: P14 cells d8 post LCMV Cl13 infection


title: mESC_MeRIPseq.Dox_rep1_IP

value: embryo

value: mouse embryonic stem cell


title: Control_1cell1

value: early embryo

value: Control


title: Mouse #91 Lin-

city: Hannover

first: Tobias

last: Maetzig

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (v 1.4.2). The pipeline uses Nextflow ( v20.01.0) workflow tool and includes read trimming (Trim Galore! v0.6.4), alignment (STAR v2.6.1d), and counting (featureCounts  v1.6.4).
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table”, “Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering”, all of which were set to “True”.
Assembly: GRCm38.p6; release M25
Supplementary files format and content: Tab-delimited text files include normalized espression values as a matrix table for all samples (DESeq2 output)

source_name: Bone marrow

extract_protocol:
For RNA isolation, the Qiagen RNeasy Micro Kit (Qiagen, Hilden, Germany) was used according to the manufacturer’s protocol.
Library generation:   2ng of total RNA (except for sample N2591: 1ng) were used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (#634413; Takara/Clontech) according to conditions recommended in user manual #063017. Generated libraries were barcoded by dual indexing approach and were finally amplified with 12 cycles of pcr. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).    Sequencing run:   Equal molar amounts of nine libraries were pooled along with additional unrelated libraries for a common sequencing run. Each of the nine analyzed libraries constitutes 10% of overall flowcell capacity. The library pool was denatured with NaOH and was finally diluted to 2pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for single reads (20024906; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 38 bases each; Index reads 1 and 2 with 8 bases each.

value: bone marrow

value: Lin-cKit+ progenitor cells (Lin-)


title: mESC_MeRIPseq.Dox_rep2_IP


title: mESC_MeRIPseq.DMSO_rep2_input


title: Mouse #57 Lin-


title: 19577X105 C11 Bead

value: Blood


title: Pt13, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt13_PD_Week4_Blood


title: 19577X104 C11 Washed Plts

value: platelets


title: 19577X103 C10 Filter


title: mESC_MeRIPseq.DMSO_rep1_input


title: Quad_D8_PD1KO_rep1 [S23]

description: P14 cells d8 post LCMV Cl13 infection

value: PD1 knockdown


title: Mouse #56 Lin-


title: Pt13, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt13_PD_Day15_Blood


title: 19577X108 UD09 Bead

value: Leukocyte-bead depletion Isolation


title: mESC_MeRIPseq.DMSO_rep2_IP


title: Mouse #87 Lym

value: lymphoid cells (Lym+)


title: Pt4, Stable Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt4_SD_Week4_Tumor

value: Tumor

value: CT-0508 CAR Macrophages


title: Mouse #63 Lym


title: mESC_MeRIPseq.DMSO_rep1_IP


title: 19577X101 C10 Washed Plts


title: Mouse #62 Lym


title: 19577X99 UU22 Washed Plts


title: Pt4, Stable Disease, Screening, Tumor, TCR-seq

description: Library name: Pt4_SD_Screening_Tumor

value: Screening


title: Pt4, Stable Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt4_SD_Day15_Blood


title: Pt4, Stable Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt4_SD_Day8_Tumor


title: 19577X98 UU21 Bead


title: ChLPS_scRNAseq

city: Edmonton

first: Jason

middle: R

last: Plemel

state: AB

country: Canada

institute: University of Alberta

description: 10x Genomics

data_processing:
The BCL file was demultiplexed to a FASTQ file and aligned to a custom Rattus norvegicus (6.0) reference genome manually annotated to include Clec7a, a polymorphic pseudogene. The samples were aligned to the genome with the count function from the 10x cell ranger pipeline (v3.0.0) to generate barcoded and sparse matrices.
Assembly: Rattus norvegicus (6.0)
Supplementary files format and content: A .h5 file that has been filtered by the CellBender (v0.3.0; https://github.com/broadinstitute/CellBender) pipeline to remove ambient RNA.

organism: Rattus norvegicus

source_name: Spinal Cord

extract_protocol:
Rats were euthanized with 1 mL of Euthanyl injected intraperitoneally, and then transcardially perfused with Hanks’ Balanced Salt Solution (HBSS, ThermoFisher, 14175-103). All spinal cords were dissected and a 2 cm section surrounding the lesion site was isolated within 90 min after perfusion and maintained on ice for the duration of the cell sorting experiment. Spinal cords were diced in HBSS and then collected and placed into Dulbecco’s Modified Eagle Medium (DMEM, Gibco, 11960069) and deoxyribonuclease (5 μg/mL, Worthington, L3002007). Collected tissue was mechanically dissociated and dounced 5 times with a loose-fitted dounce homogenizer; following which the suspension was passed through 70 μm and 40 μm filters. Cells were then pelleted, resuspended in 5.4 mL of HBSS and myelin debris was removed using 1800 μl of Debris Removal Solution (Miltenyl Biotec, 130-109-398) and centrifugation at 3000 G for 10 min. The myelin debris was removed and cells were topped up to 15 mL with HBSS and centrifuged at 1000 G for 10 min. Cells were passed through a 20 μm filter, following which cells were resuspended in Fc block Anti-Mo CD16/CD32 (1:200, Invitrogen, 14-0161-85) blocking solution for 5 min, and subsequently stained with ZombieAqua (1:50, Biolegend, 423101), DRAQ5 (1:1000, ThermoFisher, 62240) and Cd11b (1:50, BD BioSciences, 561684) for 20 min. Cells were resuspended in a solution of 1% bovine serum albumin (BSA; Sigma-Aldrich, A8806) dissolved in HBSS and then were isolated using fluorescence-activated cell sorting (FACS) on a Sony MA700 and gated for live, nucleated and Cd11b+ cells. Following sorting, cells were manually counted using a hemocytometer, pelleted and resuspended in HBSS.
The FACS-isolated cells were processed using the 10x Genomics Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics; 1000121) and sequenced on the Illumina HiSeq P150 Sequencer (Novogene). The samples were paired-end, single index sequenced to an average of 40,000 reads per cell.

treatment_protocol: C4 dorsolateral quadrant hemitransection spinal cord injury. Animals were perfused at 8 days post injury, 60 days post injury with a sham injection (ChSaline), 60 days post injury with an LPS injection (ChLPS) or spinal cord tissue was extracted from uninjured animals.

value: Spinal Cord

value: Leukocytes

tag: strain

value: Lewis

tag: Sex

value: Female

tag: group

value: chronic with LPS

value: C4 dorsolateral quadrant hemitransection injury

tag: time

value: 60 days post injury + 3 days post-LPS injection


title: FcgRIIB-/- IRF7_input1

last: Gonzalez

address: 3535 Market St

department: Translational Medicine and Human Genetics

description: FACS sorted live cells CD3- B220+CD19+IgD-

data_processing:
For ChIPseq, data was processed and analyzed in Bioconductor. Sequences were aligned to reference genome mm9. Peaks were called against input controls using Macs2. Peaks were visualized in IGV.
Assembly: mm9
Supplementary files format and content: processed data includes .bw files

source_name: spleen

extract_protocol: Not provided

value: spleen

tag: age

value: 3 month old

value: B cells

value: FcgRIIB-/-

value: female


title: FcgRIIB-/- IRF7_input2


title: Naïve_scRNAseq

description: 10x Genomics

value: naive

value: uninjured animal


title: 19577X97 UU21 Washed Plts

value: Blood

value: platelets

value: Washed Platelet Isolation


title: ChSaline_scRNAseq

description: 10x Genomics

value: Spinal Cord

value: chronic with saline

value: 60 days post injury + 3 days post saline injection


title: FcgRIIB-/- IRF7 ChIP 1


title: FcgRIIB-/-IRF7-/- scRNA 2

description: FACS sorted live cells CD3- B220+CD19+ (90% IgD- and 10% IgD+

data_processing:
Sequencing was performed on an Illumina HiSeq sequencer. Data was then processed through the Cellranger pipeline (10x Genomics). Demultiplexing and alignments were performed against the mm10 transcriptome. Analysis was performed via Seurat package (v. 4.99) within R. Cells expressing less than 200 or more than 4000 unique genes were excluded from further analysis. Cells with >10% mitochondrial genes expression were also excluded. Log normalization and scaling of features was completed before principal component dimensionality reduction, clustering, and visualization via UMAP. Pseudotime analysis was performed using the Monocle3 package in R. A wilcoxon rank sum test with a Bonferroni multiple testing correction was used to identify differentially expressed genes between FcgRIIB-/- and FcgRIIB-/-IRF7-/- groups.
Assembly: mm10
Supplementary files format and content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics). An additional processed data file set includes the resulting filtered_contig_annotations.csv file for each library which contains the "annotations of each high-confidence cellular contig" (10x Genomics)

extract_protocol:
Murine spleens processing the tissue into a single cell suspension followed by RBC lysis using Tris-Ammonium Chloride. CD3-B220+CD19+IgD- and CD3-B220+CD19+IgD+ cells were sorted from each animal and mixed at a ratio of 9:1 (IgD-: IgD+) prior to library preparation.
Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v2 per manufacturer’s instructions.


title: Pt4, Stable Disease, Screening, Blood, TCR-seq

description: Library name: Pt4_SD_Screening_Blood

value: Screening


title: 19577X102 C10 Bead

value: Leukocyte-bead depletion Isolation


title: 19577X96 UU20 Bead


title: Pt13, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt13_PD_Screening_Blood


title: Pt4, Stable Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt4_SD_Week4_Blood

value: CT-0508 CAR Macrophages


title: 19577X100 UU22 Bead


title: FcgRIIB-/- IRF7 ChIP 2


title: FcgRIIB-/-IRF7-/- scRNA 1


title: Acute_scRNAseq

description: 10x Genomics

value: Leukocytes

value: Lewis

value: Female

value: acute

value: C4 dorsolateral quadrant hemitransection injury

value: 8 days post injury