title: IPMN63, Geomx

description: Nanostring GeoMx

value: Borderline IPMN


title: B053

status: Public on Feb 15 2024

type: SRA

city: Montreal

first: Daniel

last: Sinnett

state: QC

address: 2900 Edouard Montpetit Blvd

country: Canada

institute: University of Montreal

library_source: transcriptomic

data_processing:
Raw reads were aligned to the GRCh37 genome reference using STAR v2.5.3a.
CircRNA expression counts were obtained using CIRCexplorer3.
Assembly: grch37
Supplementary files format and content: circrna expression counts

molecule: total RNA

organism: Homo sapiens

source_name: Pediatric acute lymphoblastic leukemia

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen
Ribo-Zero Gold Kit according to Illumina's protocol

tag: diagnosis

tag: tissue

value: bone marrow

tag: gender

value: F

tag: cohort

value: discovery


title: Control-4

city: Yuzhong District

first: Lili

last: Huang

state: Chongqing

address: Chongqing

country: China

institute: The Second Affiliated Hospital, Chongqing Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Supplementary files format and content: mm10
Supplementary files format and content: TXT file contain counts for each sample

organism: Mus musculus

source_name: kidney cortex

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bilateral flank incisions were made to expose the kidneys, and renal ischemia was induced for 22 min using micro-clamps and micro-clips (RS-5420/RS-5410, Roboz, UK). The micro-clamps were removed.

value: kidney cortex

tag: genotype

value: WT

tag: treatment

value: Sham


title: IPMN17, Geomx

city: Rome

first: Antonio

last: Agostini

address: Largo Francesco Vito, 1

country: Italy

institute: Università Cattolica del Sacro Cuore

description: Nanostring GeoMx

data_processing:
Sequencing data was uploaded to the Illumina BaseSpace hub and processed with DRAGEN to obtain .dcc files
Assembly: GRCh38
Supplementary files format and content: tabular .dcc files
Library strategy: GEOmx Spatial Transcriptomics

source_name: High-grade IPMN

extract_protocol:
5μm sections from to TMA were used for library construction for spatial transcriptomics
Two IPMN TMA obtained from APGI were analyzed for spatial transcriptomics using GeoMX Human Whole Transcriptome Atlas (Nanostring, USA) following the provided protocol. TMAs were stained with GeoMX morphology kit to mark neoplastic cells (PanCK), and immune cells (CD45). After staining all TMA cores that showed signs of detachment and degradation, or contained few IPMN cells (< 100 nuclei) were discarded from the analysis. From the original set of 101 tissue cores from 61 patients, a total of 80 ROI from 46 patients were selected (multiple ROI from the same patient) for segmentation to isolate only the PanCK positive areas and exclude CD45 areas to obtain the specific transcriptome of IPMN cells

value: High-grade IPMN


title: B052

value: M

value: HHD


title: IPMN16, Geomx

description: Nanostring GeoMx


title: Control-2


title: B049

value: MLL


title: Polysome_sgDap5_Rest_1

city: Amsterdam

first: Chun-Pu

last: Lin

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: NKI-AvL

data_processing:
Read mapping was performed using STAR (2.6.0c)
Read counts per gene were quantified using HTSeq (0.12.4)
Read counts were normalised using DEseq2 (1.36.0)
Assembly: mouse GRCm38
Supplementary files format and content: Raw counts

molecule: polyA RNA

source_name: splenic

growth_protocol: CD8+ T cells were maintained in CD8 T cell medium (RPMI, 10% FBS, 100U/ml penicillin, 100μg/ml streptomycin, 10ng/ml IL-2 (ImmunoTools), and 50μM 2-mercaptoethanol (Merck)) at a concentration of 1x10^6 cells/ml

extract_protocol:
For total RNA, cells were lysed with TRIzol (Thermo Fischer) and RNA purified following the manufacturer's instructions). Polysomes were isolated on sucrose gradient as described previously (PMID: 28388414). Fractions 9-13 were collected for RNA isolated using TRIzol.
Libraries were prepared for sequencing using standard Illumina protocols (PolyA-bead enrichment).

treatment_protocol: Cells were stimulated with anti-CD3 (1.25ug per/ 2x10^6 cells) on 24-well stimulation plates for 24h. Cells were then removed from the plates and harvested for sequencing.

value: splenic

tag: cell line

value: Primary OT-I cell

tag: cell type

value: CD8 T cell

value: rest

tag: fraction

value: Polysome


title: IPMN15, Geomx

description: Nanostring GeoMx


title: IPMN13, Geomx

description: Nanostring GeoMx


title: IPMN14, Geomx

description: Nanostring GeoMx


title: B047


title: Polysome_sgCtrl_Rest_2

value: wt


title: IPMN12, Geomx

description: Nanostring GeoMx


title: B043


title: Polysome_sgDap5_Rest_2


title: TotalRNA_sgDap5_Act_2

value: TotalRNA


title: B042

value: bone marrow


title: IPMN11, Geomx

description: Nanostring GeoMx


title: Nema-JC2

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
Raw FASTQ reads were refined using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Raw FASTQ reads were refined by eliminating sequences with suboptimal quality scores. A bespoke Python script ensured the alignment of the forward and reverse reads.
Curated reads were mapped to the reference genome using the Burrows-Wheeler Aligner (BWA), employing the maximal exact match approach.
Using SAMtools, we converted the mapping outcome from SAM to BAM format and sorted it according to genomic coordinates.
The Subread package and featureCounts tool tallied the reads for each coding sequence.
Gene transcript levels were assessed using the RPKM metric.
Assembly: Pinus taeda (loblolly pine) genome (v2.01) obtained from PineRefSeq database (accessed October 23, 2023)
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

organism: Pinus densiflora

source_name: seedlings

growth_protocol: Three-year-old Pinus densiflora seedlings were obtained and maintained in a greenhouse at 25 ± 5°C with daily watering. For pinewood nematode (PWN) infection, Bursaphelenchus xylophilus was cultured on fungal hyphae of Botrytis cinerea grown on potato dextrose agar medium at 25°C for 1 week. A suspension of PWN in distilled water was adjusted to a concentration of approximately 20,000 nematodes/ml. The Bacillus subtilis JCK-1398 treatment was performed by culturing in tryptic soy broth (TSB) for 24 h at 30°C under 150 rpm.

extract_protocol:
One gram of pinewood nematode-infected needles was ground in liquid nitrogen and mixed with 15 ml of extraction buffer containing 100 mM Tris-HCl (pH 8), 2% CTAB, 30 mM EDTA, 2 M NaCl, 0.05% spermidine, 2% polyvinylpolypyrrolidinone, 2% 2-mercaptoethanol, and 1.5 mg/ml proteinase K. The suspension was incubated at 42 °C for 90 min and then extracted with 15 ml chloroform-isoamyl alcohol (24:1), with total RNAs precipitated using 10 M LiCl. After washing with 70% ethanol, the RNA pellets were dissolved in DEPC water.
Using the TruSeq RNA Sample Preparation Kit (Illumina, CA, USA), 1 µg of total RNAs was processed to produce cDNA libraries. These libraries were sequenced on a HiSeq 4000 platform (Illumina) by Macrogen (Seoul, Korea), generating 101-bp paired-end reads.

treatment_protocol: After adjusting the optical density of the JCK-1398 culture to OD600 0.8, Tween-20 was added to a final concentration of 250 µg/mL. This mixture was foliar-sprayed onto seedlings with twice at 1-week intervals on pine seedlings. Pine seedlings treated with distilled water containing 250 μg/ml Tween 20 in the same manner were used as a negative control. One week after treatment, the pine seedlings were inoculated with pinewood nematodes.

tag: infection

value: Distilled water containing 250 μg/ml Tween 20

tag: age

value: three-years-old

value: wild type

value: seedlings


title: IPMN62, Geomx

description: Nanostring GeoMx

source_name: Borderline IPMN

value: Borderline IPMN


title: Nema-JC1

description: Pine seedlings treated with distilled water


title: B040

value: discovery


title: Nema-JN3

description: Pine seedlings treated with pinewood nematode

value: Bursaphelenchus xylophilus


title: Nema-JC3


title: Polysome_sgCtrl_Act_2


title: Polysome_sgCtrl_Act_1


title: TotalRNA_sgDap5_Act_1


title: Nema-JN2


title: B039

value: F


title: 12_NWC_S12_R1

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description:
NWC
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv

data_processing:
Reads for each sample were trimmed for adapters and low-quality bases using cutadapt (v 3.4) and umitools (v1.1.1). Reads were mapped to hg38 using STAR (v.2.7.6a) and were counted by htseq-count (v 0.9.1).  Differential analysis was performed using DEseq2.
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Thermo Fisher) according to the manufacture’s protocol. Following phase separation, the aqueous phase was applied to a RNeasy Mini Kit (Qiagen) and RNA was purified according to kit instructions. Libraries were prepared using the QIAseq microRNA Library Kit from Qiagen.
Libraries were prepared using the QIAseq microRNA Library Kit from Qiagen and sequnecing using Illumina NovaSeq SP.

value: renal cell carcinoma

value: WT

value: normoxia


title: Control-1

value: kidney cortex

value: Sham


title: TotalRNA_sgCtrl_Act_2

value: splenic

value: Primary OT-I cell

value: CD8 T cell


title: Nema-JN1


title: B038

value: bone marrow


title: 11_NWB_S11_R1

description:
NWB
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv


title: TotalRNA_sgCtrl_Act_1

value: wt

value: TotalRNA


title: Nema-JBC3

description: Pine seedlings treated with pinewood nematode under enhanced resistance state

value: Bacillus subtilis JCK-1398

value: three-years-old

value: wild type


title: Nema-JBC2

value: seedlings


title: B037

value: M

value: discovery


title: B036

value: F


title: 9_NCC_S9_R1

description:
NCC
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv

value: renal cell carcinoma

value: Mutant


title: Nema-JBC1

value: Bursaphelenchus xylophilus


title: B035


title: B045


title: TotalRNA_sgCtrl_Rest_2

value: rest


title: 7_NCA_S7_R1

description:
NCA
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv

value: normoxia


title: TotalRNA_sgCtrl_Rest_1

value: splenic

value: Primary OT-I cell


title: 8_NCB_S8_R1

description:
NCB
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv


title: B034

value: bone marrow


title: JN2

description: Pine seedling treated with distilled water

value: Distilled water containing 250 μg/ml Tween 20


title: B032


title: Laminin 511-E8 0.25ug/cm2 H69 3

first: David

last: Trampert

address: Meibergdreef 69-71

department: Department of Gastroenterology & Hepatology

institute: Amsterdam UMC

description: Laminin 511-E8 0.25ug per cm2 H69_samples 1-3_raw counts

data_processing:
Raw FASTQ files were obtained and adapter sequences were trimmed using Trimmomatic v0.39.
An average of 40 million reads per sample were aligned against the human reference genome (GRCh38) using HISAT2 (v2.2.1) and counted with HTSeq v0.11.0. Quality control was performed using FastQC v0.11.9 and dupRadar v1.12.1.
Count tables were made using HTSeq and for filtering genes with more than 2 counts-per-million reads (CPM) in 2 or more of the samples were kept. Counts were normalized as previously described (PMID 20196867). Genes were reannotated using Ensembl (v105) with biomaRt. Count data was transformed to log2-counts per million (logCPM).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include untransformed raw counts for each sample.

source_name: H69 cells

growth_protocol: H69 cholangiocytes were kindly provided by Dr. Douglas Jefferson (Tufts University, Boston, MS). H69 cells were cultured in a 5% CO2 incubator as previously described and were passaged twice per week (PMID 8023938).

extract_protocol:
RNA was isolated using QIAzol lysis reagent (Qiagen) according to the spin column miRNeasy Mini Kit (Qiagen) as previously used for total RNA isolation and downstream bulk RNA sequencing (GEO GSE156519). RNA concentration and quality were assessed by the Core Facility Genomics (Amsterdam UMC) using the RNA ScreenTape and RNA integrity scores (RIN) were 9-10.
Three biological replicates per group were sent in for library preparation by KAPA mRNA Hyperprep. The RNA samples were enriched for mRNA by poly(A) mRNA capture with a library length from 150 – 850 base pairs.

treatment_protocol: H69 cholangiocytes were seeded at a density of 100.000 cells in 12-well plates and grown for 48 hours to reach confluency. Then treatment commenced with 0.25µg/cm2 recombinant human laminin 511-E8 or 10uM acetazolamide for 48 hours. Growth media with treatments were refreshed 24 hours after the start of treatment and samples were harvested after 48 hours of treatment duration.

value: H69 cells

value: Cholangiocyte

value: Wilde type

value: Human recombinant laminin 511-E8 0.25ug/cm2 for 48hrs


title: JN3

value: three-years-old

value: wild type

value: seedlings


title: Laminin 511-E8 0.25ug/cm2 H69 2


title: B029

value: F

value: discovery


title: sgCtrl_Act_2

data_processing:
Read mapping was performed using STAR (2.6.0c)
Read counts per gene were quantified using HTSeq (0.11.4)
Read counts were normalised using DEseq2 (1.30.0)
the batch effect is taken into account in the DESeq model by using the batch effect as a covariate
Assembly: mouse GRCm38
Supplementary files format and content: Raw counts

extract_protocol:
Sorted CD8 T cells were washed with PBS and resuspended in the RLT buffer (Qiagen). The total RNA was isolated using the RNeasy Mini Kit (Qiagen), including an on-column DNase digestion (Qiagen).
Librararies were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated by co-cultured with OVA-expressing tumor cells for 3w. CD8+ T cells were then sorted for sequencing.

value: CD8 T cell

value: wt

value: antigen matching tumor 3w stimulation


title: JBC3

description: Pine seedlings under enhanced resistance state

value: Bacillus subtilis JCK-1398


title: Polysome_sgCtrl_Rest_1

value: splenic

value: rest

value: Polysome


title: TotalRNA_sgDap5_Rest_2

value: Primary OT-I cell

value: TotalRNA


title: JN1

value: Distilled water containing 250 μg/ml Tween 20


title: 10_NWA_S10_R1

description:
NWA
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv

value: renal cell carcinoma

value: WT

value: normoxia


title: Laminin 511-E8 0.25ug/cm2 H69 1

value: H69 cells

value: Cholangiocyte

value: Wilde type

value: Human recombinant laminin 511-E8 0.25ug/cm2 for 48hrs


title: B028

value: bone marrow

value: F

value: discovery


title: JBC2

value: Bacillus subtilis JCK-1398

value: three-years-old

value: wild type

value: seedlings


title: Acetazolamide 10uM H69 3

description: Acetazolamide 10uM H69_samples 1-3_raw counts

value: Acetazolamide 10uM for 48hrs


title: B027


title: TotalRNA_sgDap5_Rest_1

value: splenic

value: Primary OT-I cell

value: CD8 T cell

value: rest

value: TotalRNA


title: sgCtbp1_Act_2

value: antigen matching tumor 3w stimulation


title: sgCtrl_Act_3

value: wt


title: Acetazolamide 10uM H69 2

value: H69 cells

value: Cholangiocyte

value: Wilde type


title: JBC1


title: sgCtrl_Act_1


title: B026

value: bone marrow

value: F

value: HHD


title: Acetazolamide 10uM H69 1


title: B025

value: discovery


title: sgCtbp1_Act_1


title: B024


title: JJN3, CX-5461 and Panobinostat  treatment, replicate 3

city: Melbourne

first: Jian

last: Kang

state: Victoria

address: 9 Princes street, Fitzroy

department: research division

country: Australia

institute: St Vincent's institute of medical research

description:
JJN3_counts.csv
JJN3_CX+Pano_3

data_processing:
FASTQ files were uploaded to Galaxy Australia (version 21.09)
Sequencing reads were then aligned to the reference genome (hg19/GRCh37) using HISAT2 (version 2.2.1).
The number of reads mapped to genes was counted using featureCounts (version 2.0.1).
Differential expression analysis was performed using limma-voom (version 3.50.0).
Assembly: hg19/GRcj37
Supplementary files format and content: csv file includes normalized counts for each sample

growth_protocol: Cells were cultured in RPMI-1640+20mM HEPES., 10% fetal bovine serum and 1% GlutaMAXTM L-alanyl-L-glutamine dipeptide at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Mini Kit as per the manufacturer's instructions.
PolyA selective cDNA libraries were prepared using TruSeq RNA sample preparation kit (Illumina)
3'RNA-seq

treatment_protocol: JJN3 cells were treated with 500 nM CX-5461 and 50 nM  panobinostat for 24 hours

value: multiple myeloma

value: Wild type

value: CX-5461 and panobinostat

tag: p53 status


title: Ctrl H69 3

description: Ctrl H69_samples 1-3_raw counts

value: 10ul DMSO to correct for vehicle in other groups


title: sgCtbp1_Act_3

value: splenic

value: Primary OT-I cell


title: JJN3, CX-5461 and Panobinostat  treatment, replicate 2

description:
JJN3_counts.csv
JJN3_CX+Pano_2


title: B023


title: Ctrl H69 2

description: Ctrl H69_samples 1-3_raw counts


title: Ctrl H69 1

description: Ctrl H69_samples 1-3_raw counts


title: JJN3, CX-5461 and Panobinostat  treatment, replicate 1

description:
JJN3_counts.csv
JJN3_CX+Pano_1


title: B021


title: RNA-Seq-VSV-HEK293

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Reads were aligned to the hg38 using STAR version 2.7.10, with Ensembl v36 as the genome annotation.
Stringtie was used to generate expression estimates per gene from the BAM files generated by STAR
Assembly: hg38
Supplementary files format and content: txt, expression estimates for genes in Ensembl v36

growth_protocol: HEK293 cells were cultured in DMEM medium supplemented with 10% FBS and 1%penicillin and streptomycin

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: HEK293 cells were treated with/without VSV

value: Human Embryonic Kidney 293

value: VSV 6h


title: B020


title: JJN3, Panobinostat  treatment, replicate 2

description:
JJN3_counts.csv
JJN3_Pano_2

treatment_protocol: JJN3 cells were treated with 50 nM  panobinostat for 24 hours

value: panobinostat


title: RCB4

value: B cell control

value: peripheral blood CD19+

value: normal-B

value: replication


title: B019

value: bone marrow

value: M


title: RNA-Seq-CTL-HEK293


title: RCB3

value: F


title: JJN3, CX-5461 treatment, replicate 3

description:
JJN3_counts.csv
JJN3_CX_3

treatment_protocol: JJN3 cells were treated with 500 nM CX-5461 for 24 hours


title: JJN3, Panobinostat  treatment, replicate 1

description:
JJN3_counts.csv
JJN3_Pano_1


title: OATL4_24h_Lenalidomide_2

type: RNA

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent). For comparison among multiple arrays, probe set data were median-normalized per chip.

source_name: ATL

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).

extract_protocol: Total RNA from each cell line was isolated by RNeasy Mini Kit (QIAGEN) in combination with DNase treatment (RNase-Free DNase Set, QIAGEN)

value: ATL

value: 1.5µM Lenalidomide, 24h


title: B022

value: discovery


title: OATL4_24h_Lenalidomide_3


title: JJN3, CX-5461 treatment, replicate 2

description:
JJN3_counts.csv
JJN3_CX_2

value: multiple myeloma

value: Wild type


title: B013


title: JJN3, Panobinostat  treatment, replicate 3

description:
JJN3_counts.csv
JJN3_Pano_3


title: OATL4_24h_DMSO_3

value: DMSO, 24h


title: RCB2


title: OATL4_24h_Lenalidomide_1


title: OATL4_24h_DMSO_2


title: HuT102_24h_Lenalidomide_2


title: OATL4_24h_DMSO_1


title: HuT102_24h_Lenalidomide_3


title: B005

value: HHD


title: R60


title: JJN3, Vehicle treatment, replicate 2

description:
JJN3_counts.csv
JJN3_Vehicle_2

treatment_protocol: JJN3 cells were treated with vehicle for 24 hours

value: vehicle


title: B014


title: R59


title: B008


title: Fish_embryo_mRNA_germ_ring_PAL_seq_v4

city: Cambridge

first: Kehui

last: Xiang

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: Endognous mRNA, library made with PAL-seq v4, two technical replicates

data_processing:
For gene-specific tail-seq of mRNA reporters, data were processed with a custom script available at https://github.com/coffeebond/MPRA_tail_seq.
For PAL-seq v3 or v4, reads were trimmed with cutadapt v3.7 with the parameters “-m 15 --quality-base=64 -q 20,20 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7”. The trimmed reads were mapped using STAR (v2.7.1a) to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained, the genomic sequences of humans or fish, depending on which spike-in RNAs were used, and the sequences of the poly(A) standards generated previously, with the parameters “--runThreadN 16 --runMode alignReads --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outFilterType BySJout --outSAMattributes All --outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL-seq.
Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4, primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly.
Supplementary files format and content: For gene-specific tail-seq of mRNA reporters, tab-delimited text files with columns indicating 1) sequence of the variable region; 2) median tail length; 3) number of reads; 4–7) tail lengths at quantile 10, 25, 75, and 90.
Supplementary files format and content: For PAL-seq v3 or v4, tab-delimited files with columns indicating 1) gene ID or poly(A) site ID; 2) read cluster ID; 3) tail length
Library strategy: PAL-seq v4

organism: Danio rerio

source_name: embryo

extract_protocol:
Frog oocytes and embryos were lysed in ice-cold buffer RL (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% [v/v] Triton X-100, 100 µg/ml cycloheximide, cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer], and 200 units/ml SUPERase•In) in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri-reagent for RNA isolation. Fish embryos were de-chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. After removing all E3 medium, Tri-Reagent was added to the embryos for RNA isolation. Mouse GV-oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus-oocyte-complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG-induced mice (16 hr), denuded with 3 mg/ml hyaluronidase for 2 min, washed, and then collected in Tri-reagent for RNA isolation.
For gene-specific tail-seq of reporter libraries, total RNA with reporter mRNA libraries was ligated to a pre-adenylated 3ʹ adapter directly in most cases, but for the N60 library injected into fish embryos and frog oocytes, the N37-PAS-N17 library injected into fish embryos and frog oocytes, and the CPEmos-N60 and N60(LC)-PASmos libraries injected into frog oocytes, reporter library mRNAs were enriched by anti-sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009, 8 pmol KXSH010, and 2x SSC (0.3 M NaCl, 30 mM sodium citrate pH 7.0) in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads (Thermo Fisher, 65002) and incubated for 20 min at 23°C on a thermal mixer, shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined, precipitated with ethanol, and resuspended in 6.5 µl water.
The anti-sense oligo-enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre-adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330, 50 mM HEPES pH 7.5, 10 mM MgCl2, 10 mM dithiothreitol, 1 unit/µl T4 RNA ligase 1 (New England Biolabs, M0204S). The ligation reaction was incubated at 23°C for 150 min. After ligation, RNA was extracted with phenol/chloroform, precipitated with ethanol, and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl, incubated at 65°C for 5 min, and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First-Strand Buffer, 500 µM dNTPs, 5 mM dithiothreitol, 1 unit/µl SUPERase•In, and 200 units SuperScript III (Thermo Fisher, 18080044) at 50°C for 1 hr. After reverse transcription, RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min, followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio-Spin P-30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer (Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR-amplified library was cleaned up twice with AMPure XP beads (Beckman Coulter, A63881) with a beads-to-sample ratio of 1.2.
For sequencing of endogenous mRNA poly(A)-tail length, libraries were prepared with PAL-seq v3 (for frog oocytes) or PAL-seq v4 (for frog embryos, fish embryos, and mouse oocytes) as described previously (PMID: 34213414). When preparing the sequencing libraries of mRNAs from fish embryos, a different 3ʹ adapter (KXS013) was used for 3ʹ-end ligation, and poly(A)-selected mRNA from HeLa cells was used as spike-in, replacing poly(A)-selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer, shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined, precipitated with ethanol, and resuspended in 30 µl water. The oligo-depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample after monitoring consistency.

value: embryo


title: B002


title: JJN3, CX-5461 treatment, replicate 1

description:
JJN3_counts.csv
JJN3_CX_1


title: R57


title: Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4


title: HuT102_24h_DMSO_3


title: HuT102_24h_Lenalidomide_1


title: RCB1


title: MM1.S, CX-5461 and Panobinostat  treatment, replicate 2

description:
MM1S_counts.csv
MM1S_CX+Pano_2

treatment_protocol: MM1.S cells were treated with 500 nM CX-5461 and 50 nM  panobinostat for 24 hours

value: 500 nM CX-5461 and 50 nM panobinostat, 24hrs


title: CGG-Cit3

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: calvarial bone defect areas

extract_protocol:
Total RNA was extracted using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA).
Library preparation was performed at Novogene Co (Beijing, China), and the paired-end libraries were sequenced using Illumina NovaSeq 6000 platform (Illumina, USA).

value: calvarial bone defect areas

value: wild type

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: CGG-Cit hydrogel implantation


title: R56

value: bone marrow

value: M

value: replication


title: JJN3, Vehicle treatment, replicate 3

description:
JJN3_counts.csv
JJN3_Vehicle_3


title: HuT102_24h_DMSO_2

value: ATL


title: Fish_embryo_mRNA_128cell_PAL_seq_v4


title: B004

value: discovery


title: MM1.S, CX-5461 and Panobinostat  treatment, replicate 3

description:
MM1S_counts.csv
MM1S_CX+Pano_3

value: multiple myeloma


title: R58


title: B001


title: Fish_embryo_mRNA_sphere_PAL_seq_v4


title: MM1.S, Panobinostat  treatment, replicate 3

description:
MM1S_counts.csv
MM1S_Pano_3

treatment_protocol: MM1.S cells were treated with 50 nM  panobinostat for 24 hours

value: Wild type

value: 50 nM panobinostat, 24hrs


title: R55

value: F


title: JJN3, Vehicle treatment, replicate 1

description:
JJN3_counts.csv
JJN3_Vehicle_1

value: vehicle


title: Fish_embryo_mRNA_1024cell_PAL_seq_v4

value: embryo


title: CGG-Cit2


title: CGG-Cit1


title: Fish_embryo_mRNA_8cell_PAL_seq_v4


title: Fish_embryo_mRNA_1cell_PAL_seq_v4


title: MM1.S, CX-5461 and Panobinostat  treatment, replicate 1

description:
MM1S_counts.csv
MM1S_CX+Pano_1

value: 500 nM CX-5461 and 50 nM panobinostat, 24hrs


title: CGG2

value: calvarial bone defect areas

value: CGG hydrogel implantation


title: R54

value: HHD


title: R52


title: CGG3

value: wild type

value: Sprague-Dawley

value: male


title: MM1.S, Panobinostat  treatment, replicate 2

description:
MM1S_counts.csv
MM1S_Pano_2


title: R51

value: bone marrow

value: M


title: MM1.S, CX-5461 treatment, replicate 3

description:
MM1S_counts.csv
MM1S_CX_3

treatment_protocol: MM1.S cells were treated with 500 nM CX-5461 for 24 hours


title: R53

value: replication


title: HuT102_24h_DMSO_1

value: ATL

value: DMSO, 24h


title: bone marrow mesenchymal stem cell,CKO2

city: Guangzhou

first: Chuan

last: Li

address: Zhongshan 2th Road

institute: Sun yat-sen university

data_processing:
Genes exhibiting a fold change of 2 and P-value < 0.05 were identified as significantly differentially expressed. GO and KEGG pathway enrichment of differentially expressed genes were analyzed using online tool of DAVID Bioinformatics Resources 2021.
Assembly: mm9
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 RPKM  values for each sample

source_name: bone marrow

growth_protocol: MSCs were grown in α-MEM containing 1% penicillin-streptomycin solution and 10% FBS in a 37°C incubator with 5% CO2

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were prepared using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, USA) and sequenced them on Illumina sequencing platform according to manufacturer's instructions.

value: mesenchymal stem cell

value: Mapk7 conditional knock out


title: R50

value: MLL


title: MM1.S, Panobinostat  treatment, replicate 1

description:
MM1S_counts.csv
MM1S_Pano_1

value: multiple myeloma

value: Wild type

value: 50 nM panobinostat, 24hrs


title: (6-4)PP XR-seq rep2

city: Istanbul

first: Sezgi

last: Kaya

state: Tuzla

address: Orta Mahalle, Universite Cad, No: 27

country: Turkey

institute: Sabanci University

library_source: genomic

data_processing:
The reads were processed with cutadapt to trim the adapter sequences (TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG) from the 3′-end. Bowtie2was used to align XR-seq reads onArabidopsisgenome (Araport11) with the following parameters: --seed 1 --reorder. File conversions were processed with samtoolsand bedtools. Read duplications were filtered out by keeping the unique genomic regions only.
Assembly: Araport11
Supplementary files format and content: BigWig files include plus read counts on Araport11 genomic windows
Supplementary files format and content: BigWig files include minus read counts on Araport11 genomic windows
Library strategy: XR-seq

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Ten-day-old seedlings ofArabidopsis thalianaColumbia (Col-0) accession were used in this study. Plants were grown under a long-day condition (16 h light/8 h dark) with a cool white, fluorescent light at 24 °C. Eight milligrams of seeds for each sample were surface-sterilized, and stratified for 2 days at 4 °C, and then planted on a Murashige and Skoog plate. The seedlings were collected at circadian timepoint of ZT20.

extract_protocol:
After 30-min incubation in the dark at 24 °C, the seedlings were frozen with liquid nitrogen, and were ground using mortar and pestle. The resulting powder was resuspended in 400 µl of STES buffer (200 mM Tris⋅HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 10 mM EDTA) and 400 µl of phenol:chloroform (20:1). The sample was homogenized by vortexing with acid-washed glass beads for 30 min at 4 °C, followed by centrifugation at 14,000 rpm for 10 min at room temperature. The supernatant was treated with 10 µl of RNAseA (R4642; Sigma) for 1 h at 37 °C, then with 10 µl of proteinase K (P8107S; NEB) for 1 h at 60 °C. The excision products were obtained by ethanol precipitation and purified by immunoprecipitation with a (6-4)PP-specific antibody obtained from Cosmo Bio. (NMDND001).
5′ and 3′ adapters compatible with the Illumina TruSeq Small RNA protocol were ligated to excision products. Ligation products were immunoprecipitated with (6-4)PP antibodies(CosmoBio USA), and photoreversed with purified photolyase to remove(6-4)PPs interfering with following PCR approaches. Analytical PCR was performed using one percent of the sample to decide the minimum number of cycles required for preparative scale PCR amplification. The repaired ligation products were PCR-amplified using 50- and 63-nt-long primers adding specific barcodes compatible with the Illumina TruSeq Small RNA kit. The correct size PCR products representing the library were gel purified, and then sequenced in the Illumina HiSeq 4000 platform, and single-end 50-nt reads were generated.

treatment_protocol: Ten-day-old seedlings were irradiated with 1 J/(m2s) UVC (254 nm) for 2 min (120 J/m2UVC).

value: Seedling

tag: antibody

value: anti-(6-4)PP from Cosmo Bio. (#NMDND001)

value: WT

value: UV


title: bone marrow mesenchymal stem cell,CKO1


title: (6-4)PP XR-seq rep1


title: bone marrow mesenchymal stem cell,CKO3


title: MM1.S, CX-5461 treatment, replicate 2

description:
MM1S_counts.csv
MM1S_CX_2


title: R48

value: HHD


title: bone marrow mesenchymal stem cell,WT3


title: MM1.S, Vehicle treatment, replicate 3

description:
MM1S_counts.csv
MM1S_Vehicle_3

treatment_protocol: MM1.S cells were treated with vehicle for 24 hours

value: vehicle


title: MM1.S, CX-5461 treatment, replicate 1

description:
MM1S_counts.csv
MM1S_CX_1


title: bone marrow mesenchymal stem cell,WT2

value: bone marrow


title: CGG1

value: calvarial bone defect areas

value: wild type

value: Sprague-Dawley

value: male

value: CGG hydrogel implantation


title: R44

value: F

value: replication


title: bone marrow mesenchymal stem cell,WT1

value: mesenchymal stem cell


title: Withdrawal from chronic ethanol liquid diet, 17VTA

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

data_processing:
About 100,000,000 raw reads were obtained persequencedsample and followingsequence quality controlusingFASTQC(v. 0.11.4)and processing,reads were aligned to thereferenceRattusNorvegicusRnor6.0 genome from NCBI (release 106),using STAR (v. 2.5.2a).
Gene counts were generated from uniquely aligned reads usingFeatureCounts(v. 1.5.0),which counts mapped reads for exon features, then sums to gene-level. These have been included as Processed Data.
Raw counts were imported into R (v. 3.3.3) for statistical analysis. A total of 18,118 genes were kept for differential expression(DE)analysis. Following surrogate variable analysis, we used limma-voomto calculate a one-way ANOVA across all 3 treatments.
Assembly: Rnor 6.0
Supplementary files format and content: .txt

source_name: Ventral Tegmental Area tissue

extract_protocol:
Brains were collected for the dissection of VTA. Followed by total RNA extraction using the miRNEasy protocol, which was used for RNA-sequencing (paired-end) using the Illumina platform. cDNA fragments were 80bp to 500bp, with an average length of 250bp.
RNA integrity numbers (RIN)for eachRNA sampleweredetermined using an AgilentTapestationandwereallabove 8.0. Illumina True-Seq Stranded libraries were prepared and quantitated by qPCR. Reads were 100nt in length.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand, whereas Read 2 aligns to the SENSE strand.  The libraries were quantitated by qPCR and sequenced on 11 lanes (8 lanes on one flowcell, 3 lanes on another flowcell) for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.  Adaptors have been trimmed from the 3'-end of the reads.

treatment_protocol: Adult Sprague-Dawley male rats received control (C) or chronic ethanol (9% v/v) Lieber-DeCarli diets for 15 or 16 days. Chronic ethanol fed rats were withdrawn for 0 h(Chronic Ethanol)and 24h (Withdrawal), as described by us (Pandey et al., 2008, Journal of Neuroscience 28 (14), 3729-3737).

value: Ventral Tegmental Area tissue

tag: animal id

value: Sprague Dawley

value: Withdrawal


title: Withdrawal from chronic ethanol liquid diet, 16VTA


title: Withdrawal from chronic ethanol liquid diet, 18VTA


title: R41


title: R40


title: MM1.S, Vehicle treatment, replicate 1

description:
MM1S_counts.csv
MM1S_Vehicle_1

value: multiple myeloma

value: Wild type


title: Human CM, Input

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

description: ChIP-seq control

data_processing:
ChIA-PET data were processed using ChIA-PET Utilities  (https://github.com/cheehongsg/CPU) on hg19 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses.
ChIP-seq fastq files were trimmed with trim_galore (v0.4.0)  with error rate 0.2 and min quality 30, then mapped with bwa aln. ChIP vs Input peaks were called using MACS version 2.1.0.20151222  (options: --nomodel --extsize 250 -B --SPM)
Assembly: hg19
Supplementary files format and content: ChIA-PET: non-redundant paired BAM files and Chiasig output interaction files (coordinates of 2 anchors at the first six columns, interaction frequency at the 8th).
Supplementary files format and content: ChIP-seq: narrowPeak and BAM alignment files

source_name: CM

extract_protocol:
10 million for formaldehyde crosslinked cells were suspended with 100  μl 0.55% SDS and incubated at RT for 10 min, 62°C for 10 min and 37°C for 10 min to permeabilize nuclei, which was followed by adding 25 μl 20% TritonX-100 with an incubation of 30 min at 37°C to quench SDS, and then 50 μl of blunt-end four-cutter AluI (cat# R0137L, NEB), 50 μl 10 × CutSmart buffer and 275 μl H2O incubating at 37°C overnight for in situ digestion. After pelleted and washed once with 1 ml 1× CutSmart buffer, the nuclei were suspended in 500 μl A tailing solution composed of 50 μl 10 × CutSmart buffer, 10 μl BSA (cat#B9000S, NEB), 10 μl 10 mM dATP (cat#N0440S, NEB), 10 μl Klenow (3’-5’ exo-) (cat#M0202L, NEB), and 420 μl H2O and incubated at RT for 1 hr.  The in situ proximity ligation with biotinylated bridge linker was performed by adding 200 μl 5 × ligation buffer (cat#B6058S, NEB), 6 μl Bridge linker (200 ng/ul), 10 μl T4 DNA ligase (cat#M0202L, NEB) and 284 μl H2O and incubating at 16°C overnight.
The nuclei with in situ proximity ligation were then subjected to sonication and chromatin immunoprecipitation with anti-RNApolII antibody (8WG16, cat# 920102, Biolegend, San Diego, CA), Tn5 tagmentation, biotin selection, PETs were amplified by PCR and sequenced.
in-situ ChIA-PET nuclear proximity ligation

tag: developmental stage

value: Differentiation day 35 cells

value: CM

value: human CM

tag: chip antibody


title: R38

data_processing:
Raw reads were aligned to the GRCh37 genome reference using STAR v2.5.3a.
CircRNA expression counts were obtained using CIRCexplorer3.
Assembly: grch37
Supplementary files format and content: circrna expression counts

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen
Ribo-Zero Gold Kit according to Illumina's protocol

tag: diagnosis

tag: tissue

value: bone marrow

value: HHD


title: Withdrawal from chronic ethanol liquid diet, 14VTA

value: WT


title: R36

tag: gender

value: M

tag: cohort


title: Withdrawal from chronic ethanol liquid diet, 15VTA

tag: genotype

tag: treatment


title: Chronic Ethanol liquid diet, 12VTA

value: Chronic Ethanol


title: H1048_AU15330_4h_ATAC-seq_R2

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

data_processing:
The program bwa mem was run for alignment.
Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates and chrM).
Peaks were called using macs2 (with options: -g hs -f BAMPE -B -q 0.001 --nolambda --SPMR 2).
Assembly: hg38
Supplementary files format and content: bigwigs
Supplementary files format and content: beds from macs peaks

growth_protocol: Cells were cultured in ATCC-formulated RPMI with 10% FBS and penicillin.streptomycin except NCI-H929, which using ATCC-formulated RPMI with 0.05mM 2-mercaptoethanol, 10% FBS and penicillin

extract_protocol: ATAC-seq was performed as previously described in Buenrostro et al. 2013 Nat Methods. In brief, 50,000 cancer cells were washed in cold PBS and resuspended in cytoplasmic lysis buffer (CER-I from the NE-PER kit, Invitrogen, cat. no. 78833). This single-cell suspension was incubated on ice for 5 min. The lysate was centrifuged at 1,300g for 5 min at 4 °C. Nuclei were resuspended in 50μl of 1× TD buffer, then incubated with 0.5-3μl Tn5 enzyme (depending on the cell line) for 30 min at 37 °C (Nextera DNA Library Preparation Kit; cat. no. FC-121-1031). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol27. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881).

treatment_protocol: Cell were plated at 70-80% confluence in a 6-well plate and treated with AU-15330 dissolved in DMSO at 1uM concentration for labeled durations (4-6h).

tag: cell line


title: Human CM, H3K27ac, ChIP

description: H3K27ac ChIP-seq

tag: cell type


title: H1048_AU15330_4h_ATAC-seq_R1


title: R35

first: Daniel

last: Sinnett

address: 2900 Edouard Montpetit Blvd

institute: University of Montreal


title: MM1.S, Vehicle treatment, replicate 2

description:
MM1S_counts.csv
MM1S_Vehicle_2

value: vehicle


title: R31


title: Chronic Ethanol liquid diet, 11VTA


title: R28

value: F


title: Chronic Ethanol liquid diet, 10VTA


title: R33

value: replication


title: H1048_DMSO_4h_ATAC-seq_R1

value: DMSO


title: Chronic Ethanol liquid diet, 9VTA

value: Ventral Tegmental Area tissue


title: H69_AU15330_6h_ATAC-seq_R2


title: Chronic Ethanol liquid diet, 8VTA

value: Sprague Dawley


title: H69_AU15330_6h_ATAC-seq_R1


title: R26


title: Chronic Ethanol liquid diet, 7VTA


title: WT omit replicate 3

data_processing:
Read quality analysis was performed with FastQC. Following the recommendation of Herzog et al., read 2 was discarded. Demultiplexed fastq files were applied to the SLAMDUNK pipeline (v/0.4.2) and mapped against hg38. The optional --multimappers flag was enabled. Following the pipeline, the output count file was collapsed used the included SLAMDUNK Alleyoop collapse module. Curve fitting was performed according to a first-order decay reaction in R (v3.6.3)
SLAMDUNK pipeline (v 0.4.2)
Assembly: hg38
Supplementary files format and content: tsv count file

extract_protocol:
At select time points of interest, “chase” media was removed, and cells were lysed in using Trizol Reagent according to the manufacture’s protocol with the following modifications: RNA isolation was performed in the dark and DTT was added to the aqueous phase to keep samples under reducing conditions.
Library preparation was performed using QuantSeq 3' mRNA library prep kit for Illumina using the manufacturer’s protocol and recommended maximum input amount

treatment_protocol: Metabolic labeling to determine RNA half-life followed the method of Herzog et al. Cells were seeded the day before the experiment at approx. 50% confluency.  The morning of the experiment, media was removed and replaced with cell media supplemented with 100 µM 4-thiouridine to begin the “pulse”. 4SU-containing media was exchanged every 8 hr during the 24 hr “pulse” period to increase the efficiency of labeling. Following 24 hr labeling, the “pulse” media was removed. Cells were washed 2X with PBS. Cell culture growth medium containing 10 mM uridine (i.e., 100X excess over 4SU) was added to the cells to begin the “chase”.

value: renal cell carcinoma

value: omit

tag: time


title: WT omit replicate 2


title: R24


title: Withdrawal from chronic ethanol liquid diet, 13VTA

value: Withdrawal


title: H69_DMSO_6h_ATAC-seq_R2


title: Control liquid diet, 6VTA

value: Control


title: R34


title: WT omit replicate 1


title: H69_DMSO_6h_ATAC-seq_R1


title: R22


title: H1048_DMSO_4h_ATAC-seq_R2


title: H526_AU15330_4h_ATAC-seq_R2


title: R20

value: MLL


title: R18


title: Control liquid diet, 4VTA


title: WT 12 hr replicate 2

value: 12 hr


title: WT 12 hr replicate 1


title: H526_AU15330_4h_ATAC-seq_R1


title: R15

value: bone marrow


title: H526_DMSO_4h_ATAC-seq_R1


title: WT 6 hr replicate 3

value: 6 hr


title: R17


title: Control liquid diet, 5VTA

value: WT


title: R14

value: M


title: Control liquid diet, 2VTA


title: MM1S_AU15330_4h_ATAC-seq_R2


title: WT 6 hr replicate 2


title: R13


title: MM1S_AU15330_4h_ATAC-seq_R1


title: WT 6 hr replicate 1


title: WT 12 hr replicate 3


title: H526_DMSO_4h_ATAC-seq_R2


title: WT 0 hr replicate 3

value: 0 hr


title: Control liquid diet, 1VTA


title: MM1S_DMSO_4h_ATAC-seq_R2


title: R12


title: WT 0 hr replicate 2


title: MM1S_DMSO_4h_ATAC-seq_R1


title: R11


title: Control liquid diet, 3VTA


title: PBT147 human glioma tumor cell lines treated with ICG-001 at 10 µM and 72 hrs

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

hyb_protocol: RNA was hybridized with the Codeset from the gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed on nSolver (NanoString Technologies).

scan_protocol: Scanning was done using NanoString nCounter system, following manufacturer's instructions.

data_processing: All raw data were first normalized with internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Statistically significant (p<0.05) and |fold change|≥1.5 differential expressed genes were analyzed for different cell lines and treatments.

source_name: primary PBT147 glioma human tumor

label_protocol: Human patient-derived glioma cell lines were labeled like PBT030-10 (ICG001 concentration)-24h (or 72h)

growth_protocol: PBT tumor cells lines are derived from patient with brain tumors (IRB07074) dissociated and grown in DMEM/F12 medium, supplemented with heparin, hepes, glutamax, and B27. Epidermal growth factor (EFG) and fibroblast growth factor (FGF) are added at the time of culture, as described previously(63). ICG-001 was provided by M. Kahn’s laboratory.

extract_protocol: RNA was isolated from cell culture pellets (untreated or ICG001 treated with 5 and 10 mM) and used for Nanostring analysis

treatment_protocol: Co-culture assay of PBT cell lines were grown as described above and seeded to 100,000 cells/2 ml in 6-well plates. ICG-001 was added to cell cultures in concentrations 0, 5, and 10 mM for 24–72h.

tag: cell lines

value: PBT147 patient-derived glioma cell lines

value: ICG001 treated

tag: treatment dose

value: 10 uM

tag: treatment time

value: 72 hours


title: WT 0 hr replicate 1


title: Run 1 UOK262 WT RNA-seq--Replicate 3

data_processing:
Read quality was checked with FastQC. Reads of the samples were trimmed for adapters using Cutadapt (v2.5) and aligned against a costume genome of repetitive sequences before alignment with the hg38 reference genome (gencode v35) using STAR v2.7.6a. PCR duplicates were marked and removed with Picard’s MarkDuplicates (v 2.25.0). Sample counts were obtained with HTSeq’s count (v 0.9.1) and differential gene expression was analyzed with DeSeq2.
Assembly: hg38
Supplementary files format and content: count matrix

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent according to the manufacture’s protocol. Following phase separation, the aqueous phase was applied to a Qiagen RNeasy Mini Kit column and RNA was purified according to kit instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit v2 and sequenced on NextSeq 500 using paired-end sequencing

value: Renal Cell Carcinoma

value: normoxia


title: R5

city: Montreal

value: HHD

value: replication


title: Run 1 UOK262 WT RNA-seq--Replicate 2


title: R4

value: F


title: PBT147 human glioma tumor cell lines treated with ICG-001 at 5 µM and 24 hrs

value: 5 uM

value: 24 hours


title: PBT147 human glioma tumor cell lines treated with ICG-001 at 5 µM and 72 hrs


title: R9


title: PBT147 human glioma tumor cell lines untreated at 72 hrs

value: ICG001 untreated


title: Run 1 UOK262 WT RNA-seq--Replicate 1


title: PBT147 human glioma tumor cell lines treated with ICG-001 at 10 µM and 24 hrs


title: Mut omit replicate 2

value: renal cell carcinoma

value: Mutant

value: omit


title: R2

value: bone marrow

value: M


title: Mut omit replicate 1


title: B086

value: discovery


title: PBT147 human glioma tumor cell lines untreated at 24 hrs

value: PBT147 patient-derived glioma cell lines


title: PBT030 human glioma tumor cell lines treated with ICG-001 at 10 µM and 72 hrs

source_name: primary PBT030 glioma human tumor

value: PBT030 patient-derived glioma cell lines

value: ICG001 treated

value: 10 uM


title: Mut 12 hr replicate 3

value: 12 hr


title: Run 1 UOK262 Mutant RNA-seq--Replicate 2

value: Renal Cell Carcinoma

value: normoxia


title: Run 1 UOK262 Mutant RNA-seq--Replicate 1


title: B085

value: F


title: Mut omit replicate 3


title: PBT030 human glioma tumor cell lines treated with ICG-001 at 10 µM and 24 hrs


title: B084


title: PBT030 human glioma tumor cell lines treated with ICG-001 at 5 µM and 72 hrs

value: 5 uM

value: 72 hours


title: PBT030 human glioma tumor cell lines treated with ICG-001 at 5 µM and 24 hrs

value: 24 hours


title: Run 1 UOK262 Parent RNA-seq--Replicate 3

value: Parent


title: Run 1 UOK262 Mutant RNA-seq--Replicate 3

value: Mutant


title: R270X astrocytes_pair3

city: stony brook

first: Jialin

last: Sun

state: New York

address: 100 Nicolls Road

institute: Stony Brook University

data_processing:
The RNA samples were sequenced on Illumina NovaSeq 6000 Sequencing System, yielded about 20-30 million pairs of 150 bp pair-end reads per sample.
Raw reads were first trimmed for 10 bases at the 5’end to remove reads with biased nucleotide (ACGT) distribution.
Trimmed reads were then aligned to the Homo sapiens genome (GRCh38p12, GENCODE, primary assembly), using STAR aligner (Dobin et al., 2013)(version 2.6.0a).
Differential gene expression (DEG) analyses on the read counts were performed using DESeq2 (Love et al., 2014) (v1.24.0) in R environment.
Genes with sum of read counts across all samples with less 10 were filtered out from analysis. A gene was considered significantly dysregulated if the adjusted p-value was less than 5% and with a minimum average read counts of 10 in either genotype.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text with read counts for all the genes

source_name: astrocytes

growth_protocol: The mutant astrocytes and their isogenic WT control were generated by three differentiation steps: ESCs to neural progenitor cells (NPCs); NPCs to astrocyte progenitor cells (APCs); APCs to astrocytes. Human ESC cultures were differentiated to NPCs with SB431542, Dorsomorphin in N2B27 medium. The NPCs were expanded with EGF, bFGF and LIF and further differentiated into APCs by culturing on Matrigel-coated plates and passaging in N2B27 medium supplemented with BMP4 (10 ng/ml, Peprotech) and bFGF (20 ng/ml) for 21-25 days, after which they were FACS-sorted for CD44 and propagated. The CD44-positive APCs were then differentiated to astrocytes by culturing in astrocyte maturation medium containing N2B27 medium supplemented with CNTF (10 ng/ml), LIF (10 ng/ml) and FGF1 (50 ng/ml) for up to 48 days.

extract_protocol:
RNA were harvested using miRNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. The quality was assessed by Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Mut 12 hr replicate 1

value: renal cell carcinoma


title: Run 1 UOK262 Parent RNA-seq--Replicate 2


title: h1_seedling_Hi-C

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
MNase-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. NuMap was then performed to compute nucleosome positions.
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read.
w1: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
w50: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb and 25 kb contact matrix (hic files).
Genome_build: TAIR10
Supplementary_files_format_and_content: MNase-seq: BED files of nucleosome positions.
Supplementary_files_format_and_content: Bisulfite-Seq: GFF files of fractional methylation data either for individual cytosines (w1) or in 50 bp windows (w50).
Supplementary_files_format_and_content: Hi-C: matrix and regions files of different resolutions generated by Fan-C contain genomic contacts and corresponding index information, respectively.

source_name: h1 seedling

growth_protocol: Plants were grown under long day (16 hr light; 8 hr dark) conditions at 22 °C.

extract_protocol:
Ten-day-old seedlings were harvested and fixed with 20 ml 2% formaldehyde solution for 15 min in vacuum conditions at room temperature and then quenched by adding 2.162 ml 2.5 M glycine. Fixed seedling tissue was rinsed with water three times and dried with tissue paper.   The nuclei were released by grinding in liquid nitrogen and then resuspended with 25 ml of extraction buffer I (0.4 M sucrose, 10 mM Tris HCl pH 8, 10 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 13 μl protease inhibitor). Nuclei were filtered through miracloth (Calbiochem) and then centrifuged at 4000 rpm for 20 min at 4 °C. The supernatant was discarded whilst the pellet was resuspended with 1 ml of extraction buffer II (0.25 M sucrose, 10 mM Tris HCl pH 8, 10 mM MgCl2, 1% Triton X-100, 5mM β-mercaptoethanol, 0.1mM PMSF, 13 μl protease inhibitor). Then, the mixture was centrifuged at 14000 rpm for 10 min at 4 °C and the pellet was resuspended with 300 μl of extraction buffer III (1.7 M sucrose, 10 mM Tris HCl pH 8, 0.15% Triton X-100, 2 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 1 μl protease inhibitor), load the mixture onto the top of an equal amount of clean extraction buffer III, then centrifuge at 14000 rpm for 10 min.
The Hi-C library construction and sequencing were conducted by Annoroad Gene Technology Co., Ltd (Beijing, China). Briefly, The pelleted nuclei were washed twice with 1x ice cold CutSmart buffer and finally resuspended in 0.5 ml volume. SDS was applied to permeabilize nuclei at 65 °C for 10 min, Triton X-100 was added to quench SDS. Thereafter, chromatin was digested with 400 units MboI overnight at 37 °C with gentle rocking. MboI was then denatured to cease activity. Digested chromatin underwent DNA end repair with biotin-14-dCTP insertion followed by blunt-end ligation. After decrosslinking with proteinase K at 65 °C, DNA was purified by phenol chloroform extraction method. Biotin-14-dCTP was removed from non-ligated DNA fragment ends using T4 DNA polymerase. DNA was sheared to a range of 200 to 600 bp by sonication. Next, the fragments underwent end repair and were pulled down by streptavidin C1 magnetic beads to enrich for fragments containing contact information. Fragment ends were then A-tailed, sequencing adapters were ligated, and libraries were amplified by PCR for 12-14 cycles. Following purification, libraries were sequenced using the Illumina HiSeq platform with 2×150 bp length.

tag: ecotype

value: ten-day-old seedlings


title: Mut 6 hr replicate 3

value: 6 hr


title: WT astrocytes_pair3

value: wild-type


title: Run 1 UOK262 Parent RNA-seq--Replicate 1


title: Mut 6 hr replicate 2


title: WT astrocytes_pair2


title: H929_DMSO_4h_ATAC-seq_2

value: DMSO


title: R270X astrocytes_pair2


title: Mut 6 hr replicate 1


title: Mut 12 hr replicate 2


title: PBT030 human glioma tumor cell lines untreated at 24 hrs

value: PBT030 patient-derived glioma cell lines

value: ICG001 untreated


title: PBT030 human glioma tumor cell lines untreated at 72 hrs


title: H929_AU15330_4h_ATAC-seq_2


title: R270X astrocytes_pair1


title: H929_DMSO_4h_ATAC-seq_1


title: Mut 0hr replicate 2

value: 0 hr


title: Mut 0hr replicate 3


title: WT astrocytes_pair1


title: Mut 0hr replicate 1


title: High salt-1

status: Public on Feb 14 2024

city: Beijing

first: Shuai

last: Lin

address: No.22, Zhongguancun South Avenue

institute: Peking University School of StomatologyNo.22, Zhongguancun South Avenue

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: primary bone marrow mesenchymal stem cells

value: 30mM NaCl 48h


title: High salt-2


title: Control-2

value: Control


title: 22RV1 Ctrl

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Samples were hybridized with GeneChip Human Clariom D Arrays (Affymetrix) and scanned at the Kaohsiung Chang Gung Memorial Hospital Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis was conducted with Partek.
RMA expression value derived from Expression Console software; core-exon analysis
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: Empty vector control in 22RV1 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: PC3 and 22RV1 cells were cultured in F-12 and RPMI media, respectively. All media were supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin.

extract_protocol: Total RNA was extracted using TRIzol reagent. The quality of total RNA was analyzed by the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit.

treatment_protocol: PC3 and 22RV1 cells were transfected with shCD267 RNA and its empty vector and selected as stable cells.

value: Prostate cancer cells

tag: genotype/variation

value: Empty vector control


title: 22RV1 shCD267

source_name: TNFRSF13B (CD267) knockdown in 22RV1 cells

value: TNFRSF13B (CD267) knockdown


title: H929_AU15330_4h_ATAC-seq_1


title: Control-1


title: LoVo_KO_rep2

city: Beppu,

first: Yusuke

last: Nakano

address: 4546 Tsurumibaru

department: Department of Surgery

institute: Kyushu University Beppu Hospital

data_processing:
The in-house pipeline Genomon 2.6.3  (https://genomon-project.github.io/GenomonPagesR)  was used for quality control and mapping.
The sequencing libraries generated from the RNA were analyzed by DNBSEQ-G400. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the reads were aligned to the human reference sequence and the gene annotations (UCSC hg19) using Tophat2 v2.1.1. with following parameters; --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --alignSJstitchMismatchNmax -1 -1 -1 -1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12.
STAR v2.7.10b was used to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) values.
Genome_build: UCSC hg19 with Gencode v28 annotations
Assembly: hg19
Supplementary files format and content: tab-delimited text files of read counts per gene

source_name: LoVo

extract_protocol:
Total RNA was extracted from the cells using ISOGEN II (Nippon Gene).
Total RNA samples were first enriched for mRNA with poly A tails using oligo dT beads, then fragmented into small pieces, and synthesized into first strand cDNA using random primers. The second strand cDNA was synthesized using dUTP instead of dTTP, followed by end-repair and 3' adenylation of the synthesized cDNA, with adaptors ligated to these ends. The U-labeled second-strand template was digested with Uracil-DNA-Glycosylase (UDG) and amplified by PCR, after which the library underwent quality control, circularization, and amplification to create DNA nanoballs (DNB), which were then sequenced using the DNBSEQ Technology platform.

value: LoVo

value: colon adenocarcinoma

value: SHARPIN knockout


title: LoVo_KO_rep3


title: LoVo_NT_rep3

value: non-target


title: LoVo_NT_rep2


title: LoVo_NT_rep1


title: Irf3_LPS

city: Los Angeles

first: Carolina

last: Chavez

address: 10833 LeConte Ave

institute: UCLA

data_processing:
Samples were sequenced and base calls performed on Illumina HiSeq 3000.
Reads were trimmed of adapter sequences, then mapped to mm10 genome with bowtie2. Duplicated reads were removed using Picard MarkDuplicates.
For ChIP-seq, MACS2 or MACS3 were used in broad mode to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary with extension size of average fragment length.
Assembly: mm10
Supplementary files format and content: Raw count tables are provided (unnormalized). For the ChIP-seq data, genomic regions of interest were defined by merging the WT H3K4me1 peaks from either the unstimulated and LPS stimulated or unstimulated and IFNγ stimulated samples. These genomic locations were used to determine the counts in the knockout cells.

growth_protocol: BMDMs were generated by isolating bone marrow from the femurs and tibias of age and sex-matched mice. Bone marrow cells were incubated in L929-conditioned media (RPMI + 30% L929 media, 10% FBS, 100 IU/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine, 55 µM 2-mercaptoethanol) at 37C in 15cm plates. On Day 4, cells were detached using a cell lifter and replated into experimental culture plates.

extract_protocol:
H3K4me1 ChIP was performed on lysed and sonicated chromatin using rabbit anti-H3K4me1 (Abcam ab8895).
H3K4me1 ChIP-seq libraries were prepaed with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645) according to manufacturer's instructions.

treatment_protocol: Cells were stimulated on Day 7 with IFNβ (1U/mL), LPS (100ng/mL), or IFNγ (100ng/mL) for 8 hours or as indicated.

value: bone marrow-derived macrophage

value: LPS 100ng/mL


title: LoVo_KO_rep1


title: Irf1_input_rep1


title: Irf3_Uns

value: Unstimulated


title: PC3 shCD267

source_name: TNFRSF13B (CD267) knockdown in PC3 cells


title: Irf1_input_rep2


title: Irf1_IFNg_rep2

value: IFNgamma 100ng/mL


title: Irf1_LPS_rep2


title: Irf1_IFNg_rep1


title: Irf1_LPS_rep1


title: Ifnar_LPS_rep2

value: Ifnar-/-


title: Irf1_Uns_rep1


title: Ifnar_input_rep1


title: Irf1_Uns_rep2


title: PC3 Ctrl

source_name: Empty vector control in PC3 cells


title: Ifnar_LPS_rep1


title: Ifnar_Uns_rep1


title: WT_input_rep3

value: WT


title: WT_input_rep1


title: Ifnar_input_rep2


title: WT_input_rep2


title: WT_IFNg_rep1


title: WT_IFNg_rep2


title: Irf3_LPS_IFNb

value: LPS 100ng/mL + IFNbeta  10 U/mL


title: WT_LPS_144h

value: 8hr LPS 100ng/mL + 136hr wash


title: Ifnar_Uns_rep2


title: WT_LPS_24h

value: 8hr LPS 100ng/mL + 16hr wash


title: WT_LPS_8h


title: WT_LPS_rep3


title: WT_LPS_48h

value: 8hr LPS 100ng/mL + 40hr wash


title: WT_Uns_rep3


title: WT_Uns_rep1


title: ATAC-Seq Irf1_4h

data_processing:
Samples were sequenced and base calls performed on Illumina HiSeq 3000.
Reads were trimmed of adapter sequences, then mapped to mm10 genome with bowtie2. Duplicated reads were removed using Picard MarkDuplicates.
For ATAC-seq, MACS2 version 2.1.0 was used in broad mode to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary.
Assembly: mm10
Supplementary files format and content: Raw count tables are provided (unnormalized).

extract_protocol:
ATAC-seq samples were prepared as described in Buenrostro et al, 2013 using Tn5 transposase from Illumina.
ATAC-seq libraries were prepared with the Nextera DNA Library Preparation Kit (Illumina, FC-121).

treatment_protocol: Cells were stimulated on Day 7 with 100 ng/mL of LPS for the indicated times.


title: ATAC-Seq Ifnar_4h


title: WT_LPS_96h

value: 8hr LPS 100ng/mL + 88hr wash


title: WT_LPS_rep2


title: ATAC-Seq Irf1_2h


title: ATAC-Seq Irf1_1h


title: WT_Uns_rep2


title: ATAC-Seq Irf1_0h


title: ATAC-Seq Ifnar_2h


title: WT_IFNb

value: IFNbeta  1U/mL


title: ATAC-Seq Ifnar_0h


title: ATAC-Seq WT_4h


title: ATAC-Seq WT_0h


title: ATAC-Seq Ifnar_1h


title: WT_LPS_72h

value: 8hr LPS 100ng/mL + 66hr wash


title: ATAC-Seq WT_2h


title: ATAC-Seq WT_1h


title: N1E115_4%O2_CTCF

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Data were analyzed by the HiChIP pipeline developed by the Mayo Clinic Bioinformatics Core
ChIP-seq reads were aligned to the mm10 genome assembly using BWA
Paired-end reads were aligned by BWA against the mm10 genome build. Duplicated reads were filtered out with Picard. Peak calling was performed with Sicer and MACS.
Genome_build: mm10
Supplementary_files_format_and_content: Peak file is in bed format with header of  chr, peak_start, peak_end, peakname, pileup, peakCall,fold-change, -10logpvalue, -10logqvalue, peak_summit_position

source_name: NOS1+ N1E115 mouse neuroblastoma cells

growth_protocol: NOS1+ N1E115 mouse neuroblastoma cells were cultured under normoxia (20% O2) and hypoxia (4% O2) for 3 days

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed on fixed and fragmented DNA isolated from N1E115 cells using anti-CTCF, RAD21, POLR2, POLR2S2, POLR2S5, and H3K9ac antibodies.
ThruPLEX DNA-seq Kit

treatment_protocol: 4% and 20% oxygen

value: brain

value: neuroblast

tag: agent

value: 4percent O2

tag: antibody

value: CTCF


title: N1E115_20%O2_input2

value: 20percent O2


title: N1E115_20%O2_POLR2S2


title: WT_LPS_rep1

value: bone marrow-derived macrophage

value: LPS 100ng/mL


title: N1E115_4%O2_input2


title: N1E115_20%O2_CTCF


title: N1E115_20%O2_POLR2S5


title: N1E115_20%O2_POLR2


title: N1E115_20%O2_RAD21


title: N1E115_20%O2_H3K9ac


title: N1E115_20%O2_input1


title: N1E115_4%O2_H3K9ac


title: N1E115_4%O2_RAD21


title: N1E115_4%O2_input1


title: N1E115_4%O2_H3K4me3

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed on fixed and fragmented DNA isolated from N1E115 cells using anti-H3K27ac, H3K27me3, H3K36me3, H3K4me1, and H3K4me3 antibodies.
ThruPLEX DNA-seq Kit

value: 4percent  O2


title: N1E115_4%O2_H3K4me1


title: N1E115_4%O2_H3K27me3


title: N1E115_4%O2_input3


title: N1E115_4%O2_H3K36me3


title: N1E115_4%O2_H3K27ac


title: N1E115_20%O2_H3K27ac


title: N1E115_20%O2_H3K4me1


title: N1E115_4%O2_POLR2S5


title: N1E115_20%O2_H3K4me3


title: N1E115_20%O2_H3K36me3


title: N1E115_20%O2_input3


title: N1E115_20%O2_H3K27me3


title: 20%O2_replicate3

data_processing:
Data were analyzed by the MAP-RSeq pipeline developed by the Mayo Clinic Bioinformatics Core (Kalari et al., BMC Bioinformatics 2014;15:224)
RSeQC software was used for estimating the distance between paired end reads, evaluating the sequencing depth for alternate splicing analysis, determining the rate of duplicate reads, evaluating coverage of reads across genes, and more
Paired-end reads were aligned by TopHat 2.0.6 against the mm10 genome build using the bowtie1 aligner option
Gene counts were generated using HTseq software and gene annotation files are obtained from Illumina
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene counts with corresponding RPKM values

extract_protocol:
Qiagen miRNeasy
Illumina TruSeq mRNA Sample Preparation Kit v2

tag: oriented tissue


title: 4%O2_replicate1


title: 20%O2_replicate2


title: 4%O2_replicate2


title: N1E115_4%O2_POLR2


title: No_20%_N1E115_HiC rep1

data_processing:
Map fastq files to reference genome using bowtie2
Cut the unmapped reads using dpnI and II cutsites
Map again using bowtie2
Merge global bam and local umapped bam using Samtools, and sort.
Merge R1 and R2 using Samtools
Perform Hi-C filtering using mapped_2hic_fragments.py
validPairs files are merged into allValidPairs, and duplicates are removed.
Genome_build: mm10
Supplementary_files_format_and_content: AllValidPairs fils are used to build .HiC files using Juicer (hicpro2juicebox.sh)

extract_protocol:
Cells were cross-linked with 1% formaldehyde and quenched by 2.5 mol/L glycine, and then were resuspended in lysis buffer provided in the Arima HiC kit (Arima, Cat# A510008, CA)
libraries were prepared using KAPA Hyper Prep kit (Roche, Cat# KK8500, IN)


title: 4%O2_replicate3


title: N1E115_4%O2_POLR2S2


title: testicular tissue, HO-1-WT-3 (miRNA)

city: Hangzhou

first: Ning

last: He

state: Zhejiang

address: No. 79 Qingchun Road

department: Department of Urology

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by BWA.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression were calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×106 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×10^6. Differential expression between two sets of samples was calculated by edgeR algorithm according to the criteria of |log2(Fold Change)|≥1 and P-value < 0.05.
TargetScan, miRDB, miRTarBase and miRWalk were used to predict targets gene of selected miRNA. KOBAS was used to further Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis.
Assembly: rn6
Supplementary files format and content: all.miRNA_expression.txt (RPMs)

source_name: testicle

extract_protocol:
Total RNA was isolated by using Trizol (Invitrogen,USA). The quantity and integrity of RNA yield was as-sessed by using the Qubit®2.0 (Life Technologies, USA) and  Agilent 2200 TapeStation (Agilent Technologies, USA) separately. 1μg total RNA of each samples were used to prepare small RNA libraries by NEBNext® Multi- plex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions.
The libraries were sequenced by HiSeq 2500 (Illumina,USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio,China).

value: testicle

tag: Sex

value: Male

tag: strain

value: Sprague Dawley

value: testis cell

value: the testicle suffered from reperfusion 3 days after ischemia 2 hours


title: testicular tissue, HO-1-WT-1 (miRNA)

tag: tissue

value: WT


title: testicular tissue, HO-1-WT-2 (miRNA)


title: testicular tissue, HO-1-1-3 (miRNA)

value: HO-1 knockout


title: P1+CP2+CP3+CP4, gdVDJ-derived cDNA

city: Bethesda

first: Chaim

middle: A

last: Schramm

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

description:
TRG/TRD enriched from polyA RNA via 10x Chromimum
allPTCRA_TCR.tsv

data_processing:
10X single-cell transcriptome libraries were processed with Cellranger (v6.1.1) and Seurat (v4.0.4).
The TCR-⍺β and TCR-γδ libraries were demultiplexed and cell barcodes were assigned with Minnn (v10.1).  TCR libraries were annotated with MiXCR (v3.0.13) and then separated by subject. The numbers of αβ or γδ TCRs for the patients and controls were calculated by counting the numbers of cells expressing both TRA and TRB V-J genes and both TRG and TRD V-J genes.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: tab-delimited HTO assignments for each cell
Supplementary files format and content: tab-delimited TCR gene assignments and CDR3s
Supplementary files format and content: RDS-formatted R data files with complete Seurat objects
Library strategy: scTCR-seq

source_name: PBMC

extract_protocol:
Cryopreserved peripheral blood mononuclear cells (PBMC) in R10 medium (RPMI 1640, 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin) were thawed and immediately centrifuged to obtain a cell pellet. The cells were then incubated for 15 min at 37°C under an atmosphere containing 5% CO2 in the presence of Benzonase (Millipore Sigma, cat. 70664) diluted 1:1000 in R10 medium.  The cells were then washed once in R10 and once in FACS buffer (2% FBS in PBS). For staining, cells were resuspended in 50 µl of a mixture of LIVE/DEAD Fixable Blue Dead Cell Stain (cat. L34962) diluted 1:200 in PBS and anti-CCR7 APC-Cy7 antibody (Biolegend, cat. 353212), and incubated for 10 min at 37°C under an atmosphere containing 5% CO2. Cells were then labeled with 1µL oligonucleotide-linked hashing antibody (Totalseq-C, Biolegend) and stained by incubation with 50 µL antibody cocktail diluted in Brilliant Stain Buffer (BD Biosciences, cat. 566349) for 20 min at room temperature. The antibody cocktail contained the following antibodies: anti-CD14 BV510 (Biolegend, cat. 301842), anti-CD19 BV510 (Biolegend, cat. 302242), anti-CD56 BV510 (Biolegend, cat. 362534), anti-CD8 BV785 (Biolegend, cat. 301046), anti-CD4 PECy7 (Biolegend, cat. 300512), anti-CD95 AlexaFluor 700 (Biolegend, cat. 305648), anti-PD-1 BV750 (Biolegend, cat. 329966), anti-CD69 FITC (Biolegend, cat. 310904), anti-CD40L BV421 (Biolegend, cat. 310824), anti-CD3 BUV805 (BD Biosciences, cat. 741999), anti-CD45RA PECF594 (BD Biosciences, cat. 562298), anti-CD25 BUV661 (BD Biosciences, cat. 741685), anti-CXCR3 BV711 (BD Biosciences, cat. 563156), anti-HLA-DR PECy5.5 (Invitrogen, cat. MHLDR18), anti-CXCR5 APC (Invitrogen, cat. 17-9185-42). The cells were washed twice with FACS buffer and resuspended in R10 for sorting. 12,000 T cells (CD3+CD14−CD19−CD56−Live/Dead−) were sorted from each sample with a BD FACSymphony S6 Cell Sorter instrument (BD Biosciences) running BD FACSDiva Software version 9.5.1 (BD Biosciences). Sorted cells were pooled four by four, and each pool was loaded in a different lane of the 10x Genomics Chromium Chip for sequencing.
For the sequencing of single-cell V(D)J repertoires for sorted T cells, the cell suspension was loaded on the 10x Genomics Chromium Instrument according to the manufacturer’s protocol for the Next GEM Single-Cell 5′ Kit v1.1 (10x Genomics PN-1000165) to generate gel bead-in-emulsions, and to perform GEM-RT and the amplification of total cDNA. Following purification with SPRIselect beads (Beckman Coulter), specific TCR targets were amplified from the cDNA with the PTCR1 primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3′) and constant region primers: TRB (5′-TGCTTCTGATGGCTCAAACACAGCGACCT-3′), TRA (5′-TCTCAGCTGGTACACGGCAGGGTCAGGGT-3′), TRG (5′-GAAGGAAGAAAAATAGTGGGCTTGGGGGAAAC-3′), or TRD (5′-CACCAGACAAGCGACATTTGTTCC-3′) with a barcode and the P7 sequence added to the constant region primers. The Illumina-ready libraries were sequenced by paired-end MiSeq with 2×300 base-pair reads to obtain VDJ sequences
scRNA-seq with FeatureSeq and scAIRR-seq

value: PBMC

value: CD3+ T cells

tag: library type

value: mRNA

tag: tags


title: P2+CP5+CP6, gdVDJ-derived cDNA


title: CA1+CA2+CA5+CP1, abVDJ-derived cDNA

description:
TRA/TRB enriched from polyA RNA via 10x Chromimum
allPTCRA_TCR.tsv


title: CA1+CA2+CA5+CP1, gdVDJ-derived cDNA


title: testicular tissue, HO-1-1-1 (miRNA)

tag: genotype

tag: treatment


title: P1+CP2+CP3+CP4, abVDJ-derived cDNA

tag: cell type


title: 20%O2_replicate1

value: brain

value: neuroblast


title: mp26_FFT_LN1_4

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

data_processing:
Sequencing reads were processed with MiXCR software (MiLaboratories) in order to extract TCRβ CDR3 clonotypes. MiXCR aligns reads to human V, D and J TCR gene segments.
VDJtools software was used for processing of MiXCR output TCR repertoire data, calculation of TCR repertoire diversity, and pre-processing of TCR repertoires (i.e., pooling of joined TCR repertoires and down-sampling of TCR repertoires)
Supplementary_files_format_and_content: Tab delimeted text files include the TCR clonotype tables in VDJtools output format

source_name: Freshly frozen TILs (FFT)

growth_protocol: TILs were expanded from the separate tumor fragments in different cultivation conditions. For patient mp26 conditions were - IL2(300IU/ml); IL2(200 IU/ml)+IL21(25ng/ml); Nivolumab(20 μg/mL)+IL2+IL21; Nivolumab+IL2+IL21+IFNγ(100 μg/ml). For patients mp34 and mp41 conditions were: IL2(300IU/ml); IL2(200 IU/ml; IL2(200 IU/ml)+IL21(25ng/ml); Nivolumab(20 μg/mL)+IL2+IL21).

extract_protocol:
RNA from fresh-frozen tumor fragments was isolated using TRIzol reagent(Invitrogen). RNA from RLT-lysed cells was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. RNA concentration was measured with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, US). No more than 500 ng of total RNA was used for cDNA synthesis.
cDNA libraries were generated using the Human RNA TCR Multiplex kit (MiLaboratories), according to the manufacturer's protocol.
other: targeted RNA-seq (TCR amplicon seq)

treatment_protocol: CD39+PD-1+ (double-positive, DP) and non-DP CD4+ and CD8+ T cells from TILs freshly isolated from lymph node metastases from 8 melanoma patients.

tag: subset

value: Bulk TILs

tag: patient

value: melanoma patient 26

tag: tcr chain

value: TCR beta


title: mp26_FFT_LN2_4


title: mp26_FFT_LN1_3


title: P3+P4+CA3+CA4, abVDJ-derived cDNA


title: mp26_FFT_LN2_3


title: P2+CP5+CP6, abVDJ-derived cDNA


title: mp26_cult_IL21_niv_LN2_6

source_name: Bulk TILs cultivated with Nivolumab(20 μg/mL)+IL2+IL21 for 9 days


title: Hy_4%_N1E115_HiC rep1


title: mp26_cult_IL21_niv_LN2_4


title: mp26_cult_IL21_niv_LN2_3


title: mp26_cult_IL21_niv_LN2_2


title: testicular tissue, HO-1-1-2 (miRNA)


title: mp26_cult_IL21_niv_LN1_5


title: mp26_cult_IL21_niv_LN1_1


title: mp26_cult_IL21_niv_LN1_2


title: mp26_cult_IL21_niv_LN2_5


title: P3+P4+CA3+CA4, gdVDJ-derived cDNA


title: mp26_cult_IL21_niv_ifn_LN2_4

source_name: Bulk TILs cultivated with Nivolumab+IL2+IL21+IFNγ(100 μg/ml) for 9 days


title: mp26_cult_IL21_niv_ifn_LN2_3


title: mp26_cult_IL21_LN2_6

source_name: Bulk TILs cultivated with IL2(200 IU/ml)+IL21(25ng/ml) for 9 days


title: mp26_cult_IL21_niv_ifn_LN2_5


title: mp26_cult_IL2_high_LN2_6

source_name: Bulk TILs cultivated with IL2 (3000 IU/ml) for 9 days


title: mp26_cult_IL21_LN2_5


title: mp26_cult_IL21_LN1_5


title: mp26_cult_IL21_LN1_4


title: mp26_cult_IL21_niv_LN1_4


title: mp26_cult_IL21_niv_LN2_1


title: mp26_cult_IL2_high_LN2_4


title: mp26_cult_IL2_high_LN1_5


title: mp26_cult_IL2_high_LN1_6


title: mp40_CD8_DP_1

source_name: CD39+ PD-1+ CD8+ melanoma TILs

value: melanoma patient 40


title: mp40_CD8_nDP_1

source_name: CD39 PD-1 not-double-positive (not-DP) CD8+ melanoma TILs

value: CD8+ CD39 PD-1 not-DP


title: mp26_cult_IL2_high_LN1_4


title: mp36_CD8_notDP2_LN

value: melanoma patient 36


title: SP_D8_10xStress+Recovery

city: Kobe

first: Tomoyuki

last: Furuyashiki

state: Hyogo

address: 7-5-1 Kusunoki-cho Chuo-ku

institute: Kobe University

description: instrument model: Illumina NovaSeqXPlus

data_processing:
Read quantification was performed using Kallisto (version 0.46.1) with mouse cDNA sequences from Ensemble GRCm38.
Differential gene expression analysis was conducted using Sleuth, with quantified transcript expression levels in TPM (transcripts per million) merged to determine the expression of a given gene.
Assembly: mouse reference genome GRCm38
Supplementary files format and content: tab-delimited text files include transcripts per kilobase million (TPM) values for each Sample.

source_name: Spleen

growth_protocol: Femur bone marrow was flushed with ice-cold RPMI buffer and collected cells were processed with RNA isolation kit. Spleen was harvested and its RNA was purified using the same kit.

extract_protocol:
RNA was isolated using the NucleoSpin RNA Plus kit (Macherey-Nagel) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded mRNA Library Prep, according to the manufacturer’s instructions.

treatment_protocol: The study involved subjecting mice to social defeat stress for 1, 4, or 10 times (one per day). A subset of the mice, after experiencing stress 10 times, were left without any intervention for a period of one week. In contrast, the control group of mice did not undergo any social defeat stress.

value: Spleen

value: wild-type


title: mp40_CD8_nDP_2


title: SP_D2_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus


title: SP_D3_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus


title: KO_R.DraR1,no_stress,rep2

first: Chenxiang

last: Shi

state: Zhejiang province

address: Sandun Zhen Yuhangtang Road 866

institute: Zhejiang University

data_processing:
The library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Assembly: Deinococcus radiodurans R1
Supplementary files format and content: table delimited text files include FPKM values for each sample

organism: Deinococcus radiodurans

source_name: cells

growth_protocol: tryptone glucose yeast extract (TGY) liquid media at 30◦C

extract_protocol:
Total RNA was isolated using the Trizol method.1% denaturing agarose gels were used to assess RNA degradation and contamination. RNA concentration and RNA integrity were measured using an RNA Nano 6000 Assay kit and Bioanalyzer 2100 system.
A total of 3G RNA text per sample was used as the input material for library preparation.

value: cells


title: SP_D1_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus


title: KO_R.DraR1,no_stress,rep1


title: R1,no_stress,rep1


title: mp36_CD8_DP1_LN


title: mp26_cult_IL2_high_LN2_5


title: SP_D9_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: mp35_CD8_notDP2

value: melanoma patient 35


title: mp36_CD8_DP2_LN


title: R1,no_stress,rep2


title: mp35_CD8_DP2


title: SP_D4_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: SP_D7_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: mp35_CD8_DP1


title: mp35_CD8_notDP1


title: SP_D6_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: mp36_CD8_notDP1_LN


title: mp40_CD8_DP_2


title: SP_D13_4xStress

description: instrument model: Illumina NovaSeqXPlus


title: mp40_CD4_DP_2

source_name: CD39+ PD-1+ CD4+ melanoma TILs


title: mp40_CD4_nDP_1

source_name: CD39 PD-1 not-double-positive (not-DP) CD4+ melanoma TILs

value: CD4+ CD39 PD-1 not-DP


title: SP_D15_1xStress

description: instrument model: Illumina NovaSeqXPlus


title: SP_D10_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: SP_D16_1xStress

description: instrument model: Illumina NovaSeqXPlus


title: mp40_CD4_DP_1


title: SP_C3_Control

description: instrument model: Illumina NovaSeqXPlus

value: Control


title: mp35_CD4_DP1


title: mp35_CD4_DP2


title: mp35_CD4_notDP1


title: mp40_CD4_nDP_2


title: SP_C4_Control

description: instrument model: Illumina NovaSeqXPlus


title: SP_C1_Control

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D8_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus

source_name: Bone Marrow

value: Bone Marrow


title: SP_C2_Control

description: instrument model: Illumina NovaSeqXPlus


title: SP_D14_4xStress

description: instrument model: Illumina NovaSeqXPlus


title: mp35_CD4_notDP2


title: SP_D5_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: TL4-2A 2

city: Ames

first: Ravindra

middle: N

last: Singh

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

institute: Iowa State University

data_processing:
Mapping was performed using HISAT2
Reads were assigned to genes according to the Gencode v33 human transcriptome annotation using the featureCounts script from the Subread software package
Differential expression was estimated using the DESeq2 R package
Assembly: GRCh38
Supplementary files format and content: readCounts.csv is a table view of raw read counts for each annotated gene for all samples
Supplementary files format and content: circResults.csv and linResults.csv are outputs of DESeq2 comparing induced samples to control cells

source_name: T-REx

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Invitrogen, Cat No. 15596018). RNA was digested with RQ1 RNase-free DNase (Promega, Cat No. M6101) to remove contaminating genomic DNA, followed by phenol:chloroform extraction and ethanol precipitation.
NEBNext rRNA depletion kit v2 (Human/Mouse/Rat) followed by NEBNext Ultra II directional RNA library prep kit for Illumina

treatment_protocol: For induction of expression, TC4-2A, TL4-2A and control T-REx cells were seeded at a density of 2 × 105 cells per 100 mm dish. After incubating for 18 hours (h), the cell culture medium was replaced with fresh medium containing Dox. After 48 h of incubation, the cell culture medium was replaced with fresh medium containing Dox. The cells were collected 48 h after the second addition of Dox (96 h of induction in total).

tag: cell line

value: T-REx


title: TC4-2A 3


title: TL4-2A 1


title: BMC_D3_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D1_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D2_10xStress+Recovery

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D10_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: TC4-2A 1


title: BMC_D9_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: TC4-2A 2


title: Control 2


title: BMC_D6_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: TL4-2A 3


title: BMC_D7_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: Control 3


title: Control 1


title: BMC_D12_4xStress

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D18_1xStress

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D14_4xStress

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D5_10xStress

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D17_1xStress

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D11_4xStress

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D16_1xStress

description: instrument model: Illumina NovaSeqXPlus


title: Caco-2 cells, Uninfected-rep1

city: Guangzhou

first: Yuting

last: Fang

state: Guangdong, China

address: No. 1023-1063 Shatai South Road, Baiyun District

institute: School of Public Health, Southern Medical University

data_processing:
StringTie (v2.1.1) was used for gene and transcript quantification.
Differential gene expression analysis and GSEA of the EHEC and ΔespF groups were performed with DESeq2 and ClusterProfiler (v4.2.2), respectively.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples.

extract_protocol:
Total RNA was extracted using AG RNAex Pro Reagent (Accurate Biotechnology) according to the manufacturer’s instructions.RNA quality evaluation, library construction and sequencing were performed by APE ×Bio Technology LLC. 2 μg of total RNA was used for the constuction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Tn5 DNA library Prep Kit for Illumina (APE ×Bio Technology LLC) following the manufacturer’s protocol

value: Colon adenocarcinoma cell

tag: infection

value: uninfected


title: Caco-2 cells, Uninfected-rep3


title: Caco-2 cells, EHEC post-infection-rep3

value: EHEC


title: Caco-2 cells, ΔespF post-infection-rep3

value: ΔespF


title: Caco-2 cells, EHEC post-infection-rep2


title: Caco-2 cells, ΔespF post-infection-rep1


title: BMC_C4_Control

description: instrument model: Illumina NovaSeqXPlus


title: BMC_C2_Control

description: instrument model: Illumina NovaSeqXPlus


title: Caco-2 cells, EHEC post-infection-rep1


title: BMC_C1_Control

description: instrument model: Illumina NovaSeqXPlus


title: BMC_D15_1xStress

description: instrument model: Illumina NovaSeqXPlus


title: barcoded_ss3_cortex

city: Solna

first: Carl-Johan

middle: Wilheard Torkel

last: Eriksson

state: Stockholm

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institute

description: smart-seq3 libraries of barcoded single cells isolated from S1 via single-cell sorting of EGFP+ cells into 384-well plates

library_source: transcriptomic single cell

data_processing:
zUMIs v2.9.7
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: RDS, raw counts, UMI-counts, intron, exon, downsampled counts

source_name: brain

extract_protocol:
Single cell FACS
Smartseq3

value: brain

value: wildtype

value: lentivirus injection during embryogenesis