title: RNA-seq, Naive, rep1

description:
RNAseq1.count_mat.csv.gz
naive_1

tag: strain


title: RNA-seq, LCMV cl13, D8, rep3

status: Public on Sep 01 2023

type: SRA

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

country: China

institute: Nanjing Medical University

description:
RNAseq1.count_mat.csv.gz
Cl13_early_3

library_source: transcriptomic

data_processing:
Illumina HCS 1.2.0 and RTA 3.7.17 software used for sequencing and basecalling.
ATAC-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v2.4.2), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.2.7.1).
RNA-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v2.4.2) and STAR (v2.7.7a), read counts by HTSeq-count (v2.0.1).
Assembly: mm10
Supplementary files format and content: RNA-seq: csv, gene count matrix
Supplementary files format and content: ATAC-seq: bigWig, normalized signal

molecule: total RNA

organism: Mus musculus

source_name: CD8+ T

extract_protocol:
P14 CD8+ T cells were FACS-purified from spleens.
ATAC-seq: Nuclei were extracted using the ATAC-Seq Kit (Active Motif). Tagmented DNA was then column-purified and immediately used for PCR amplification and library generation.
RNA-Seq: Library preparation using the  Qiagen RNeasy Mini Kit.

tag: genotype

value: GOT1 WT

tag: cell type

value: CD8+ T

tag: treatment

value: infected with LCMV clone 13

tag: timepoint

value: d8 post infection

tag: treatment 2

tag: replicate


title: normal, NA, 67, 13

city: Santa Cruz

first: Daniel

last: Kim

state: California

address: McLaughlin Dr

department: Biomolecular Engineering

country: USA

institute: UC Santa Cruz

description:
n31
panc_normal_normalized_counts_20230703.csv
normal_13

data_processing:
RNA sequencing reads (FASTQ) were trimmed with Trimmomatic (v0.39), quality assessed using FASTQC (v0.11.9) and visualized using MultiQC (v1.11). Quantification was performed using Salmon (v1.9.0).
Assembly: Hg38
Supplementary files format and content: csv, normalized gene counts
Supplementary files format and content: tsv, normalized gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood Plasma

extract_protocol:
The ExoRNeasy kit (Qiagen) was used to isolate cell-free RNA from blood plasma of de-identified healthy controls (Discovery Life Sciences, blood collected in K2EDTA tubes) and pancreatic cancer patients (BioIVT, blood collected in K2EDTA tubes). Samples were initially filtered through a 0.8 um filter to remove any contaminants such as buffy coat. Filtered plasma was then processed using the ExoRNeasy kit to isolate cell-free RNA according to manufacturer instructions.
Full-length cDNA was synthesized from cell-free RNA from pancreatic cancer and healthy control samples (Takara SMART-Seq HT kit). Size distribution of cell-free RNA and resulting cDNA were evaluated using an Agilent bioanalyzer. Final libraries were made using the Illumina Nextera XT DNA Prep kit. These libraries were then sequenced (PE150) on an Illumina NextSeq 500.  Nanopore full-length cDNA libraries were prepared as described above, followed by manufacturer instructions for the Oxford Nanopore ligation kit LSK109. Sequencing for each library was performed on an Oxford Nanopore MinION device with R9.4 flowcells.

tag: tissue

value: Blood Plasma

tag: subject status

value: normal healthy donor

tag: age

tag: subject id


title: WJL2998_RLF_N026

city: Stanford

first: Jinglong

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

library_source: genomic

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg19
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS, JoinT-seq

molecule: genomic DNA

growth_protocol: K562 and its derived cell lines were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4). HEK293T and its derived cell lines were cultured at 37 °C and 5% CO2 in DMEM supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1/G0-arrested K562-Bcl2, K562-Bcl2 PKcs-/- and K562-iCas9 cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with pX330-Cas9-sgRNA or pMCB320-sgRNA to generated twined or genome-wide DSBs in different conditions, such as DMSO, 0.5 μM DPKi #1 (Nu7441), 20 μM DPKi #2 (Nu7026) and 10 μM ATMi (Ku60019).

tag: cell line

value: lymphoblast cells

value: Pal + Nu7026

tag: dsb induction (bait site)

tag: dsb induction (prey sites)

tag: number of normalized reads


title: RNA-seq, LCMV cl13, D8, rep2

description:
RNAseq1.count_mat.csv.gz
Cl13_early_2


title: WJL3003_RLF_N026

value: Pal + Nu7441


title: normal, NA, 61, 7

description:
n21
panc_normal_normalized_counts_20230703.csv
normal_7


title: RNA-seq, LCMV cl13, D8, rep1

description:
RNAseq1.count_mat.csv.gz
Cl13_early_1


title: WJL3002_RLF_N026


title: WJL2999_RLF_N026


title: normal, NA, 62, 8

description:
n22
panc_normal_normalized_counts_20230703.csv
normal_8


title: RNA-seq, LCMV cl13, D30, rep2

description:
RNAseq1.count_mat.csv.gz
Cl13_later_2

value: d30 post infection


title: RNA-seq, LCMV cl13, D30, rep3

description:
RNAseq1.count_mat.csv.gz
Cl13_later_3


title: normal, NA, 69, 22

description:
n45
panc_normal_normalized_counts_20230703.csv
normal_22


title: normal, NA, 68, 15

description:
n33
panc_normal_normalized_counts_20230703.csv
normal_15


title: normal, NA, 67, 17

description:
n35
panc_normal_normalized_counts_20230703.csv
normal_17


title: normal, NA, 47, 19

description:
n42
panc_normal_normalized_counts_20230703.csv
normal_19


title: normal, NA, 70, 18

description:
n41
panc_normal_normalized_counts_20230703.csv
normal_18


title: normal, NA, 78, 21

description:
n44
panc_normal_normalized_counts_20230703.csv
normal_21


title: normal, NA, 61, 16

description:
n34
panc_normal_normalized_counts_20230703.csv
normal_16


title: normal, NA, 59, 20

description:
n43
panc_normal_normalized_counts_20230703.csv
normal_20


title: normal, NA, 79, 6

description:
n16
panc_normal_normalized_counts_20230703.csv
normal_6


title: WJL3001_RLF_N026


title: E. coli promoter activity, FACS, rep1 bin11, LB

city: Saint Louis

first: Yichao

last: Han

state: MO

address: 1 Brookings Dr

department: Department of Energy, Environmental & Chemical Engineering

institute: Washington University in St Louis

description: amplicon

library_source: other

data_processing:
align read1 to sgRNA library and read2 to E. coli MG1655 genome using bowtie2, santools, and bedtools
calculate read counts for each promoter-sgRNA pair in each bin
fit the binned distribution of each promoter-sgRNA pair to a log-normal distribution
Supplementary files format and content: GSE213624_PPTP_Ecoli_summary_updated.csv

molecule: other

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli

growth_protocol: For each replicate, 100 μL glycerol stocks of the combinatorial library were thawed and inoculated in 250 mL of LB medium. When an OD600 of 0.5 was reached, 1 mL of cells was diluted into 25 mL of a target medium (either M9 glucose, M9 glycerol, or LB medium). After a few hours of adaptation, 500 μL of the cultures were added to 50 mL of the target medium containing 1 μM aTc as inducer. The induced cells were grown at 37°C until OD600 reached 0.1-0.2. At this point, the cell cultures were supplemented with 250 μg/mL chloramphenicol to halt protein production and were kept on ice until sorting.

extract_protocol:
Reporter plasmids were purified from 3 mL aliquots of overnight cell cultures from each bin using miniprep kits.
50 ng purified plasmids for each bin were amplified by the KAPA HiFi PCR Kit (Kapa Biosystems) for 20 cycles using primers prYH071 and prYH087. The PCR products were purified using the DNA Clean & Concentrator kit, and then were ligated with Illumina sequencing adapters via Golden Gate assembly. The ligation products were gel-purified to select DNA size between 400 bp and 1.5 kb and were subjected to another PCR with primers prYH128 and prYH129 for 8 cycles by the KAPA HiFi to enrich ligated products. The samples from each binned population were mixed at an estimated ratio to ensure that the number of reads sequenced is approximately proportional to the number of cells sorted for each bin in each replicate experiment.
Other: PPTP-seq (pooled promoter responses to transcription factor perturbations sequencing)

value: replicate 1

tag: facs gate

value: cell sorting according to log(GFP)

value: E. coli


title: E. coli promoter activity, FACS, rep1 bin10, LB

description: amplicon


title: E. coli promoter activity, FACS, rep1 bin12, LB

description: amplicon


title: WJL2997_RLF_N026

value: Pal + DMSO


title: E. coli promoter activity, FACS, rep1 bin9, LB

description: amplicon


title: normal, NA, 65, 5

description:
n15
panc_normal_normalized_counts_20230703.csv
normal_5


title: RNA-seq, LCMV Arm, D8, rep3

description:
RNAseq1.count_mat.csv.gz
Arm_early_3

value: infected with LCMV Armstrong


title: RNA-seq, LCMV Arm, D8, rep2

description:
RNAseq1.count_mat.csv.gz
Arm_early_2


title: WJL2996_RLF_N026


title: WJL2995_RLF_N026


title: WJL2828_RLF_N025

value: epithelial-like cells


title: normal, NA, 59, 3

description:
n13
panc_normal_normalized_counts_20230703.csv
normal_3


title: E. coli promoter activity, FACS, rep1 bin8, LB

description: amplicon


title: normal, NA, 67, 2

description:
n12
panc_normal_normalized_counts_20230703.csv
normal_2


title: E. coli promoter activity, FACS, rep1 bin7, LB

description: amplicon


title: RNA-seq, LCMV cl13, D30, rep1

description:
RNAseq1.count_mat.csv.gz
Cl13_later_1


title: normal, NA, 82, 4

description:
n14
panc_normal_normalized_counts_20230703.csv
normal_4


title: RNA-seq, LCMV Arm, D8, rep1

description:
RNAseq1.count_mat.csv.gz
Arm_early_1


title: panc, III, 50, 9

description:
panc.10.1.2
panc_normal_normalized_counts_20230703.csv
panc_9

value: pancreatic cancer patient

tag: Stage

value: III


title: normal, NA, 60, 1

description:
n11
panc_normal_normalized_counts_20230703.csv
normal_1


title: WJ1932_RLF_N020


title: WJL2825_RLF_N025


title: E. coli promoter activity, FACS, rep1 bin6, LB

description: amplicon


title: RNA-seq, LCMV Arm, D30, rep2

description:
RNAseq1.count_mat.csv.gz
Arm_later_2

tag: strain

value: GOT1 WT

value: CD8+ T


title: panc, II-B, 64, 7

description:
panc.7.1.1
panc_normal_normalized_counts_20230703.csv
panc_7

value: II-B


title: panc, II-B, 77, 10

description:
panc.6.1.1
panc_normal_normalized_counts_20230703.csv
panc_10

value: Blood Plasma


title: WJL2829_RLF_N025

tag: genotype


title: E. coli promoter activity, FACS, rep1 bin5, LB

description: amplicon

tag: cell type


title: WJ1935_RLF_N020

tag: treatment


title: E. coli promoter activity, FACS, rep1 bin2, LB

description: amplicon


title: RNA-seq, LCMV Arm, D30, rep3

description:
RNAseq1.count_mat.csv.gz
Arm_later_3

tag: timepoint


title: RNA-seq, withoutNH3, rep3

description:
RNAseq2.count_mat.csv.gz
withoutNH3_3

value: infected with LCMV clone 13

value: d8 post infection

tag: treatment 2

value: cultured without ammonium hydroxide


title: E. coli promoter activity, FACS, rep1 bin3, LB

description: amplicon

tag: replicate


title: panc, II-B, 72, 8

description:
panc.9.1.1
panc_normal_normalized_counts_20230703.csv
panc_8

tag: tissue


title: WJL2826_RLF_N025


title: RNA-seq, withoutNH3, rep2

description:
RNAseq2.count_mat.csv.gz
withoutNH3_2


title: panc, III, 64, 6

description:
panc.8.2.5
panc_normal_normalized_counts_20230703.csv
panc_6

tag: subject status


title: WJL2827_RLF_N025

value: DMSO


title: RNA-seq, withNH3, rep3

description:
RNAseq2.count_mat.csv.gz
withNH3_3

value: cultured with ammonium hydroxide


title: WJ1934_RLF_N020


title: E. coli promoter activity, FACS, rep3 bin15

data_processing:
align read1 to sgRNA library and read2 to E. coli MG1655 genome using bowtie2, samtools, and bedtools
calculate read counts for each promoter-sgRNA pair in each bin
fit the binned distribution of each promoter-sgRNA pair to a log-normal distribution
Supplementary files format and content: PPTP_Ecoli_summary.csv
Library strategy: PPTP-seq (pooled promoter responses to transcription factor perturbations sequencing)

source_name: bacterial cell

growth_protocol: For each replicate, 100 μL glycerol stocks of the combinatorial library were thawed and inoculated in 250 mL of LB medium. When OD600 of 0.5 was reached, 1 mL of cells were diluted into 25 mL M9 medium. After 3 h, 500 μL of cells were added to 50 mL M9 medium with 1μM aTc. The induced cells were grown to an OD600 of 0.1-0.2 in 7 h. At this point, the cell cultures were supplemented with 250 μg/mL chloramphenicol to halt protein production and were kept on ice until sorting.

extract_protocol:
Reporter plasmids were purified from 3 mL aliquots of overnight cell cultures from each bin using miniprep kits.
50 ng purified plasmids for each bin were amplified by the KAPA HiFi PCR Kit (Kapa Biosystems) for 20 cycles using primers prYH071 and prYH087. The PCR products were purified using the DNA Clean & Concentrator kit, and then were ligated with Illumina sequencing adapters via Golden Gate assembly. The ligation products were gel-purified to select DNA size between 400 bp and 1.5 kb and were subjected to another PCR with primers prYH128 and prYH129 for 8 cycles by the KAPA HiFi to enrich ligated products. The samples from each binned population were mixed at an estimated ratio to ensure that the number of reads sequenced is approximately proportional to the number of cells sorted for each bin in each replicate experiment.

value: replicate 3

value: bacterial cell

tag: molecule type

value: plasmid


title: WJ1931_RLF_N020


title: panc, I-B, 57, 5

description:
panc.5.4.5
panc_normal_normalized_counts_20230703.csv
panc_5

value: I-B

tag: age

tag: subject id


title: RNA-seq, withNH3, rep1

description:
RNAseq2.count_mat.csv.gz
withNH3_1


title: E. coli promoter activity, FACS, rep1 bin4, LB

description: amplicon

value: replicate 1

value: cell sorting according to log(GFP)

value: E. coli


title: panc, IV, 64, 4

description:
panc.4.3.9
panc_normal_normalized_counts_20230703.csv
panc_4

value: pancreatic cancer patient

value: IV


title: RNA-seq, withoutNH3, rep1

description:
RNAseq2.count_mat.csv.gz
withoutNH3_1

value: GOT1 WT

value: CD8+ T


title: RNA-seq, GOT1, WT, rep3

description:
RNAseq2.count_mat.csv.gz
GOT1_WT_P14_3


title: E. coli promoter activity, FACS, rep1 bin1, LB

description: amplicon


title: E. coli promoter activity, FACS, rep3 bin16


title: E. coli promoter activity, FACS, rep3 bin12


title: E. coli promoter activity, FACS, rep3 bin14


title: E. coli promoter activity, FACS, rep3 bin13


title: RNA-seq, LCMV Arm, D30, rep1

description:
RNAseq1.count_mat.csv.gz
Arm_later_1

value: infected with LCMV Armstrong

value: d30 post infection


title: WJ1933_RLF_N020

tag: cell line

value: epithelial-like cells

tag: dsb induction (bait site)


title: RNA-seq, withNH3, rep2

description:
RNAseq2.count_mat.csv.gz
withNH3_2

value: infected with LCMV clone 13

value: d8 post infection


title: CORALEEN patient 007 week_03 Ribociclib H3K4me2_ig_input

city: Salamanca

first: Darek

last: Kedra

state: Castilla y León

address: Campus Miguel de Unamuno

department: Cancer Research Center

country: Spain

institute: University of Salamanca

description: FiT-seq, breast tumor

data_processing:
clumpify from BBMap for FASTQ reads clusterin and removal of optical duplicates
ChIP-seq reads were aligned to the GRCh38.p13  genome using bwamem2 v2.2.1.
BAM files from the corresponding sample replicas were merged using samtools v1.16.
Duplicate reads were removed using samtools markdup
BAM files were converted to BED files containing chromosomes 1-22 and X using bedtools (ver 2.30). Simultaneously we excluded mappings to blacklisted regions6 (ENCODE, file obtained from: https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz).
Peak calling was done using sicer2  (ver 1.0.3) at FDR 0.01
Assembly: GRCh38.p13
Supplementary files format and content: combined island.bed (sicer2 island.bed peaks only)  with scoreisland. Six columns BED with peak_name, score and “.” for the strand

source_name: primary breast tumor

extract_protocol:
Two sections of 10 μm thickness of formalin-fixed paraffin-embedded (FFPE) tissue microscopy- guided were microdissectioned to obtain >70% of breast tumor epithelial of patients from CORALEEN clinical trial. To remove all traces of paraffin, FFPE tissue sections were washed three times with xylene before being rehydrated in an ethanol (%)/water (%) series (95/5, 80/20, 70/30, 50/50, 20/80, 0/100). An incubation of 10 min at 4 °C in a rotator platform end-to-end and a 5 min centrifugation at 14.000 xg at 4°C were carried out between each step. Samples were resuspended in dilution buffer (1% (vol/vol) Triton X-100, 150 mM NaCl, 20 mM tris-HCl, 2 mM EDTA pH 8 and 1 tablet of cOmplete). Samples were heated for 1 h at 50 °C at 900 rpm on the shaker. When samples were cooled down, they were treated with 40 ng/µl of proteinase K (Roche) for 5 min. Enzyme was subsequently inactivated with AEBSF (AG Scientific). The material was sonicated (Bioruptor) for 12 cycles (30s ON, 30s OFF, at low intensity 4 mA). After sonication, samples were centrifuged for 20 min at 14.000 xg at 4 °C. Supernatant was collected to perform the chromatin immunoprecipitation (ChIP) protocol and 10 µl of chromatin were taken aside as an input. Magnetic Dynabeads A (Invitrogen) (100 µl/ChIP) were pre-blocked by coupling them with 10 µg of antibody against H3K4me2 (Millipore 07-030) and incubating them at 4 °C overnight on an end-to-end rotator platform. After washing the beads with PBS/BSA, beads were resuspended with sonicated chromatin, and it was topped up (until 2 mL) with dilution buffer.
Beads, chromatin and the coupled antibody were incubated overnight at 4 °C on an end-to-end rotator platform. Beads were washed 5 times with RIPA buffer (50 mM HEPES pH 7.6, 1 mM EDTA, 0.7% (wt/vol) sodium deoxycholate, 1% (vol/vol) NP-40 and 0.5 M LiCl). DNA from the beads and from the input was eluted with elution buffer (1% (wt/vol) SDS, 0.1 M NaHCO3). Eluted samples were treated with 10 µg of RNAse A (Invitrogen) and were incubated at 37 °C for 30 min at 900 rmp (shaker). Reverse crosslink was performed by adding proteinase K (final concentration of 1 µg/µl) and samples were incubated overnight at 65 °C at 900 rpm (shaker). They were purified by performing an ethanol purification (adding phenol-chloroform-isoamyl, 3M Na-acetate pH 5.5, 100% ethanol and glycogen as a carrier) and leaving the samples overnight at -80 °C. Samples were finally washed twice with 70% ethanol and resuspended in 10 mM tris HCl, pH 8. Soluble chromatin was quantified fluorometrically using q-bit (ThermoFischer Scientific).
DNA libraries were prepared using ThruPLEX-FD kits (Takeda) using the manufacturer's protocols and sequenced on a Illumina Nextseq 500 instrument

treatment_protocol: Letrozole (2.5 mg/day) and CDK4 inhibitor Ribociclib (600 mg/day) for three weeks

tag: subject

value: patient 007

value: primary breast tumor

value: Letrozole+Ribociclib

tag: chip antibody

value: H3K4me2 (Millipore 07-030)


title: panc,  IV,  65,  1

description:
panc.1.2.3
panc_normal_normalized_counts_20230703.csv
panc_1

value: Blood Plasma

tag: Stage


title: WJ1930_RLF_N020

value: DMSO

tag: dsb induction (prey sites)

tag: number of normalized reads


title: RNA-seq, GOT1, WT, rep1

description:
RNAseq2.count_mat.csv.gz
GOT1_WT_P14_1

tag: strain

tag: genotype

tag: cell type


title: E. coli promoter activity, FACS, rep3 bin11

value: replicate 3

tag: facs gate

tag: treatment

value: cell sorting according to log(GFP)

value: bacterial cell

value: plasmid


title: RNA-seq, GOT1, KO, rep3

description:
RNAseq2.count_mat.csv.gz
GOT1_KO_P14_3

value: GOT1 KO

tag: timepoint

tag: treatment 2

tag: replicate


title: WJL2955_RLF_N026

source_name: K562-Bcl2 PKcs-/- backup

value: K562-Bcl2 PKcs-/- backup

value: lymphoblast cells

value: Bcl2 PKcs-/-

value: Pal + Nu7026


title: panc, III, 85, 3

description:
panc.3.2.5
panc_normal_normalized_counts_20230703.csv
panc_3

tag: tissue

tag: subject status

value: pancreatic cancer patient

value: III

tag: age


title: E. coli promoter activity, FACS, rep3 bin10

tag: molecule type


title: CS107_RLF_N025

tag: cell line

tag: dsb induction (bait site)


title: CORALEEN patient 006 week_03 Ribociclib_h3k4me2

description: FiT-seq, breast tumor

tag: subject

value: patient 006

tag: chip antibody


title: CORALEEN patient 007 week_00 no_treatment ig_input

description: FiT-seq, breast tumor

value: patient 007

value: primary breast tumor

value: none (input)


title: WJL2824_RLF_N025

value: epithelial-like cells

tag: dsb induction (prey sites)

tag: number of normalized reads


title: RNA-seq, GOT1, WT, rep2

description:
RNAseq2.count_mat.csv.gz
GOT1_WT_P14_2

tag: strain

tag: genotype

value: GOT1 WT

value: CD8+ T

value: infected with LCMV clone 13

value: d8 post infection


title: E. coli promoter activity, FACS, rep3 bin8

value: replicate 3

tag: facs gate

value: cell sorting according to log(GFP)

tag: cell type

value: bacterial cell

value: plasmid


title: RNA-seq, GOT1, KO, rep1

description:
RNAseq2.count_mat.csv.gz
GOT1_KO_P14_1

value: GOT1 KO

tag: treatment

tag: timepoint


title: panc, IV, 89, 2

description:
panc.2.2.7
panc_normal_normalized_counts_20230703.csv
panc_2

value: Blood Plasma

tag: Stage

value: IV

tag: subject id


title: WJL2957_RLF_N026

value: K562-Bcl2 PKcs-/- backup

value: lymphoblast cells

value: Bcl2 PKcs-/-

value: Pal + Nu7441


title: CORALEEN patient 006 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor

value: patient 006

tag: tissue

value: primary breast tumor

value: H3K4me2 (Millipore 07-030)


title: CORALEEN patient 006 week_00 no_treatment ig_input

description: FiT-seq, breast tumor

value: none (input)


title: E. coli promoter activity, FACS, rep3 bin9

tag: replicate


title: CS108_RLF_N025


title: ATAC-seq, Naive, rep2

value: GOT1 WT

value: CD8+ T

tag: treatment 2


title: CORALEEN patient 007 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor

value: patient 007


title: E. coli promoter activity, FACS, rep3 bin6

value: replicate 3

value: cell sorting according to log(GFP)

tag: molecule type


title: ATAC-seq, Naive, rep3


title: WJL2956_RLF_N026

tag: cell line

value: Pal + Nu7026

tag: dsb induction (bait site)


title: E. coli promoter activity, FACS, rep3 bin3

value: bacterial cell

value: plasmid


title: E. coli promoter activity, FACS, rep3 bin7


title: E. coli promoter activity, FACS, rep3 bin4


title: E. coli promoter activity, FACS, rep3 bin5


title: ATAC-seq, Naive, rep1


title: CORALEEN patient 005 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor

tag: subject

value: patient 005

tag: chip antibody


title: CORALEEN patient 005 week_03 Ribociclib_h3k4me2

description: FiT-seq, breast tumor

value: Letrozole+Ribociclib


title: RNA-seq, GOT1, KO, rep2

description:
RNAseq2.count_mat.csv.gz
GOT1_KO_P14_2

value: GOT1 KO

value: infected with LCMV clone 13

value: d8 post infection


title: ATAC-seq, LCMV cl13, D8, rep3


title: WJL2954_RLF_N026

value: K562-Bcl2 PKcs-/- backup

value: lymphoblast cells

value: Bcl2 PKcs-/-

value: Pal + DMSO

tag: dsb induction (prey sites)

tag: number of normalized reads


title: ATAC-seq, LCMV cl13, D30, rep3

tag: strain

tag: genotype

value: GOT1 WT

value: d30 post infection


title: E. coli promoter activity, FACS, rep3 bin1

tag: facs gate

tag: cell type


title: CORALEEN patient 005 week_00 no_treatment ig_input

description: FiT-seq, breast tumor

value: primary breast tumor

tag: timepoint

tag: treatment

value: none (input)


title: ATAC-seq, LCMV cl13, D8, rep2

value: CD8+ T


title: CORALEEN patient 004 week_03 Ribociclib_h3k4me2

description: FiT-seq, breast tumor

value: patient 004

value: H3K4me2 (Millipore 07-030)


title: WJL2952_RLF_N026

source_name: K562-Bcl2 PKcs-/-

value: K562-Bcl2 PKcs-/-

value: Pal + Nu7441


title: WJL2953_RLF_N026


title: CORALEEN patient 003 week_03 Ribociclib_h3k4me2

description: FiT-seq, breast tumor

value: patient 003

value: Letrozole+Ribociclib


title: CS106_RLF_N025


title: ATAC-seq, LCMV cl13, D8, rep1

value: infected with LCMV clone 13


title: E. coli promoter activity, FACS, rep3 bin2

value: replicate 3

value: cell sorting according to log(GFP)

value: bacterial cell

value: plasmid


title: WJL2950_RLF_N026

value: lymphoblast cells

value: Bcl2 PKcs-/-

value: Pal + Nu7026


title: CORALEEN patient 004 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor

value: primary breast tumor


title: WJL2949_RLF_N026


title: CS104_RLF_N025


title: CORALEEN patient 004 week_00 no_treatment ig_input

description: FiT-seq, breast tumor

value: none (input)


title: CORALEEN patient 003 week_00 no_treatment ig_input

description: FiT-seq, breast tumor


title: WJL2951_RLF_N026


title: CORALEEN patient 002 week_03 Ribociclib_h3k4me2

description: FiT-seq, breast tumor

value: patient 002


title: E. coli promoter activity, FACS, rep2 bin16

value: replicate 2


title: ATAC-seq, LCMV Arm, D8, rep2

value: GOT1 WT

value: CD8+ T

value: infected with LCMV Armstrong

value: d8 post infection


title: ATAC-seq, LCMV cl13, D30, rep2

value: d30 post infection


title: ATAC-seq, LCMV cl13, D30, rep1

value: infected with LCMV clone 13


title: E. coli promoter activity, FACS, rep2 bin15


title: CORALEEN patient 003 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor

value: patient 003

value: H3K4me2 (Millipore 07-030)


title: E. coli promoter activity, FACS, rep2 bin14

value: cell sorting according to log(GFP)

value: bacterial cell


title: CS105_RLF_N025

value: K562-Bcl2 PKcs-/-

value: lymphoblast cells

value: Pal + Nu7441


title: ATAC-seq, LCMV Arm, D8, rep3


title: E. coli promoter activity, FACS, rep2 bin13

value: plasmid


title: ATAC-seq, LCMV Arm, D30, rep2


title: CORALEEN patient 001 week_03 Ribociclib_h3k4me2

description: FiT-seq, breast tumor

value: patient 001

value: primary breast tumor

value: Letrozole+Ribociclib


title: ATAC-seq, LCMV Arm, D30, rep1

value: GOT1 WT


title: E. coli promoter activity, FACS, rep2 bin12

value: replicate 2


title: E. coli promoter activity, FACS, rep2 bin9


title: CORALEEN patient 001 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor


title: WJL2948_RLF_N026

value: Bcl2 PKcs-/-

value: Pal + DMSO


title: ATAC-seq, LCMV Arm, D8, rep1

value: CD8+ T

value: infected with LCMV Armstrong

value: d8 post infection


title: CORALEEN patient 002 week_00 no_treatment H3K4me2

description: FiT-seq, breast tumor

value: patient 002

value: H3K4me2 (Millipore 07-030)


title: WJL2958_RLF_N026

value: K562-Bcl2 PKcs-/- backup


title: CORALEEN patient 002 week_00 no_treatment ig_input

description: FiT-seq, breast tumor

value: none (input)


title: ATAC-seq, LCMV Arm, D30, rep3

value: d30 post infection


title: WJ517_RLF_N013

value: epithelial-like cells


title: CS103_RLF_N025

value: K562-Bcl2 PKcs-/-

value: lymphoblast cells


title: WJL2947_RLF_N026


title: E. coli promoter activity, FACS, rep2 bin10

value: cell sorting according to log(GFP)

value: bacterial cell

value: plasmid


title: E. coli promoter activity, FACS, rep2 bin8

value: replicate 2


title: ATAC-seq, withoutNH3, rep3

value: GOT1 WT

value: infected with LCMV clone 13

value: cultured without ammonium hydroxide


title: CORALEEN patient 001 week_00 no_treatment ig_input

description: FiT-seq, breast tumor

value: patient 001

value: primary breast tumor


title: WJL2991_RLF_N026


title: ATAC-seq, withoutNH3, rep2

value: CD8+ T

value: d8 post infection


title: WJ519_RLF_N013


title: bt474_FOXA1_S307A mutation

description:
ERS14484165
ERR10809415; ERR10809416

data_processing:
fastq_quality_filter -q 10 -p 97
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie v2.4.2. Only uniquely mapping reads were retained.
BAM files from the corresponding sample replicas were merged using samtools v1.11.
Peaks were called using MACS v3.0.0b1 with the significance cut-off q-value <=0.01
Assembly: hg19
Supplementary files format and content: narrowPeak, summits.bed

growth_protocol: BT474 cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% FBS and 0.01 mg/ml insulin (I9278, Sigma Aldrich).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min and then quenched with 125 mM of glycine. For FOXA1 ChIP with MCF-7 cells treated with Palbociclib, 2×106 of cells were plated into each 15cm plate in DMEM with 5% FBS. 3 days after plating, cells were treated with vehicle (control) or Palbociclib for 24h. Then cells were fixed for 10 min with 1% formaldehyde and then quenched with glycine (125mM)."
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Generation of FOXA1 serine to alanine mutants and Tet-On inducible stable cell lines Wild type human FOXA1 lentiviral expressing plasmid was purchased from Cyagen, with FOXA1 ORF downstream of a TRE element which allowed FOXA1 overexpression in a Tet-On manner. S234A and  S307A FOXA1 mutant were generated with QuikChange Lightning Site-Directed Mutagenesis Kit  (210518, Agilent) by following the manufacturer’s protocol. Lentivirus carrying wild type or mutant  FOXA1 were prepared and transduced to BT474 cells expressing Tet-On 3G transactivator protein.  Cells were selected with 2 μg/ml puromycin for two weeks before cryopreservation and further  experiments.

value: Human breast carcinoma

value: FOXA1 (Abcam, #ab23738)


title: E. coli promoter activity, FACS, rep2 bin7


title: WJL387_RLF_N012


title: E. coli promoter activity, FACS, rep2 bin11


title: ATAC-seq, withNH3, rep1

value: cultured with ammonium hydroxide


title: WJL2992_RLF_N026

value: epithelial-like cells


title: E. coli promoter activity, FACS, rep2 bin6


title: ATAC-seq, GOT1, WT, rep3


title: bt474_FOXA1_S234A mutation

description:
ERS14484164
ERR10809413; ERR10809414


title: E. coli promoter activity, FACS, rep2 bin5


title: WJL2994_RLF_N026


title: WJL2990_RLF_N026

value: DMSO


title: ATAC-seq, withNH3, rep3


title: WJL2993_RLF_N026


title: E. coli promoter activity, FACS, rep2 bin4


title: RCC#153

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Sequences were trimmed using BBDuk
Sequences were aligned to a human reference genome (hg19) using Bowtie2
Read count was calculated using Bedtools
Quantile normalization was performed using EdgeR
Assembly: hg19
Supplementary files format and content: matrix file includes raw read count for each sample

source_name: bulk tumor tissue

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit. Total RNA quality and quantity were determined using a Nanodrop 8000 UV-Vis spectrometer and 2200 TapeStation Instrument
Library construction for whole transcriptome sequencing was performed using the Truseq RNA sample preparation v2 kit.

value: bulk tumor tissue

value: primary

value: not specified

tag: Sex

value: male

tag: t stage

tag: n stage

tag: histology

value: clear cell

tag: nuclear grade


title: WJL2989_RLF_N026

tag: cell line


title: bt474_FOXA1 wild type

description:
ERS14484163
ERR10809411; ERR10809412


title: ATAC-seq, withNH3, rep2

value: GOT1 WT

tag: treatment 2

tag: replicate


title: VDJ: Peripheral Blood Mononuclear Cells, P8008_CW2

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

institute: Vanderbilt Universit Medical Center

description: 10x Genomics

data_processing:
Indiviudal samples were input into Cellranger v7.0.0 with default parameters
Reads were mapped to hg38 and UMI count matrices were computed by Cellranger with default parameters
Assembly: hgb38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Isolation of PBMCs
10X 5' Gene Expression (GEX) and Antibody Expression (ADT) Library Construction

value: peripheral bllod mononuclear cells

tag: tissue

value: blood


title: RCC#152

value: female


title: ATAC-seq, GOT1, WT, rep1

value: infected with LCMV clone 13


title: WJL389_RLF_N012

tag: dsb induction (bait site)

tag: dsb induction (prey sites)


title: ATAC-seq, withoutNH3, rep1

tag: strain

value: CD8+ T

value: cultured without ammonium hydroxide


title: ADT: Peripheral Blood Mononuclear Cells, P8008_CW2

description: 10x Genomics


title: ATAC-seq, GOT1, KO, rep3

tag: genotype

value: GOT1 KO

value: d8 post infection


title: E. coli promoter activity, FACS, rep2 bin2

value: replicate 2

tag: facs gate

value: cell sorting according to log(GFP)

value: bacterial cell

tag: molecule type

value: plasmid


title: RNA: Peripheral Blood Mononuclear Cells, P8008_CW2

description: 10x Genomics

library_source: transcriptomic single cell

tag: cell type


title: E. coli promoter activity, FACS, rep2 bin1

tag: treatment


title: E. coli promoter activity, FACS, rep1 bin16

value: replicate 1


title: ATAC-seq, GOT1, KO, rep2

tag: timepoint


title: ATAC-seq, GOT1, WT, rep2


title: ATAC-seq, GOT1, KO, rep1


title: E. coli promoter activity, FACS, rep1 bin15


title: WJ515_RLF_N013

value: epithelial-like cells

value: DMSO

tag: number of normalized reads


title: RCC#142

value: bulk tumor tissue

value: primary

value: not specified

tag: Sex

tag: t stage

tag: n stage

value: clear cell


title: RCC#150

tag: cell line

value: female

tag: histology

tag: nuclear grade


title: WJL385_RLF_N012


title: PMG, Hypo, rep4

city: Seoul

first: Jong-Il

address: Daehakro 103

institute: Seoul National University

data_processing:
Sequence reads were mapped to mm10 using STAR with RSEM (v1.3.3).
Read counts and FPKM were calculated using RSEM (v1.3.3).
Assembly: mm10
Supplementary files format and content: *.genes.results.txt: Tab-delimited text files include FPKM values.

source_name: brain

growth_protocol: Primary microglial cells were prepared from newborn mouse pups (postnatal day 1; Crl:CD1(ICR) mice). Cortices and hippocampi were scooped out from mouse pup brains and collected in ice-cold HBSS. After the meninges were carefully removed, the tissues were transferred to a 15 ml tube containing 3 ml culture media (DMEM containing FBS and P/S). The contents were triturated using a fire-polished Pasteur pipette and filtered through a 40-μm cell strainer. The resulting cells in culture media were plated on PDL-coated T75 flasks and maintained in a 37 °C, humidified 5% CO2 incubator for 11–12 days. At 11–12 DIV, floating microglial cells in T75 flasks were harvested and then replated at the appropriate density on PDL-coated plates for experiments. Adhering astrocytes in T75 flasks were further cultured for use in experiments.

extract_protocol:
RNA was harvested with Qiagen RNeasy mini kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Microglia cells were treated with vehicle or T3 (0.3 μM) in DMEM for 48 hours.

tag: tissue

value: brain

value: Primary microglia

tag: age

value: Postnatal day 1

value: no treatment


title: E. coli promoter activity, FACS, rep1 bin13

tag: replicate


title: E. coli promoter activity, FACS, rep1 bin10


title: RCC#137

value: male


title: E. coli promoter activity, FACS, rep1 bin12


title: RCC#135


title: WJL2834_RLF_N025

value: lymphoblast cells

value: Pal + Nu7026

tag: dsb induction (bait site)

tag: dsb induction (prey sites)


title: E. coli promoter activity, FACS, rep1 bin9

tag: facs gate

value: cell sorting according to log(GFP)

value: bacterial cell


title: RCC#126


title: E. coli promoter activity, FACS, rep1 bin11

value: replicate 1

tag: molecule type

value: plasmid


title: PMG, Hypo, rep1

tag: strain

tag: cell type


title: WJL2837_RLF_N025

tag: genotype

tag: treatment


title: PMG, Hypo, rep2


title: E. coli promoter activity, FACS, rep2 bin3

value: replicate 2


title: RCC#122

value: bulk tumor tissue

tag: Sex

value: papillary


title: WJL2841_RLF_N025

value: Pal + Nu7441

tag: number of normalized reads


title: WJL2839_RLF_N025

value: Pal + DMSO


title: RCC#148

value: primary

value: not specified

value: female

tag: t stage

tag: n stage

value: MiT family translocation-associated


title: PMG, Hypo, rep3

value: brain

value: Primary microglia

value: Postnatal day 1

value: no treatment


title: WJL2838_RLF_N025

tag: cell line

value: lymphoblast cells


title: RCC#114

value: male

tag: histology

value: clear cell

tag: nuclear grade


title: WJL2840_RLF_N025

value: Pal + Nu7026


title: E. coli promoter activity, FACS, rep1 bin8

value: replicate 1

value: cell sorting according to log(GFP)

value: bacterial cell

value: plasmid


title: E. coli promoter activity, FACS, rep1 bin6


title: RCC#99

tag: tissue

value: bulk tumor tissue

value: papillary


title: PMG, con, rep3

tag: age

value: Liothyronine (L-T3) treatment


title: WT_CD, WT_ID, APT_CD, APT_ID

description: 10x Genomics

data_processing:
The demultiplexing barcoded processing, gene counting were made using the Cell Ranger software (v6.0.1).
Assembly: GRCh38
Supplementary files format and content: Tab-separated valued files and matrix files (barcodes.*.tsv, features.*.tsv, matrix.*.mtx).

source_name: brain (hippocampus)

extract_protocol:
Freshly collected mouse hippocampus was dissociated with Adult Brain Dissociation Kit (Miltenyi) using manufacturer's protocols (37C_ABDK_02). Dissociated cells were stained with Fixable Viability Dye eFluorTM 660 (BD) for 30min, 4C for FACS sorting. FACS sorted cells were suspended with 0.04% BSA/PBS solution.
Libraries were generated with the manufacturer's instructions (single cell 3' v3.1 protocol with CellPlex, 10x Genomics).

treatment_protocol: Hypothyroidism was induced by feeding 16-week-old ADLP mice a low iodine deficient diet supplemented with 0.15% propylthiouracil (PTU) (Envigo, TD.95125) for 10 weeks. Control euthyroidism mice of the same age were fed a normal diet for 10 weeks.

value: ADLP

value: brain (hippocampus)

value: all cells

value: mixed sample (non-demultiplexed)

value: 26 weeks


title: WJL2833_RLF_N025

value: Pal + DMSO

tag: dsb induction (bait site)


title: E. coli promoter activity, FACS, rep1 bin5

tag: replicate


title: E. coli promoter activity, FACS, rep1 bin7

tag: facs gate


title: WJL2988_RLF_N026

value: lymphoblast cells

value: Pal + Nu7026+NVB

tag: dsb induction (prey sites)


title: WJL2836_RLF_N025


title: RCC#132

value: primary

value: not specified

value: male


title: E. coli promoter activity, FACS, rep1 bin3

value: replicate 1

value: cell sorting according to log(GFP)

tag: molecule type


title: WJL2835_RLF_N025

tag: cell type

value: Pal + Nu7441


title: PMG, con, rep2

tag: strain

value: brain

value: Primary microglia

value: Postnatal day 1


title: PMG, con, rep4

tag: treatment

value: Liothyronine (L-T3) treatment


title: PMG, con, rep1


title: RCC#97

value: bulk tumor tissue

tag: Sex

value: female

value: clear cell


title: RCC#93


title: E. coli promoter activity, FACS, rep1 bin4

value: bacterial cell

value: plasmid


title: WJL2823_RLF_N025

value: lymphoblast cells

tag: genotype

tag: number of normalized reads


title: WJL2605_RLF_N024

value: Pal + Nu7026+NVB


title: ZcKO _2cell_RNAseq_rep3

city: NanJing

first: Wenya

last: Sun

address: 140 Hanzhong Rd,Gulou, Nanjing, 210029,China

institute: NanJing Medical University

data_processing:
Sequencing reads were trimmed for adaptor sequence/low quality sequence using fastp.
Trimmed reads were aligned with the mouse genome mm10 using HISAT2 with default parameters.
Read counts were quantified using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: 2cell embryos

extract_protocol: GV oocytes were collected 46h after PMSG injection, MII oocytes were collected 14h after hCG injection, and 2cell embryos were collected 32h after insemination. Five oocytes or embryos were collected for each sample.  The RNA-seq libraries for the harvested samples were generated based on Smart-seq2. ERCC spike-ins were added for normalization. Sequence libraries were constructed using the KAPA HyperPlus Prep Kit (KK8514) according to the manufacturer's instructions.

value: 2cell embryos

value: Vps34 floxed/floxed, Zp3-Cre positive


title: E. coli promoter activity, FACS, rep1 bin2


title: WJL2822_RLF_N025

value: Pal + Nu7026+Olap


title: ZcKO _2cell_RNAseq_rep2


title: RT208_TIM_3_minus

description: #208, TTEX, anti-CD3

data_processing:
Sequences were trimmed using BBDuk
Sequences were aligned to a human reference genome (hg19) using Bowtie2
Read count was calculated using Bedtools
Quantile normalization was performed using EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM expression for each Sample

source_name: Tumor infiltrating lymphocytes

extract_protocol:
Total RNA was extracted from the sorted cells using TRIZOL reagent (Thermo Fisher Scientific), and was assessed for quantity and quality using a Bioanalyzer 2100 (Agilent).
Libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

value: Tumor infiltrating lymphocytes

value: primary

value: PD1+Tim3+ CD8 T cell


title: E. coli promoter activity, FACS, rep1 bin14

value: replicate 1

value: cell sorting according to log(GFP)


title: WJL2604_RLF_N024


title: WJL2603_RLF_N024


title: RCC#79

value: not specified

value: male

tag: t stage

tag: n stage

value: chromophobe


title: RT208_TIM_3_plus

description: #208, TTEX, anti-CD3+HPK1 inhibitor

tag: cell line

value: HPK1 inhibitor


title: RCC#90

value: bulk tumor tissue

tag: histology

value: clear cell

tag: nuclear grade


title: Vps34f/f _2cell_RNAseq_rep1

tag: age

value: Vps34 floxed/floxed


title: Cold acclimation four times, 3

city: Lanzhou

first: Zezhong

last: Su

address: YuZhong

institute: Lanzhou University

data_processing:
Prior to assembly, we removed the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) in the raw data.
Reference genome http://www.tair.org/alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.
Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
Transcript abundance estimation and differentially expressed testing.  The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).
The feference GTF annotation file used in Cufflinks was downloaded from the JGI database. Cufflink was used to de novo assemble the transcripiome at first; The second ,Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded JGI GTF file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with “q_value”less than 0.05 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression.
Assembly: Arabidopsis thaliana
Supplementary files format and content: bigWig, excel

organism: Arabidopsis thaliana

source_name: plants stems and leaves

growth_protocol: Soil culture after the germination, 2-week seedlings

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5 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.

treatment_protocol: cold memory (S1:4°C for 6 h, then at room temperature for 18 h; S4:4°C for 6 h, then at room temperature for 18 h, repeated four times), and then placed at 0°C for 6 h, and control groups with normal growth conditions.

tag: tissue

value: plants stems and leaves

value: WT

value: Cold acclimation four times

tag: time

value: Day 4


title: E. coli promoter activity, FACS, rep1 bin1

tag: replicate

tag: facs gate

value: bacterial cell

value: plasmid


title: RT208_CD28_plus

description: #208, TPEX, anti-CD3+HPK1 inhibitor

value: Tumor infiltrating lymphocytes

value: primary

value: PD1+CD28+Tim3- CD8 T cell


title: RCC#64


title: Vps34f/f _2cell_RNAseq_rep3

value: 2cell embryos


title: ZcKO _2cell_RNAseq_rep1

value: Vps34 floxed/floxed, Zp3-Cre positive


title: Vps34f/f _2cell_RNAseq_rep2


title: WJL2602_RLF_N024

value: lymphoblast cells

value: Pal + Nu7026+Olap

tag: dsb induction (bait site)

tag: dsb induction (prey sites)


title: ZcKO _MII_RNAseq_rep3

source_name: MII oocytes

tag: cell type

value: MII oocytes


title: ZcKO _MII_RNAseq_rep2


title: RT208_CD28_minus

description: #208, TPEX, anti-CD3

tag: treatment


title: Cold acclimation four times, 2


title: RT202_TIM_3_plus

description: #202, TTEX, anti-CD3+HPK1 inhibitor

value: PD1+Tim3+ CD8 T cell

value: HPK1 inhibitor


title: WJL2987_RLF_N026


title: WJL2986_RLF_N026

value: Pal + Nu7026


title: WJL2821_RLF_N025


title: Cold acclimation four times, 1

value: plants stems and leaves


title: WJL2601_RLF_N024


title: RT202_TIM_3_minus

description: #202, TTEX, anti-CD3


title: ZcKO _MII_RNAseq_rep1


title: Vps34f/f _MII_RNAseq_rep3

value: Vps34 floxed/floxed


title: RT202_CD28_plus

description: #202, TPEX, anti-CD3+HPK1 inhibitor


title: Cold acclimation once, 3

value: WT

value: Cold acclimation once

value: Day 1


title: Cold acclimation once, 1


title: Vps34f/f _MII_RNAseq_rep1


title: Cold acclimation once, 2


title: RT195_TIM_3_plus

description: #195, TTEX, anti-CD3+HPK1 inhibitor


title: WJL2820_RLF_N025

value: Pal + NVB


title: WJL2985_RLF_N026


title: control : Room temperature/or before stress, 3

value: Room temperature/or before stress

value: Day 0


title: control : Room temperature/or before stress, 2


title: RT202_CD28_minus

description: #202, TPEX, anti-CD3

value: Tumor infiltrating lymphocytes

value: primary

value: PD1+CD28+Tim3- CD8 T cell


title: ZcKO _GV_RNAseq_rep3

source_name: Germinal vesicle oocytes

value: Germinal vesicle oocytes

value: Vps34 floxed/floxed, Zp3-Cre positive


title: RT195_TIM_3_minus

description: #195, TTEX, anti-CD3


title: ZcKO _GV_RNAseq_rep2


title: 21TP

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequence and length filtering (≤18nt discarded): TrimGalore
miRNA annotation and prediction: sRNAtoolbox-sRNAbench (number of allowed mismatches: 1, minimum read count: 6) with reference to miRBase 22.1
read count extraction, normalization and differential expression analysis: DESeq2 (a Bioconductor R-project package)
Assembly: ARS-UCD1_2_
Supplementary files format and content: CSV file with normalized abundance measurements

organism: Bos taurus

source_name: mammary fat pad

extract_protocol:
Total RNA was extracted using Direct-zol RNA Mini Prep kit (Zymo Research). The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
The libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C until further use.

treatment_protocol: Immediately after slaughter, tissue samples were put in RNA Later solution (Thermo Fisher Scientific) and stored at -80°C

value: mammary fat pad

value: control


title: RT195_CD28_minus

description: #195, TPEX, anti-CD3


title: control : Room temperature/or before stress, 1


title: WJL2600_RLF_N024

value: lymphoblast cells


title: WJL2598_RLF_N024


title: Vps34f/f _GV_RNAseq_rep3


title: 19TP


title: WJL2819_RLF_N025

value: Pal + Olap


title: RT193_TIM_3_plus

description: #193, TTEX, anti-CD3+HPK1 inhibitor

value: PD1+Tim3+ CD8 T cell

value: HPK1 inhibitor


title: 18TP


title: Vps34f/f _MII_RNAseq_rep2

value: MII oocytes

value: Vps34 floxed/floxed


title: WJL2597_RLF_N024


title: RT193_TIM_3_minus

description: #193, TTEX, anti-CD3


title: WJL2599_RLF_N024


title: Vps34f/f _GV_RNAseq_rep1


title: RT193_CD28_plus

description: #193, TPEX, anti-CD3+HPK1 inhibitor


title: 16TP

value: restricted


title: WJL2596_RLF_N024


title: RT193_CD28_minus

description: #193, TPEX, anti-CD3


title: WJL2983_RLF_N026

value: Pal + DMSO


title: ZcKO _GV_RNAseq_rep1


title: 13TP


title: RT195_CD28_plus

description: #195, TPEX, anti-CD3+HPK1 inhibitor


title: 15TP

value: ad libitum


title: WJL2818_RLF_N025


title: CT26, CX3CL1+IFN-γ, biological replicate 3 [CX3CL1+IFN-γ 3]

city: Boston

first: Gordon

last: Freeman

state: MA

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA sequencing using Illumina NovaSeq 6000 at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Sequenced reads were aligned to the UCSC mm10 reference genome assembly
Gene counts were quantified using STAR (v2.7.3a)
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package (v1.22.1)
RNAseq analysis was performed using the VIPER snakemake pipeline
Assembly: mm10
Supplementary files format and content: Excel files include TPM values

extract_protocol:
RNA was isolated using RNeasy kit (Qiagen catalog 74104)
RNA libraries for RNA-seq were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kit following manufacturer's protocols.

value: tumor cell line


title: CT26, No treatment, biological replicate 3 [No treatment 3]

value: No treatment


title: WJL2595_RLF_N024


title: MCF10A Cells, untreated, Rep 2

city: Boulder

first: Amy

last: Palmer

state: Colorado

address: 596 UCB

department: BioFrontiers

institute: University of Colorado Boulder

data_processing:
Quality control of demultiplexed fastq files was performed using fastQC (v.0.11.8). Adapters were trimmed using BBDuk55 using the following flags: ktrim=r , qtrim=10,  k=23, mink=11, hdist=1, maq=10, minlen=20, tpe, tbo
Trimmed fastq files were mapped in a paired-end fashion with HISAT2 (v2.1.0) to the hg38 genome assembly
BAM files for each sequencing run were concatenated with their corresponding treatment + replicate BAM file using samtools-merge (v1.8)
Resulting BAM files were indexed with samtools (v1.8) and converted to TDFs using igvtools (v2.3.75)
Regions of open chromatin were annotated by running HMMRATAC (Tarbell and Liu, Nucleic Acids Research, 2019) on sorted BAM files
Assembly: hg38
Supplementary files format and content: tdfs for combined (Sequencing Runs 1 & 2) treatments
Supplementary files format and content: bed files containing regions of open chromatin annotated using HMMRATAC

source_name: Breast

growth_protocol: MCF10A cells were maintained in DMEM/F12 medium containing 5% Horse Serum (ThermoFisher) and 1% Penicillin/Streptomycin (ThermoFisher), supplemented with 20 ng/mL EGF (ThermoFisher), 0.5 mg/mL hydrocortisone (Sigma), 100 ng/mL cholera toxin (Sigma), and 10 µg/mL insulin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested by scraping in fresh HHBSS, and nuclei were isolated according to the OMNI-ATAC protocol as described by Corces et al (Nat. Methods, 2017).
Tagmentation was performed using the Illumina Tagment DNA TDE1 Enzyme & Buffer Kit. DNA was purified using the E.Z.N.A. Plasmid DNA miniprep kit from Omega Bio-Tek. Libraries were prepared using Nextera CD Indexes from Illumina and subjected to an additional  6  cycles of PCR amplification. Librariies were quantified via Qubit and size selected for 100-1000 bp fragments using an Agilent High Sensitivity D5000 Tapestation. Librariers were subsequently pooled and run on a Illumina NextSeq 500. To increase the sequencing depth, pooled libraries were sequenced twice.

treatment_protocol: For each treatment, approximately 50,000 MCF10A cells were pre-incubated in phosphate-free HEPES-buffered Hanks balanced salt solution (HHBSS), pH 7.6, for 30 mins. Cells were then treated with either 30 µM ZnCl2, 50 µM Tris(2-pyridylmethyl)amine (TPA), or no treatment for 30 mins prior to harvest.

value: Breast

value: Mammary epithelial

value: WT

value: Untreated


title: MCF10A Cells, ZnCl2 treated, Rep 2

value: 30 uM ZnCl2


title: CT26, IFN-γ, biological replicate 3 [IFN-γ 3]

value: IFN-γ


title: CT26, CX3CL1, biological replicate 3 [CX3CL1 3]


title: WJL2984_RLF_N026

value: lymphoblast cells


title: 10TP

value: mammary fat pad


title: 11TP


title: MCF10A Cells, Zn chelator treated, Rep 2

value: 50 uM TPA


title: Vps34f/f _GV_RNAseq_rep2

value: Germinal vesicle oocytes


title: 7TP


title: WJL2981_RLF_N026


title: MCF10A Cells, untreated, Rep 1


title: 9TP


title: WJL2594_RLF_N024


title: CT26, No treatment, biological replicate 2 [No treatment 2]


title: MCF10A Cells, Zn chelator treated, Rep 1


title: 6TP


title: WJL2976_RLF_N026

value: Pal + Nu7026


title: CT26, No treatment, biological replicate 1 [No treatment 1]


title: 8TP


title: WJL2975_RLF_N026


title: CT26, CX3CL1+IFN-γ, biological replicate 2 [CX3CL1+IFN-γ 2]


title: MCF10A Cells, ZnCl2 treated, Rep 1


title: CT26, CX3CL1+IFN-γ, biological replicate 1 [CX3CL1+IFN-γ 1]


title: CT26, IFN-γ, biological replicate 2 [IFN-γ 2]


title: WJL2980_RLF_N026


title: CT26, CX3CL1, biological replicate 2 [CX3CL1 2]


title: D gH2AX +IAA

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: conserved sited of increased DNA damage

data_processing:
Single-end BrdU-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.4.2 on the online platform Galaxy (https://usegalaxy.org; Afgan et al., 2018)
gH2AX ChIP-Seq peaks were called in the +IAA treated sample against the gH2AX ChIP-Seq in its uninduced control using MACS2 v.2.1.1
The bedtools intersect intervals function on the online platform Galaxy was used to identify the conserved gH2AX ChIP-Seq peaks in the two repeats.
Assembly: hg38
Supplementary files format and content: .txt, contains the coordinates of the peaks shared between the two replicates

source_name: colon

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (Phospho-Histone H2A.X: ab2893, Abcam; H3: ab1791, Abcam) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
NEBNext Ultra II DNA Library Preparation Kit
ChIP Seq single end on 4 Lanes (L001-L004)

treatment_protocol: For G1 cell synchronisation, asynchronous cells were treated with 20 uM Lovastatin for 24 hours. To then release cells from the G1 arrest, cells were washed 3X in pre-warmed growth media before fresh media supplemented with 2 mM Mevalonic Acid was added. Cells entered S-phase approximately 12 hours post release.

value: colon

value: colorectal carcinoma

tag: chip antibody

value: Rabbit polyclonal anti-Phospho-Histone H2A.X (Ser139), Abcam, Cat#ab2893

value: auxin-induced degradation of TRAIP


title: 5TP

value: restricted


title: D gH2AX +IAA-2

description: conserved sited of increased DNA damage


title: WJL2979_RLF_N026

tag: genotype

value: Pal + Nu7441


title: 2PAD

value: control


title: 4PTP


title: D H2AX +IAA-2

description: conserved sited of increased DNA damage

value: Rabbit polyclonal anti-histone H2AX, Merck Millipore, Cat# 07627


title: WJL2974_RLF_N026

tag: number of normalized reads


title: CT26, IFN-γ, biological replicate 1 [IFN-γ 1]

value: tumor cell line


title: 3TP

value: ad libitum


title: WJL2982_RLF_N026


title: 18W

source_name: liver

value: liver


title: D H2AX +IAA

description: conserved sited of increased DNA damage


title: WJL2977_RLF_N026


title: CT26, CX3CL1, biological replicate 1 [CX3CL1 1]


title: D H2AX unind

description: conserved sited of increased DNA damage


title: 16W


title: Sample_S44

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the mouse genome (mm10) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Gene counts were imported into R (v4.05) and analysis of differential expression between groups was done using the limma-voom pipeline
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts) and columns include samples. A single file is included for all samples.

source_name: Liver

extract_protocol:
RNA was extracted from liver tissue from individual mice in four groups (OC or veh diet, with or without VWR, n = 5 per group) using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape.
mRNA-seq libraries (n = 5 per group) were prepared using a TruSeq Stranded RNA HT Sample Prep Kit (Illumina, Cat. No. RS-122-2303) on a Perkin Elmer Sciclone G3 platform. An additional standard 1.0x manual bead cleanup was performed using AMPure XP Beads (Beckman Coulter, A63881) after the libraries were completed to remove primer-dimers. Qubit dsDNA BR Assay kit was used to determine the concentration of the completed library and a Fragment Analyzer Standard Sensitivity NGS Fragment Kit
Paired-end, opposing strand directional libraries

value: Liver

tag: activity

value: VWR

value: Con

tag: group


title: WJL2971_RLF_N026

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg19
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS, JoinT-seq

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

tag: cell line

value: lymphoblast cells

value: Pal + DMSO


title: D gH2AX unind-2

description: conserved sited of increased DNA damage


title: Sample_S8


title: 21W


title: WJL2978_RLF_N026


title: Sample_S7

value: Sed

value: OC


title: 19W


title: D H2AX unind-2

description: conserved sited of increased DNA damage

value: colon

value: colorectal carcinoma


title: MCF7_NAIL_ΔNFκB_TNFa_90min_rep2

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Raw reads were aligned to human genome hg19 by Tophat2
Differential gene expressions were analyzed via Cufflink and Cuffdiff with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: raw counts and differential gene analysis

source_name: MCF7 cell line

growth_protocol: Cells were cultured in DMEM media supplemented with 10% FBS and antibiotics.

extract_protocol:
RNA was isolated using Trizol followed by column purification.
RNA-Seq library was prepared by Illumina Truseq Total RNA sequencing kit according to manufacturer instructions.
Paired-end sequencing was performed using Illumina Hiseq, 2x76bp.

treatment_protocol: MCF7-NAILWT and MCF7-NAILΔNFκB cells were stimulated with TNF alpha (10ng/ml) for 0, 45 and 90 mins.

value: breast

value: TNFa


title: D gH2AX unind

description: conserved sited of increased DNA damage

value: Rabbit polyclonal anti-Phospho-Histone H2A.X (Ser139), Abcam, Cat#ab2893


title: MCF7_NAIL_ΔNFκB_TNFa_90min_rep1


title: Sample_S5


title: 11W


title: WJL2973_RLF_N026


title: WJL2972_RLF_N026


title: 15W


title: Sample_S34


title: Sample_S41


title: WJL2970_RLF_N026


title: 13W

value: restricted


title: MCF7_NAIL_ΔNFκB_TNFa_0min_rep2

value: control


title: WJL2969_RLF_N026


title: Sample_S39


title: MCF7_NAIL_WT_TNFa_90min_rep2


title: MCF7_NAIL_ΔNFκB_TNFa_45min_rep1


title: Sample_S3


title: 10W


title: WJL2967_RLF_N026


title: Sample_S33


title: WJL2968_RLF_N026


title: MCF7_NAIL_ΔNFκB_TNFa_0min_rep1


title: 9W


title: WJL2963_RLF_N026


title: 8W


title: Sample_S32


title: WJL2966_RLF_N026


title: WJL2964_RLF_N026


title: 5W


title: Sample_S30


title: MCF7_NAIL_WT_TNFa_45min_rep1


title: 7W


title: Sample_S31


title: 6W


title: MCF7_NAIL_ΔNFκB_TNFa_45min_rep2


title: WJL2962_RLF_N026


title: MCF7_NAIL_WT_TNFa_90min_rep1


title: WJL2961_RLF_N026

value: DMSO


title: MCF7_NAIL_WT_TNFa_45min_rep2


title: 2W


title: 3W

value: ad libitum


title: Sample_S23


title: Sample_S19


title: Sample_S22


title: WJL2965_RLF_N026


title: Sample_S2


title: MCF7_NAIL_WT_TNFa_0min_rep1


title: 4W

value: liver


title: 18PPP

source_name: mammary parenchyma

value: mammary parenchyma


title: MCF7_NAIL_WT_TNFa_0min_rep2


title: Sample_S14

value: Liver

value: VWR


title: GBM43 cells, COMBI-1

city: New York

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
the Fasq file was processed and gene set analysis was performed by using Scidap software (https://scidap.com/)
Supplementary files format and content: RPKM

source_name: Gliobalstoma

growth_protocol: GBM43 cells were cultured in DMEM + 10% FBS + primocin

extract_protocol:
total RNA by using miRNAeasy Mini Kit from QIAGEN (217004)
SIRV-Set 1 (Iso Mix E0, E1, E2) - RNA-seq  (Cat#SKU: 025.03)

treatment_protocol: GBM43 cells were treated with DMSO, 50 nM THZ1, 100 µM etomoxir, or combination of both for 24 hours in  DMEM + 1.5% FBS + primocin

value: Gliobalstoma


title: 16PPP


title: WJL2959_RLF_N026

value: lymphoblast cells


title: Sample_S10


title: GBM43 cells, COMBI-2


title: WJL2960_RLF_N026


title: GBM43 cells, ETO-2

value: ETO


title: GBM43 cells, ETO-1


title: 15PPP


title: 13PPP


title: Sample_S18

value: OC


title: GBM43 cells, THZ1-2


title: EG.7-OVA tumor, Cas9/OT-I T cells, perturb-seq (sgRNA library)

city: New Haven

first: jingjing

last: Ren

state: Connecticut

address: 200 S Frontage Rd, #0618: Hunter Building

institute: Yale University

description: 10x Genomics

data_processing:
Initial data processing was performed using the Cell Ranger version 3.0 pipeline (10X Genomics)
Post-processing, including filtering by number of genes expressed per cell, was performed using the Seurat 4.0.
Following clustering and visualization with UMAP, and identification of cell clusters was performed on the final aligned object guided by marker genes.
The sgRNA data was added into corresponding Seurat objects as the metadata and calculated accordingly
Differentially expressed gene (DEG) analysis among different cell groups were based on the non-parametric Wilcoxon rank sum test with logfc.threshold=0.25 and min.pct =0.1. Functional analyses of sgRNA perturbations were evaluated by DEG analysis of sgRNA specific groups.
Assembly: mm10
Supplementary files format and content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix and sgRNA features, "filtered_feature_bc_matrix_crispr.h5" contains gene expression and sgRNA matrix.

source_name: EG.7-OVA tumor

extract_protocol:
Live transferred tumor-infiltrating CD8+ T cells as CD8a+GFP+ T cells were sorted and washed once in cold 1x PBS containing 0.04% BSA prior to resuspending in cold 1x PBS containg 0.04% BSA at 1x10^6 cells/ml concentration.
Cells were then processed by Yale Center for Genome Analysis to generate single-cell RNA library and sgRNA library separately according to the instruction of 10x genomics 3’ V2 single cell RNA sequencing kit with sgRNA feature.

value: CD8a+ T cells

value: EG.7-OVA tumor

tag: strain

tag: Sex

value: female

value: 12 weeks old


title: EG.7-OVA tumor, Cas9/OT-I T cells, perturb-seq (scRNA-seq library)

description: 10x Genomics

tag: age


title: 11PPP

tag: tissue


title: 1W


title: HCT116 cells, LS-24H-2

type: RNA

city: Beijing

first: Haizhao

last: Yi

address: No. 52 Fucheng Rd., Haidian District

institute: Peking University Cancer Hospital & Institute

description: HCT116 cells treated with 0.1μM LS-1-2 was conducted at 24 h

hyb_protocol: The labeled cDNA targets were then hybridized on slides of Affymetrix GeneChip® Human Transcriptome Array 2.0.

scan_protocol: Slides were scanned Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Data were extracted using Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US).

label: biotin

source_name: HCT116 cell treated with LS-1-2

label_protocol: Total RNA was amplified, labeled, and purified by Affymetrix WT PLUS Reagent Kit (Cat#902280, Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin-labeled cDNA.

growth_protocol: Human CRC cell lines HCT116 were 158 purchased from American Type Culture Collection and maintained in Dulbecco’s 159 Modified Eagle medium (Gibco, Carlsbad, CA) with 10% fetal bovine serum, 100 U/mL 160 penicillin sodium, and 100 mg/mL streptomycin sulfate in humidified 5% CO2 at 37 °C.

extract_protocol: Total RNA from six cell samples was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: HCT116 cells treated with 0.1μM LS-1-2 was conducted at 6 h , 12 h, and 24 h after treatment

value: Colon

value: colon cancer cell

tag: time

value: 24H after treatment


title: Sample_S13

value: Sed


title: GBM43 cells, THZ1-1


title: HCT116 cells, LS-24H-3


title: 10PPP

value: restricted


title: HCT116 cells, LS-12H-2

description: HCT116 cells treated with 0.1μM LS-1-2 was conducted at 12h

value: 12H after treatment


title: testis, shControl, LPS, rep2

city: Yangling

first: Mengfei

last: Zhang

state: Shaanxi

address: No.3rd, Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The de-duplicated consensus sequences were used for standard RNA-seq analysis using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences using the DESeq R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: testis

extract_protocol:
Total RNAs were extracted from testes using TRIzol Reagent (Invitrogen, cat. NO 15596026).2 μg total RNAs were used for stranded RNA sequencing library preparation
RNA libraries for RNA-seq were prepared using KC-Digital Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: testis

value: male

value: WT

value: LPS


title: testis, shControl, LPS, rep1


title: GBM43 cells, DMSO-2

value: Gliobalstoma

value: DMSO


title: GBM43 cells, DMSO-1


title: testis, shSpry1, LPS, rep2

value: Spry1 knockdown


title: siSRSF1_rep3

city: Irvine

first: Cholsoon

last: Jang

state: CA

address: 839 Health Science Rd

department: Biological Chemistry

institute: University of California, Irvine

data_processing:
The reads were aligned to the human hg38 genome using STAR (2.7.10b) with following parameters: --outFilterMismatchNmax 2 --outFilterMultimapNmax 10 --outSJfilterOverhangMin 30 888 --outSAMunmapped Within KeepPairs.
Genome coverage files (bigwigs) were generated using bam2wig.py from RSeQC (v5.0.1) with following parameter: "1+-,1-+,2++,2--" -t 1000000000.
Differential gene expression analysis was done by extracting counts using featureCounts (v2.0.3) and running Deseq2 (1.34.0) to find differentially expressed genes with the cutoff of q-value < 0.01 and |(Log2FC)| > 0.5.
Assembly: hg38. Ensembl V107
Supplementary files format and content: Bigwig files generated using bam2wig.py from RSeQC
Supplementary files format and content: featureCounts_raw.txt for all samples

source_name: Kidney

growth_protocol: LAM621-101 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using PureLink™ RNA Mini Kit (Invitrogen). Extracted total RNA was treated with Dnase and purified using Quick-RNA™ Miniprep Plus (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit.

treatment_protocol: LAM621-101 cells were serum starved overnight.

value: Kidney

value: angiomyolipoma patient-derived cell line


title: 7PPP

value: mammary parenchyma

value: ad libitum


title: 8PPP


title: testis, shSpry1, LPS, rep1


title: 9PPP


title: siSRSF1_rep2


title: HCT116 cells, LS-12H-1

value: Colon


title: HCT116 cells, LS-6H-2

description: HCT116 cells treated with 0.1μM LS-1-2 was conducted at 6 h

value: colon cancer cell

value: 6H after treatment


title: HCT116 cells, LS-24H-1

value: 24H after treatment


title: HCT116 cells, LS-12H-3


title: HCT116 cells, LS-6H-3


title: HCT116 cells, C-3

description: HCT116 without treatment

source_name: HCT116 cell

value: control


title: 6PPT


title: testis, shDmrt1

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The de-duplicated consensus sequences were used for standard RNA-seq analysis using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences using the DESeq R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

value: Dmrt1 knockdown

value: 16 weeks


title: HCT116 cells, LS-6H-1

description: HCT116 cells were treated with 0.1μM LS-1-2 was conducted at 6 h


title: HCT116 cells, C-2

description: HCT116 without treatment


title: siSRSF1_rep1


title: testis, shControl

value: testis

value: male


title: M1_DC_3

city: Guangzhou

first: Jia

last: Dan

address: No.58 Zhongshan Road 2

institute: The First Affiliated Hospital, Sun Yat-sen University

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/mm10 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 files include RPKM values for each Sample

source_name: bone marrow-derived dendritic cells

growth_protocol: Bone marrow cells were collected from the tibias and femurs of C57BL/6J mice and cultured with RPMI-1640 medium containing 10% (vol/vol) FBS, 20 ng/ml mGM-CSF (315-03-250, Pepro Tech, USA) and 10 ng/ml mIL-4 (214-14-100, Pepro Tech, USA). Fresh medium supplemented with mGM-CSF and mIL-4 was added on day 3, and half of the culture medium was replaced with fresh medium on day 5. iDCs were harvested on day 7.

extract_protocol:
RNA was harvested using TRIZOL.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: DCs were cocultured with B16-F10 cells, cocultured with B16-F10 cells and treated with M1 virus, or treated with M1 virus, and purified with a EasySepTM mouse CD11c positive selection kit (18780, STEMCELL Technologies, Canada).

value: bone marrow-derived dendritic cells

value: immune cell

value: WT

value: DCs were treated with M1 virus for 24 h


title: 4PPP

value: restricted


title: siFAM120A_rep3

value: Kidney

value: angiomyolipoma patient-derived cell line


title: siFAM120A_rep2


title: 5PPT

value: mammary parenchyma


title: M1_DC_2


title: 2PAR


title: 165449-1L

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
Transcript abundances for each sample were estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown
Assembly: GRCm38
Supplementary files format and content: Excel files containing FPKM values for each gene in each sample
Supplementary files format and content: Excel files containing FPKM values for each transcript in each sample

source_name: Left kidney

extract_protocol:
Total RNA from kidney tissue was isolated using Trizol and quantified using NanoDrop ND-1000
Total RNA was used to prepare sequencing libraries with a KAPA Stranded RNA-Seq Library Prep Kit (Illumina)

value: Left kidney

value: Kdm6afl/Y Pax8Cre+

value: Unilateral ureteral obstruction


title: siFAM120A_rep1


title: 1PAR


title: EOS_10x

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
scRNA-seq
3'-end gene expression
10x genomics

data_processing:
For scRNA-seq data: 10x Genomics Cellranger v6.1.1 was used to process fastq files and generate the bam file and matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.0.
genome build: mm10
processed data files format and content: UMI counts expression matrix files were extracted from cellranger.
processed data files format and content: analyzed single cell dataset as seurat object

source_name: Small Intestine

growth_protocol: primary eosinophils

extract_protocol:
RNA were extracted from cells using AMPure XP beads (Backman)
Full-length Smart-seq2 and 10x genomics scRNA-seq

treatment_protocol: The mice were at the steady state

value: Small Intestine

value: Total eosinophils

value: Wildtype

value: 8-12 weeks

value: pooled male and female


title: M1_DC_1


title: 165448-1L


title: siNTC_rep3

value: siNTC


title: M1_tumorDC_3

value: bone marrow-derived dendritic cells

value: DCs were cocultured with B16-F10 cells for 24 h and treated with M1 virus for another 24 h


title: HCT116 cells, C-1

description: HCT116 without treatment

value: Colon

value: colon cancer cell

value: control


title: 3PP

value: ad libitum


title: siNTC_rep2

value: Kidney

value: angiomyolipoma patient-derived cell line


title: M1_tumorDC_2

value: immune cell

value: WT


title: 163361-2R

value: Left kidney

value: Kdm6afl/Y Pax8Cre+

value: Unilateral ureteral obstruction


title: siNTC_rep1


title: M1_tumorDC_1


title: Study 2, KO HFD Female, Animal 3

city: Winston Salem

first: Alexandria

last: Szalanczy

state: NC

address: 575 Patterson Ave

department: Internal Medicine/Molecular Medicine

institute: Wake Forest University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed sequence reads were mapped to Rnor_6.0 (ENSEMBL) using STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2
Gene hit counts were normalized and differential expression analyzed with DESeq2
Assembly: RN6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited excel file includes TPM values for each Sample

organism: Rattus norvegicus

source_name: Hypothalamus

growth_protocol: Rats were maintained on a HFD from 6 weeks of age to 19 weeks of age, pair-housed

extract_protocol:
Sections of hypothalamus were dissected at -20 C from snap-frozen brain, then total RNA extracted using Qiagen Rneasy Plus Universal mini kit. All samples had a concentration of at least 200 ng/uL
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina according to manufacturer's instructions

value: F

value: Hypothalamus

value: KO

value: HFD

tag: study


title: tumorDC_3

value: bone marrow-derived dendritic cells

value: DCs were cocultured with B16-F10 cells for 48 h


title: 163361-1R


title: Study 2, KO HFD Female, Animal 2


title: Study 2, KO HFD Female, Animal 4


title: tumorDC_2


title: Study 2, KO HFD Female, Animal 1


title: PFA_rep1

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institute of Pathology

country: Germany

institute: University Medical Centre Göttingen

data_processing:
Raw reads were mapped to human genome (build hg38) using STAR.
Mapped reads were quantified using FeatureCounts considering only primary aligned, properly paired reads.
Differential gene expression was computed using DESeq2.
For gene set enrichment, Metascape was run on the significantly changing genes (Padj≤0.05, |log2FC|>0.6)
Assembly: hg38
Supplementary files format and content: Bigwig files of read coverage for each sample.

extract_protocol:
Nascent RNA from ~10 million U2OS cells was isolated according to “factory-seq” protocol.
Following standard strand-specific cDNA library preparation using the TruSeq kit (Illumina), sequencing was performed on a NovaSeq6000 platform (Illumina) to >40 million paired-end reads.

treatment_protocol: U2OS cells in PFA groups were treated or with FA (200μM, 2 hours).

value: with epithelial morphology

value: FA retreatment

tag: fraction

value: nascent RNA


title: 165451-1R

value: Sham Surgey


title: HCT116 short-read RNA-seq

city: Hong Kong

first: Sojung

last: LEE

address: 21 Sassoon Rd, Pok Fu Lam

department: Faculty of Medicine

country: Hong Kong

institute: The Hong Kong University

data_processing:
For RNA-seq, raw reads were mapped to the human genome (hg38) using STAR aligner (version 2.5.3a).
Read counts were computed by lasTEq (Our developed TE quantified tool) based on transposable elements defined in RepeatMasker.
Assembly: hg38
Supplementary files format and content: RNA-Seq expression matrix (txt)

growth_protocol: HCT116 cells were cultured in McCoy’s 5A media supplemented with 10% FBS and seeded into 35 cm dishes.

extract_protocol:
At 80% confluence, RNA was extracted using Qiagen RNeasy Mini kit (74104) following manufacturer’s directions
For short read RNA-seq, samples were sent to Novogene Co., Ltd (Beijing) for library preparation and illumina sequencing. Briefly, mRNA was enriched with oligo(dT) beads and then fragmented randomly. cDNA was synthesised from fragmented mRNA using random hexamers as primers and then subject to second-strand synthesis, end-pair, dA-tailing and ligation of sequencing adapters. Sequencing was performed on an Illumina Novaseq 6000 instrument.

value: Human colorectal carcinoma cell line


title: 165451-1L


title: iDC_1

value: untreated DCs


title: 165450-1L


title: DMSO_rep2

value: control


title: PFA_rep2

value: WT


title: DMSO_rep1


title: 165450-1R

value: Left kidney


title: tumorDC_1

value: immune cell


title: Hypo48hr-3

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

institute: Altis Biosystems

data_processing:
Transcript quantification and pseudoalignment: Gene level expression was obtained through pseudo alignment of reads to human genome GRCh38 using Kallisto
Normalization: Expression values for plotting were obtained by TMM normalization across all samples using EdgeR package and differential expression between normoxic and hypoxic samples at each time point was calculated from raw counts with DESeq2
Assembly: GRCh38
Supplementary files format and content: csv - TMM normalized gene expression values per sample
Supplementary files format and content: h5ad - annotated matrix with read counts per gene x sample

source_name: 48 hours Hypoxia

growth_protocol: Crypts or dissociated monolayers were placed on the top of 1.0 mg/mL collagen hydrogels (1 ml into each well of 6-well plate (T1006; Denville, Holliston, MA)) at a density of 5,000 crypts/ well and overlaid with 4 ml of Expansion Media (EM) containing 10 mmol/L Y-27632 (S1049; SelleckChem). EM contains a mixture of advanced Dulbecco’s modified Eagle medium/F12 medium (12634010; ThermoFisher) and Wnt-3A, R-spondin 3, noggin (WRN) conditioned medium (WRN medium prepared in lab from L-WRN cells (CRL- 3276; ATCC) following a published protocol98 at a volumetric ratio of 1:1, and supplemented with GlutaMAX (35050061; ThermoFisher), B27 supplement without vitamin A (12587010; ThermoFisher), 10 mM HEPES (15630-080; ThermoFisher), 1.25 mM N-acetyl cysteine (194603; MP Bio, Santa Ana, CA), 10 mM nicotinamide (N0636; Sigma-Aldrich), 50 ng/mL epidermal growth factor (315-09; Peprotech), 2.0 nM gastrin (AS-64149; Anaspec), 10 nM prostaglandin E2 (14010; Cayman Chemicals), 3.0 µM SB202190 (S1077; Selleckchem), 100 U/mL penicillin-streptomycin (15140122; ThermoFisher), and 50 mg/mL primocin (ant-pm-1; InvivoGen, San Diego, CA). EM was used to expand the epithelial cell numbers as monolayers or organoids. Y-27632 was present only in the first 48 hours of cell culture and was not added to subsequent media changes. The medium was changed every 48 hours. When the cell coverage was greater than 80% (typically 5 to 7 days), the epithelium was dissociated to fragments to seed onto the intestinal MPS or passaged for further expansion.

extract_protocol:
To investigate the dynamic response of hISC to hypoxia at the whole transcriptomic level, we performed RNA-seq on human intestinal epithelium exposed to 6 hours, 24 hours, or 48 hours of hypoxia inside intestinal MPS, along with normoxic control intestinal MPS which were cultured for each respective time point with no hypoxia exposure. RNA samples were collected from each intestinal MPS, and Total RNA was extracted using RNAqueous-Micro Total RNA Isolation Kit (AM1931; ThermoFisher) according to manufacturer’s protocols and stored at −80°C.
Three technical replicates were collected from each duration of normoxia or hypoxia. RNA was extracted via the RNAqueous-Micro Total RNA Isolation Kit (AM1931; ThermoFisher, Waltham, MA) according to the manufacturer’s protocol. To assess RNA quality prior to submission for sequencing, an RNA integrity number (RIN) was measured using the Agilent 2100 Bioanalyzer. After confirmation that each sample had a RIN of at least 8, integrated fluidic circuits (IFCs) for gene expression and genotyping analysis were prepared using the Advanta™ RNA-Seq NGS Library Prep Kit for the Standard Biotools Juno™. Bulk sequencing was run on a NovaSeq 6000 instrument using one lane of an S4 v1.5 flow cell (Illumina).

value: Healthy human jejunal epithelium

value: 48 hours of hypoxic culture


title: Study 2, WT HFD Female, Animal 1

value: F

value: Hypothalamus


title: Study 2, WT HFD Female, Animal 2

value: HFD


title: Study 2, WT HFD Female, Animal 4


title: Study 2, WT HFD Female, Animal 3


title: iDC_2

value: bone marrow-derived dendritic cells


title: iDC_3


title: 163363-1L

value: Kdm6afl/Y Pax8Cre+


title: 165453-B

value: Unilateral ureteral obstruction


title: P15_OL_Mogpos_invivo

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
The standalone version of sRNAbench version 05/2014 (https://bioinfo2.ugr.es/srnatoolbox/standalone/) was used to align reads to miRBase 20 miRNAs and the mm9 genome
The multi-mapping read alignment strategy was used. Expression of mature sense miRNAs was assessed, and levels were RPM normalized using the reads that mapped to the library as the baseline
Genome_build: mm9
Supplementary_files_format_and_content: GEO sRNA RPM and DE.xlsx

source_name: oligodendrocytes (OLs) in vivo MOG positive

growth_protocol: Data were generated using OPCs generated from epiblast stem cell (EpiSC) lines EpiSC5 and 129O1, which were derived from mouse strain 129SvEv and 129S1/SvImJ as described previously except SHH was not used for the maintenance nor differentiation of OPCs (Najm et al., 2011). All OPC and immature oligodendrocyte cultures were maintained on plates or glass coverslips coated with 100 µg/mL poly(L-ornithine), followed by 10 µg/ml laminin. OPC growth media consisted of DMEM/F12 supplemented with N2 Max, B27, 20ng/mL bFGF, and 20ng/mL PDGFA and was changed every 48 hours. After 4 passages, these EpiSC derived OPCs were purified by fluorescence activated cell sorting using conjugated CD140a and NG2-AF488 antibodies. Sorted OPCs were then expanded and purity was verified by staining for markers of OPCs, astrocytes, and oligodendrocytes and frozen down in aliquots.

extract_protocol:
Samples were lysed and RNA isolated using the miRNeasy kit according to manufacturers instructions
Samples were prepped according to manufacturer instructions for the Illumina TruSeq small RNA kit

value: oligodendrocyte lineage

tag: timepoint

value: postnatal day 15

tag: molecule subtype

value: small RNA


title: P15_OPC_invivo

source_name: oligodendrocyte progenitor cells (OPCs) in vivo from Barres lab

tag: cell type


title: 163361-1L

tag: treatment


title: 165453-1L


title: P7_OPC

source_name: oligodendrocyte progenitor cells (OPCs) in vivo from Barres lab expanded

value: postnatal day 7


title: P15_OL_GalCpos_invivo

source_name: oligodendrocytes (OLs) in vivo from Barres lab GalC positive MOG negative


title: Study 1, KO HFD Female, Animal 2

value: KO


title: 163358-2L


title: 163358-2R


title: Hypo48hr-2


title: Hypo48hr-1


title: Hypo24hr-3-1

source_name: 24 hours Hypoxia

value: 24 hours of hypoxic culture


title: 163358-1L


title: Study 1, KO HFD Female, Animal 3


title: Study 1, WT HFD Female, Animal 4

value: WT


title: Hypo24hr-2


title: 165454-B

value: Left kidney

value: Sham Surgey


title: 165454-1R


title: Study 1, WT HFD Female, Animal 3


title: Study 1, WT HFD Female, Animal 2


title: EpiSC9_OPC

source_name: oligodendrocyte progenitor cells (OPCs)

value: in vitro


title: Hypo6hr-3

source_name: 6 hours Hypoxia

value: Healthy human jejunal epithelium

value: 6 hours of hypoxic culture


title: 163360-B


title: Study 1, KO HFD Female, Animal 4

value: F

value: Hypothalamus


title: P7_OPC_invivo


title: Hypo24hr-3-2


title: EpiSC9_OL

source_name: oligodendrocytes (OLs)


title: Hypo6hr-2


title: Study 1, WT HFD Female, Animal 1

value: HFD


title: 163360-1R


title: Study 1, KO HFD Female, Animal 1


title: CKD RASi/SGLT2i/MRA 3

city: München

first: ZHIHUI

last: ZHU

address: Geiselgasteigstr. 62, 2.0G

institute: LMU Klinikum

data_processing:
After QC, Fastq was mapped to the mm39 by hisat2. DESeq2 for downstream analyze.
Assembly: mm39
Supplementary files format and content: count, rpkm matrix

source_name: kidney

extract_protocol:
Total RNA was isolated using an RNA extraction kit (Life Technologies, Darmstadt, Germany) according to the manufacturer´s instructions, and RNA quality was assessed using agarose gels. RNA-seq of total RNA samples was conducted on the Illumina DNBSEQ-G400 platform, producing 100bp paired-end reads.
Strand-specific transcriptome library construction is completed by enriching mRNA from total RNA, sequenced by DNBSEQ high-throughput platform, and followed by bioinformatics analysis.

treatment_protocol: Col4a3-/- mice were treated with food admix of either vehicle, 10 mg/kg ramipril, 10 mg/kg ramipril plus 30 mg/kg empagliflozin, and 10 mg/kg ramipril plus 30 mg/kg empagliflozin plus 10 mg/kg finerenone. The different types of food preparations were marked by different food colors starting from 6 weeks of age for 8 weeks.

value: kidney

value: primary cell

value: Ramipril/Empagliflozin/Finerenone


title: EpiSC9_R12_D39

source_name: EpiSC9 Epiblast stem cell

value: EpiSC9 Epiblast stem cell


title: 12901_OPC

value: oligodendrocyte lineage

value: small RNA


title: 12901_OL


title: Norm48hr-3

source_name: 48 hours Normoixa

value: 48 hours of normoxic culture


title: Hypo24hr-1

value: 24 hours of hypoxic culture


title: CKD RASi/SGLT2i/MRA 2