title: Liver_Fibrosis.C10

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

data_processing:
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
The high quality reads were aligned to the reference genome/transcriptome with Tophat package.The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The feference GTF annotation file was downloaded from NCBI, Ensembl or NCBI database. CIRCExplorer was used to denovo assemble the mapped reads to circular RNAs at first; The second ,these assembled circular RNAs from all samples were generate unique circular RNAs. Circular RNA expressions from different samples or groups were caculated by scripts in house. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes. was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: count and FPKM

source_name: Liver Fibrosis

growth_protocol: six human liver fibrotic tissues were obtained from patients undergoing surgery.

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs.The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp).

tag: disease state

value: fibrosis


title: Liver_Fibrosis.C3

status: Public on Dec 22 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: Liver


title: Liver_Fibrosis.C9


title: MGHc_CIN009

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

label: biotin

source_name: liver biopsy

extract_protocol: RNA was isolated using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

value: liver

tag: diagnosis

value: chronic hepatitis C

tag: future fibrosis progression (2 or more f stages within 5 years)

value: No


title: Liver_Fibrosis.C11


title: Liver_Fibrosis.C12


title: MGHc_CIN004

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: RNA-Seq N2_Naive_WT_P14_S14

city: Boston

first: Jim

last: Kaminski

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
All RNA-seq reads were trimmed using Trimmomatic (60) to remove primer and low-quality bases.
Reads were then passed to FastQC (61) to check the quality of the trimmed reads.
The single-end reads were then aligned to the Mus_musculus.GRCm38.82 transcriptome from Ensembl using RSEM (62) with the parameters “--num-threads 4 --bowtie2 --sampling-for-bam --output-genome-bam --sort-bam-by-coordinate --sort-bam-memory-per-thread 1G --estimate-rspd --fragment-length-mean 200 --fragment-length-sd 80’.
Normalized counts obtained using DESeq2, applied to each of the three datasets separately.
Genome_build: Mus_musculus.GRCm38.82 transcriptome
Supplementary_files_format_and_content: Tab-delimited files of normalized counts for each replicate

organism: Mus musculus

source_name: P14 CD8+ T cells

growth_protocol: In vitro P14 CD8+ T cells: naïve CD8+ T cells were isolated with Miltenyi kit (Cat#130-096-543), stimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI (supplemented with HEPES, NEAA, sodium pyruvate, 2-Mercaptoethanol, 10% FBS) in the presenece of 100 U/ml IL-2. In vivo P14 CD8+ T cells were sorted directly from LCMV infected mice. NIH/3T3 fibroblast: cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were lysed and RNA was extracted with Qiagen RNeasy Plus Kits (Qiagen Cat#74034) according to manufacturer's protocol.
mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and the RNA-seq libraries were generated with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760) according to manufacturer’s instructions.

treatment_protocol: In vitro P14 CD8+ T cells: on day 6, cells were left untreated or activated with 50 ng/ml PMA and 1 uM ionomycin for 3 hours before harvest for RNA-seq. In vivo P14 CD8+ T cells: no treatment. NIH/3T3 fibroblast: cells were transduced with doxycycline-inducible TF-expressing lentivirus. Fibroblasts were left untreated or treated with 4 ug/ml doxycline for 72 hours for TFs induction before harvest for RNA-seq.

tag: sample group

tag: timepoint

value: Day 0

tag: condition

value: in vivo WT Naive T Cells


title: HUc028

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: non-alcoholic fatty liver disease (NAFLD)

value: liver biopsy


title: HUc032


title: HUc031


title: RNA-Seq F1_WT_P14_S6

value: Day 3.5

value: in vivo WT


title: RNA-Seq N1_Naive_WT_P14_S7


title: HUc030


title: HUc029


title: HUc025


title: HUc027


title: Liver_Fibrosis.C13


title: HUc024


title: HUc023


title: RNA-Seq D2_Irf4_cKO_P14_S11

value: in vivo Irf4 f/f with Cre = Irf4 cKO


title: RNA-Seq C2_WT_Irf4_floxed_Cre_P14_S10

value: in vivo Irf4 f/f without Cre


title: HUc021


title: HUc022


title: HUc033


title: RNA-Seq F2_WT_P14_S13


title: RNA-Seq B2_WT_Batf_floxed_Cre_P14_S9

value: in vivo Batf f/f without Cre


title: RNA-Seq C1_WT_Irf4_floxed_Cre_P14_S3


title: HUc020


title: RNA-Seq E2_WT_iCre_P14_S12

value: in vivo WT, with Cre


title: HUc019


title: RNA-Seq B1_WT_Batf_floxed_Cre_P14_S2


title: HUc018


title: RNA-Seq E1_WT_iCre_P14_S5


title: HUc016

value: Yes


title: RNA-Seq A2_Batf_cKO_P14_S8

value: in vivo Batf f/f with Cre = Batf cKO


title: RNA-Seq Day6_Act_3_S24

value: Day 6

value: in vitro WT, 6 days post antiCD3/28 stimulation + PMA/ionomycin restimulation


title: RNA-Seq A1_Batf_cKO_P14_S1


title: RNA-Seq Day6_Act_2_S23


title: HUc014


title: RNA-Seq Day6_Act_1_S22


title: RNA-Seq Day6_3_S21

value: in vitro WT, 6 days post antiCD3/28 stimulation


title: RNA-Seq Day6_2_S20


title: HUc012


title: HUc011


title: RNA-Seq Day6_1_S19


title: HUc013


title: HUc010


title: RNA-Seq Day5_3_S18

value: Day 5

value: in vitro WT, 5 days post antiCD3/28 stimulation


title: HUc009

value: No


title: HUc008


title: HUc007


title: RNA-Seq Day5_2_S17


title: HUc006


title: RNA-Seq Day4_2_S14

value: Day 4

value: in vitro WT, 4 days post antiCD3/28 stimulation


title: RNA-Seq Day3_2_S11

value: Day 3

value: in vitro WT, 3 days post antiCD3/28 stimulation


title: HUc015

value: non-alcoholic fatty liver disease (NAFLD)

value: liver biopsy


title: HUc002


title: RNA-Seq Day3_3_S12


title: HUc004


title: RNA-Seq Day3_1_S10


title: RNA-Seq Day2_2_S8

value: Day 2

value: in vitro WT, 2 days post antiCD3/28 stimulation


title: RNA-Seq Day5_1_S16


title: HUc005


title: RNA-Seq Day4_1_S13


title: HUc001


title: AW231_STM165

tag: fibrosis stage

tag: pls risk prediction

value: Low


title: RNA-Seq Day2_1_S7


title: AW232_STM339

value: Intermediate


title: AW230_STM492


title: RNA-Seq Day1_2_S5

value: Day 1

value: in vitro WT, 24 hours post antiCD3/28 stimulation


title: RNA-Seq Day4_3_S15


title: AW343_WCA090


title: AW342_WCA220


title: RNA-Seq Day0_3_S3

value: Day 0

value: in vitro WT, no stimulation


title: AW344_WCA151

value: High


title: HUc003


title: RNA-Seq Day0_2_S2


title: AW341_WCA107


title: RNA-Seq Day0_1_S1


title: AW340_WCA261


title: RNA-Seq Day1_1_S4


title: RNA-Seq NoDox_Irf4_Tbet_rep1_S13

source_name: NIH/3T3 Fibroblasts

value: Yes


title: RNA-Seq Day1_3_S6


title: AW339_WCA184


title: AW229_STM430


title: AW337_WCA036


title: RNA-Seq NoDox_Irf4_Runx3_rep2_S10

value: No


title: RNA-Seq NoDox_Irf4_Runx3_Tbet_rep2_S18


title: AW335_WCA322


title: AW228_STM405


title: AW338_WCA143


title: RNA-Seq NoDox_Batf_Tbet_rep2_S2


title: RNA-Seq NoDox_Irf4_Runx3_rep1_S9


title: RNA-Seq NoDox_Batf_Tbet_rep1_S1


title: AW227_STM183


title: RNA-Seq NoDox_Batf_Runx3_rep1_S5


title: RNA-Seq NoDox_Irf4_Runx3_Tbet_rep1_S17


title: AW331_WCA164


title: AW333_WCA211


title: RNA-Seq Dox72h_Irf4_Tbet_rep2_S16


title: RNA-Seq NoDox_Batf_Runx3_rep2_S6


title: AW332_WCA039


title: RNA-Seq Dox72h_Irf4_Tbet_rep1_S15


title: RNA-Seq Dox72h_Irf4_Runx3_Tbet_rep2_S20


title: RNA-Seq Dox72h_Irf4_Runx3_Tbet_rep1_S19


title: AW336_WCA236


title: RNA-Seq Dox72h_Irf4_Runx3_rep2_S12


title: AW328_WCA019


title: RNA-Seq Dox72h_Irf4_Runx3_rep1_S11


title: AW327_WCA006


title: AW326_WCA246


title: AW325_WCA260


title: AW324_WCA172


title: RNA-Seq Dox72h_Batf_Tbet_rep2_S4


title: AW323_WCA177


title: RNA-Seq D1_Irf4_cKO_P14_S4

value: Day 3.5

value: in vivo Irf4 f/f with Cre = Irf4 cKO


title: RNA-Seq Dox72h_Batf_Tbet_rep1_S3


title: AW322_WCA153


title: AW334_WCA099


title: AW321_KCN490


title: RNA-Seq Dox72h_Batf_Runx3_rep1_S7


title: AW330_WCA043


title: AW320_WCA152


title: RNA-Seq NoDox_Irf4_Tbet_rep2_S14


title: RNA-Seq NoDox_Runx3_Tbet_rep2_S10


title: AW319_WCA312


title: RNA-Seq NoDox_Runx3_rep2_S2


title: AW318_WCA087


title: AW317_WCA276


title: AW316_WCA207


title: AW315_WCA188


title: AW314_WCA251


title: RNA-Seq NoDox_Batf_Runx3_Tbet_rep2_S18


title: RNA-Seq Dox72h_Batf_Runx3_rep2_S8


title: RNA-Seq NoDox_Batf_Runx3_Tbet_rep1_S17


title: AW311_WCA197


title: AW310_WCA182


title: RNA-Seq NoDox_Batf_Irf4_Runx3_rep2_S14


title: AW309_WCA125


title: RNA-Seq Dox72h_Tbet_rep2_S8


title: AW312_WCA133


title: RNA-Seq NoDox_Batf_Irf4_Runx3_rep1_S13


title: RNA-Seq NoDox_Tbet_rep2_S6


title: RNA-Seq NoDox_Runx3_rep1_S1


title: AW308_WCA254


title: RNA-Seq NoDox_Tbet_rep1_S5


title: RNA-Seq Dox72h_Tbet_rep1_S7


title: AW307_STM271


title: RNA-Seq Dox72h_Runx3_Tbet_rep2_S12


title: RNA-Seq NoDox_Runx3_Tbet_rep1_S9


title: AW306_STM308


title: RNA-Seq Dox72h_Runx3_Tbet_rep1_S11


title: AW305_STM318


title: RNA-Seq Dox72h_Runx3_rep2_S4


title: AW304_STM253


title: AW303_STM263


title: RNA-Seq Dox72h_Batf_Runx3_Tbet_rep2_S20


title: RNA-Seq Dox72h_Batf_Irf4_Runx3_rep2_S16


title: RNA-Seq Dox72h_Batf_Irf4_Runx3_rep1_S15


title: AW302_STM244


title: RNA-Seq Dox72h_Batf_Runx3_Tbet_rep1_S19


title: RNA-Seq NoDox_Batf_Irf4_Tbet_2_S24


title: RNA-Seq NoDox_Irf4_2_S10


title: RNA-Seq NoDox_Batf_Irf4_Tbet_1_S17


title: RNA-Seq NoDox_Batf_Irf4_Runx3_Tbet_2_S22


title: RNA-Seq NoDox_Irf4_1_S9


title: 5_ControlDiet_Vehicle_rep1

city: Atlanta

first: Ken

last: Liu

state: GA

address: 615 Michael Street, Suite 225

institute: Emory University

description: p20209-s005_Liver_PBS_CD_5-trans_S5_L001_R1_001

data_processing:
BioJupies Cloud-based RNAsequencing pipeline
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Liver

extract_protocol:
Livers were removed from mice, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Liver

tag: age

value: post natal day 64

tag: background

value: Germ-Free

tag: diet

value: Control

tag: treatment

value: Vehicle


title: 5_ControlDiet_Vehicle_rep2

description: p20209-s005_Liver_PBS_CD_5-trans_S5_L002_R1_001


title: 4_ControlDiet_Vehicle_rep1

description: p20209-s004_Liver_PBS_CD_4-trans_S4_L001_R1_001


title: 3_ControlDiet_Vehicle_rep2

description: p20209-s003_Liver_PBS_CD_3-trans_S3_L002_R1_001


title: RNA-Seq NoDox_Batf_Irf4_2_S22


title: AW299_STM310


title: AW297_STM254


title: AW298_STM301


title: RNA-Seq NoDox_Batf_Irf4_Runx3_Tbet_1_S21


title: 3_ControlDiet_Vehicle_rep1

description: p20209-s003_Liver_PBS_CD_3-trans_S3_L001_R1_001


title: AW296_STM319


title: 2_ControlDiet_Vehicle_rep2

description: p20209-s002_Liver_PBS_CD_2-trans_S2_L002_R1_001


title: RNA-Seq NoDox_Batf_Irf4_1_S21


title: RNA-Seq NoDox_Batf_2_S6


title: AW295_STM274


title: RNA-Seq NoDox_Batf_1_S5


title: AW300_STM291


title: RNA-Seq NoDox_3T3_2_S2


title: 4_ControlDiet_Vehicle_rep2

description: p20209-s004_Liver_PBS_CD_4-trans_S4_L002_R1_001


title: 2_ControlDiet_Vehicle_rep1

description: p20209-s002_Liver_PBS_CD_2-trans_S2_L001_R1_001


title: AW294_STM248


title: RNA-Seq NoDox_3T3_1_S1


title: RNA-Seq Dox72h_Irf4_2_S12


title: RNA-Seq Dox72h_Runx3_rep1_S3


title: 1_ControlDiet_Vehicle_rep2

description: p20209-s001_Liver_PBS_CD_1-trans_S1_L002_R1_001


title: RNA-Seq Dox72h_Irf4_1_S11


title: RNA-Seq Dox72h_Batf_Irf4_Tbet_2_S20


title: RNA-Seq Dox72h_Batf_Irf4_Tbet_1_S19


title: 1_ControlDiet_Vehicle_rep1

description: p20209-s001_Liver_PBS_CD_1-trans_S1_L001_R1_001


title: RNA-Seq Dox72h_Batf_Irf4_Runx3_Tbet_1_S23


title: 5_WesternDiet_VB_rep2

description: p20209-s020_Liv-T_VB5-WD_S20_L002_R1_001

value: Western Diet

value: VB


title: AW292_STM247

value: Intermediate


title: AW293_STM249


title: RNA-Seq Dox72h_Batf_Irf4_2_S23


title: RNA-Seq Dox72h_Batf_Irf4_1_S15


title: AW291_STM322


title: RNA-Seq Dox72h_Batf_Irf4_Runx3_Tbet_2_S24


title: 5_WesternDiet_VB_rep1

description: p20209-s020_Liv-T_VB5-WD_S20_L001_R1_001


title: RNA-Seq Dox72h_Batf_1_S7


title: AW289_STM303

value: Low


title: RNA-Seq Dox72h_Batf_2_S8


title: RNA-Seq Dox72h_3T3_2_S4


title: 4_WesternDiet_VB_rep1

description: p20209-s019_Liv-T_VB4-WD_S19_L001_R1_001


title: AW288_STM261


title: 3_WesternDiet_VB_rep2

description: p20209-s018_Liv-T_VB3-WD_S18_L002_R1_001


title: RNA-Seq Dox72h_3T3_1_S3


title: 3_WesternDiet_VB_rep1

description: p20209-s018_Liv-T_VB3-WD_S18_L001_R1_001


title: HiChIP_3T3_Batf_Irf4

description: HiChIP with BATF antibody on NIH/3T3 fibroblasts, ectopically expressing Batf

library_source: genomic

data_processing:
Data were aligned with  HiC-Pro_2.10.0
Loops were called using HiChipper v0.7.1, which uses Mango to calculate FDR for loops
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file of mango output with the following columns:  Anchor1_chr,Anchor1_start,Anchor1_End,Anchor2_chr,Anchor2_start,Anchor2_End,Count_Of_Paired_End_Tags,Mango_FDR

molecule: genomic DNA

growth_protocol: P14 CD8+ T cells: naïve CD8+ T cells were isolated with Miltenyi kit (Cat#130-096-543), stimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI (supplemented with HEPES, NEAA, sodium pyruvate, 2-Mercaptoethanol, 10% FBS) in the presenece of 100 U/ml IL-2. NIH/3T3 fibroblast: cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde and lysed according to the published HiChIP protocol (Mumbach et al., Nature Methods 2016). Briefly, nuclei were isolated, digested with MboI restriction enzyme, filled-in with biotin-dATP, lysed with sonication, immunoprecipitated with indicated antibody and then the biotin labeled DNA was pulled-down with streptavdin beads.
Libraries were constructed based on the published HiChIP protocol (Mumbach et al., Nature Methods 2016). Briefly, the pulled-down DNA was fragmented with Tn5 transposase, PCR amplified and barcoded with Illumina dual indexes. The amplified DNA fragments were size-selected (300-700 bp) wih AMPureXP beads.
HiChIP

treatment_protocol: P14 CD8+ T cells: on day 6, cells were activated with 50 ng/ml PMA and 1 uM ionomycin for 3 hours before harvest for HiChIP experiment. NIH/3T3 fibroblast: cells were transduced with doxycycline-inducible TF-expressing lentivirus. Fibroblasts were treated with 4 ug/ml doxycline for 72 hours for TFs induction before harvest for HiChIP experimenet.

tag: hichip antibody

value: BATF


title: HiChIP_3T3_CTCF

description: HiChIP with CTCF  antibody on NIH/3T3 fibroblasts

value: CTCF


title: HiChIP_3T3_Batf


title: AW286_STM324


title: AW287_STM270


title: 2_WesternDiet_VB_rep2

description: p20209-s017_Liv-T_VB2-WD_S17_L002_R1_001


title: AW285_STM198


title: AW290_STM313


title: ChIP-Seq April2017_Day6BATFKO_Input

data_processing:
All ChIP-seq reads were trimmed using Trimmomatic to remove primer and low-quality bases.
These single-end reads were then aligned to the mm10 reference genome using bowtie2, allowing maximum insert size of 2000 bp, with the “--no-mixed” and “--no-discordant” parameters added.
Reads with a mapping quality (MAPQ) below 30 were removed.
Duplicates were removed with Picard Tools, and the reads mapping to the blacklist regions and mitochondrial DNA were also removed.
Each combination of transcription factor and condition had two replicates, with the exception of Runx3 in WT, which we limited to one high-quality replicate. ChIP-seq peaks were called in each replicate, versus a control sample (listed as "Corresponding Input Sample for Peak Calling" in this dataset) , using MACS2 with a q-value cutoff of 0.05. Overlapping peaks among replicates were merged. A region was considered a valid peak for a transcription factor if it had a q-value below 0.05 in at least two replicates, and a q-value below 0.001 in at least one of the replicates.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files of peaks identified with macs2, merged across replicates. Peaks considered valid if below qvalue of 0.05 in both replicates and below 0.001 in at least one replicate.

growth_protocol: Naïve P14 CD8+ T cells were isolated with Miltenyi kit (Cat#130-096-543), stimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI (supplemented with HEPES, NEAA, sodium pyruvate, 2-Mercaptoethanol, 10% FBS) in the presenece of 100 U/ml IL-2.

extract_protocol:
Briefly, cells were fixed with 1% formaldehyde and genomic DNA was fragmented by Covaris sonicator (E220). The fragmented DNA was then subjected to immunoprecipitation with transcription factor-specific antibodies.
Briefly, the NEBNext ChIP-seq Library Prep Kit (NEB #E6240L) was used to end-repair and adding adaptor to the immunoprecipitated DNA fragments according to the manufacurer's protocol. NEBNext Multiplex Oligos for Illumina Index Primers Sets were then used to PCR amplify and barcode the libraries.

treatment_protocol: On day 6, cells were left untreated or activated with 50 ng/ml PMA and 1 uM ionomycin for 3 hours before harvest for ChIP-seq.

tag: replicate group

tag: tf

tag: corresponding input sample for peak calling


title: ChIP-Seq BatfKO_input_S18


title: ChIP-Seq BATFKO_InputForEts1_Day6


title: 4_WesternDiet_VB_rep2

description: p20209-s019_Liv-T_VB4-WD_S19_L002_R1_001

tag: tissue


title: ChIP-Seq BATFKO_Input_June2017


title: AW284_STM251


title: HiChIP_TCell_Ctcf

description: HiChIP with CTCF antibody on P14 CD8+ T Cells

source_name: P14 CD8+ T Cells


title: AW283_STM285


title: 2_WesternDiet_VB_rep1

description: p20209-s017_Liv-T_VB2-WD_S17_L001_R1_001


title: ChIP-Seq BATFKO_Input_Day6


title: ChIP-Seq BATFKO_Tbet_5ug_Day6

value: Tbet


title: AW282_STM268


title: RNA-Seq Day2_3_S9

value: Day 2

value: in vitro WT, 2 days post antiCD3/28 stimulation


title: HiChIP_3T3_Batf_Irf4_Runx3_Tbet

description: HiChIP with BATF antibody on NIH/3T3 fibroblasts, ectopically expressing Batf, Irf4, Runx3, and T-bet


title: AW281_STM216


title: HiChIP_TCell_Batf

description: HiChIP with BATF antibody on P14 CD8+ T Cells


title: 5_WesternDietDiet_Vehicle_rep2


title: ChIP-Seq BatfKO_Stat5_10ug_S17


title: 5_WesternDietDiet_Vehicle_rep1


title: ChIP-Seq BatfKO_Stat5_2ug_S16


title: 1_WesternDiet_VB_rep2

description: p20209-s016_Liv-T_VB1-WD_S16_L002_R1_001


title: ChIP-Seq BATFKO_Day6_Stat3_5ug


title: 4_WesternDietDiet_Vehicle_rep2


title: AW280_STM250


title: ChIP-Seq BATFKO_Day6_Stat3_10ug


title: ChIP-Seq BATFKO_Day6_Runx3_05ug


title: ChIP-Seq BATFKO_Day6_Jund_05ug

value: JunD


title: AW279_STM284


title: 1_WesternDiet_VB_rep1

description: p20209-s016_Liv-T_VB1-WD_S16_L001_R1_001


title: 3_WesternDietDiet_Vehicle_rep2


title: ChIP-Seq BATFKO_Day6_IRF4_10ug


title: ChIP-Seq BATFKO_Day6_Jund_10ug


title: AW277_STM480


title: ChIP-Seq BATFKO_Day6_Fosl2_10ug


title: ChIP-Seq BATFKO_Day6_IRF4_5ug


title: ChIP-Seq BATFKO_Day6_Fosl2_5ug


title: 3_WesternDietDiet_Vehicle_rep1


title: ChIP-Seq BATFKO_Tbet_10ug_Day6


title: AW275_STM416


title: AW278_WCA057


title: 2_WesternDietDiet_Vehicle_rep2


title: ChIP-Seq BATFKO_Ets1_10ug_Day6


title: AW274_STM446


title: 2_WesternDietDiet_Vehicle_rep1


title: ChIP-Seq BATFKO_Day6_Runx3_02ug


title: AW273_STM443


title: ChIP-Seq BATFKO_Ets1_5ug_Day6


title: 4_WesternDietDiet_Vehicle_rep1


title: ChIP-Seq BATFKO_Eomes_2ug_Day6

value: Eomes


title: 1_WesternDietDiet_Vehicle_rep2


title: AW272_STM410


title: ChIP-Seq BATFKO_Eomes_5ug_Day6


title: ChIP-Seq WT_Input_June2017

value: WT


title: 1_WesternDietDiet_Vehicle_rep1

value: Liver


title: ChIP-Seq April2017_Day6WT_Input


title: ChIP-Seq WT_input_S15


title: ChIP-Seq WT_InputForEts1_Day6_Set2


title: AW271_STM431


title: 5_ControlDiet_VB_rep2

description: p20209-s010_Liver_VB_CD_10-trans_S10_L002_R1_001

value: post natal day 64


title: 5_ControlDiet_VB_rep1

description: p20209-s010_Liver_VB_CD_10-trans_S10_L001_R1_001

value: Germ-Free


title: AW270_STM414


title: ChIP-Seq WT_Tbet_5ug_s8


title: ChIP-Seq WT_Stat5_10ug


title: ChIP-Seq WT_Stat5_2ug


title: 4_ControlDiet_VB_rep2

description: p20209-s009_Liver_VB_CD_9-trans_S9_L002_R1_001

value: Control


title: ChIP-Seq WT_Day6_Stat3_10ug


title: 4_ControlDiet_VB_rep1

description: p20209-s009_Liver_VB_CD_9-trans_S9_L001_R1_001


title: ChIP-Seq WT_Tbet_10ug_s8


title: ChIP-Seq WT_Runx3_2ul_s8


title: 3_ControlDiet_VB_rep2

description: p20209-s008_Liver_VB_CD_8-trans_S8_L002_R1_001


title: AW268_STM420


title: AW267_STM429


title: ChIP-Seq WT_Day6_Jund_05ug


title: AW266_STM459


title: ChIP-Seq WT_Day6_Stat3_5ug


title: 3_ControlDiet_VB_rep1

description: p20209-s008_Liver_VB_CD_8-trans_S8_L001_R1_001


title: ChIP-Seq WT_Day6_Jund_10ug


title: AW265_STM327


title: ChIP-Seq WT_Input_s8


title: ChIP-Seq WT_Day6_IRF4_5ug


title: ChIP-Seq WT_Day6_IRF4_10ug


title: AW264_STM427


title: 2_ControlDiet_VB_rep2

description: p20209-s007_Liver_VB_CD_7-trans_S7_L002_R1_001


title: ChIP-Seq WT_Day6_Fosl2_10ug


title: ChIP-Seq WT_Ets1_5ug_Day6_Set2


title: AW263_STM460


title: ChIP-Seq WT_Day6_Fosl2_5ug


title: ChIP-Seq WT_Ets1_10ug_Day6_Set2


title: ChIP-Seq WT_Eomes_5ug_s8


title: 1_ControlDiet_VB_rep2

description: p20209-s006_Liver_VB_CD_6-trans_S6_L002_R1_001


title: AW262_STM193


title: 1_ControlDiet_VB_rep1

description: p20209-s006_Liver_VB_CD_6-trans_S6_L001_R1_001


title: CD14+_ bottom 10% HLA-DRneg/low(Mo-MDSC)_healthy patient 2 [Sample 6]

city: Cleveland

first: david

middle: C

last: Soler

state: OH

address: 2109 Adelbert rd BRB Bldg 547B

department: Neuro-Surgery

institute: Case Western Reserve University

description: mRNA

hyb_protocol: Following fragmentation and labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Clariom™ S Assay for rat Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were converted into spreadsheets of observation data using the RMA normalization feature in Affymetrix's Expression Console.

source_name: purified CD14 cells from peripheral blood

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Plus protocol from 150 ng total RNA (GeneChip WT PLUS Reagent Kit, Affymetrix).

extract_protocol: Qiagen RNAeasy micro kit (74004) was used to extract the RNA from FACS-purified cells

value: blood

tag: cell type

value: CD14+ HLA-DR-neg/low (bottom 10%)

tag: disease state

value: healthy


title: ChIP-Seq WT_Eomes_2ug_s8


title: AW260_STM374

value: Intermediate


title: AW261_STM160

value: Low


title: ATAC-Seq A1_Batf_cKO_P14

data_processing:
ATAC-seq reads were trimmed using Trimmomatic to remove primer and low-quality bases.
The paired-end reads were then aligned to the mm10 reference genome using bowtie2, allowing maximum insert sizes of 2000 bp, with the “--no-mixed” and “--no-discordant” parameters added.
Reads with a mapping quality (MAPQ) below 30 were removed.
Duplicates were removed with PicardTools, and the reads mapping to the blacklist regions and mitochondrial DNA were also removed.
Reads mapping to the positive strand were moved +4 bp, and reads mapping to the negative strand were moved -5bp following the procedure outlined by Buenrostro et al.  to account for the binding of the Tn5 transposase.
Peaks were called using macs2 qith a qvalue of 0.001.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files of peaks identified with macs2 using a qvalue of 0.001

extract_protocol:
Cell nuclei were extracted and proceed directly to the Tn5 transposition reaction and library preparation.
Briefly, Tn5 transposase (Illumina #FC-121-1030) was used for genomic DNA fragmentation and the transposed DNA fragments were PCR amplified and barcoded with Illumina Nextera Index Kit (FC-121-1011).

treatment_protocol: In vitro P14 CD8+ T cells: on day 6, cells were left untreated or activated with 50 ng/ml PMA and 1 uM ionomycin for 3 hours before harvest for ATAC-seq. In vivo P14 CD8+ T cells: no treatment. NIH/3T3 fibroblast: cells were transduced with doxycycline-inducible TF-expressing lentivirus. Fibroblasts were left untreated or treated with 4 ug/ml doxycline for 72 hours for TFs induction before harvest for ATAC-seq.

tag: sample group

value: in vivo Batf f/f with Cre = Batf cKO

tag: primary stimulation

value: LCMV Arm challenge

tag: restimulation


title: ATAC-Seq A2_Batf_cKO_P14

tag: timepoint

tag: condition


title: ATAC-Seq B1_WT_Batf-floxed_Cre_P14

value: in vivo Batf f/f without Cre


title: CD14+_ top 10% HLA-DR+_healthy patient 2 [Sample 5]

description: mRNA

value: CD14+HLA-DR-high (top 10%)


title: ChIP-Seq WT_Day6_BATF_5ug

value: BATF


title: AW258_STM187

tag: fibrosis stage

tag: pls risk prediction


title: AW259_STM475


title: ATAC-Seq D2_Irf4_cKO_P14

value: in vivo Irf4 f/f with Cre = Irf4 cKO


title: CD14+_ bottom 10% HLA-DRneg/low(Mo-MDSC)_healthy patient 2 [Sample 4]

description: mRNA


title: AW257_STM496


title: CD14+_ top 10% HLA-DR+_healthy patient 2 [Sample 3]

description: mRNA


title: 2_ControlDiet_VB_rep1

description: p20209-s007_Liver_VB_CD_7-trans_S7_L001_R1_001

tag: strain

tag: age

tag: background

value: VB


title: ATAC-Seq D1_Irf4_cKO_P14


title: Total ribosome fooprints from HeLa cells

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ

data_processing:
Adapter sequences and randomized nucleotides were trimmed from raw reads using cutadapt.
Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
Then, the remaining reads were separately aligned to the human transcriptome (Refseq Transcripts, GrCH38, Version of November 2018) using BBmap.
Reads in coding sequences and Transcripts were counted using custom scripts supplied in the supplemental file to the manuscript.
Supplementary_files_format_and_content: xlsx, contain counted reads within each ENSEMBL transrcript coding sequence normalized to sequencing depth

source_name: HeLa Cells

growth_protocol: HeLa cells and MEF cells were cultured in DMEM +10% fetal bovine serum +100 U/ml Penicillin/Streptomycin (Gibco 15140122). Cells were sub-cultured using Trypsin-EDTA for dissociation.

extract_protocol:
HeLa cells were seeded in ten 10 cm dishes at 1.5 million cells per dish in 10 ml growth medium. MEF cells were seeded in three 15 cm dishes per condition at 3 million cells in 20 ml growth medium.  Two days later, cells were harvested for Ribo-seq. Cells were briefly rinsed with ice-cold PBS containing 10 mM MgCl2, 200 μM cycloheximide (CHX). This solution was poured off, removed by gently tapping the dish onto paper towels, and cells were lysed with 200 µl of lysis buffer (0,1 M HEPES pH 7.5, 20 mM MgCl2, 0.4 M KCl, 2% NP40, 400 μM CHX, 0.2 M NaF, 0.022 g/ml β-Glycerophosphate, 4 mM Sodium Vanadate, PhosSTOP™ (Roche 04 906 845 001) and cOmplete™ Mini (Roche 11836153001) both at 2x the suppliers indicated concentration, tablet dissolved in water) per plate. Cells were scraped off and lysate was collected in a 1.5mL tube. The collected volume was roughly 400 µl per plate. After brief vortexing, lysate was clarified by centrifuging for 10 minutes at 20.000 g at 4C. Approximate RNA concentration was measured using a Nanodrop system and 100U of Ambion RNAse 1 was added per 120 µg of measured RNA. To prepare undigested polysome profiles RNAse was omitted. Lysates were incubated with RNAse for 5 minutes on ice.  Lysates were then pipetted onto 17.5-50% sucrose gradients ,which were produced by freezing and layering 50% (2.5ml), 41.9% (2.5ml), 33.8% (2.5ml), 25,6% (2.5ml) and 17.5% (1.8ml) sucrose solutions (10 mM Tris HCl pH 7.4, 10 mM MgCl2, 140 mM KCl, 200 µM CHX) in Seton Scientific Polyclear Tubes 9/16x3-3/4 IN, and centrifuged at 35.000 rpm for 3.5 hours in Beckmann SW40 rotor. Gradients were fractionated using a Biocomp Gradient Profiler system and 80S fractions were collected for footprint isolation and immunoprecipitation. 500 µl of 80S fractions were saved for total footprint isolation. For immunoprecipitation, antibodies were bound to protein A magnetic dynabeads (Thermo 10001D) according to the manufacturer’s instructions. For the IP from HeLa cells lysates, 100 µl magnetic beads and 60 µl anti-p-RPS6 (Ser235/236) (Cell signaling #4857) were used. For the preparative IP from MEFs, 180 µl magnetic beads and 100 µl antibody were used. Beads were washed three times and then added to the 80S fractions. Fractions with beads were incubated for 2 hours, rotating at 4°C. Then beads were washed three times with bead wash buffer (20 mM Tris pH 7.4, 10 mM MgCl2, 140 mM KCl, 1% NP40), including a change of tube during the last wash. Bead volume was increased to ~500µl with bead wash buffer. 10% of the sample volume was saved for western blotting analysis of the IP. Total footprint fractions and IPed fractions were then subjected to RNA extraction: 55 µl (1/9th of volume) of 20% SDS was added, 650 µl Acid-Phenol Chloroform (Ambion) was added and the mixture was incubated at 65°C with 1300 rpm shaking for 45 minutes. Tubes were then placed on ice for 5 minutes, spun for 5 min at 20.000 g and the supernatant was washed once with acid-phenol chloroform and twice with chloroform. RNA was then precipitated with isopropanol, analyzed on an Agilent Bioanalyzer system to asses RNA integrity, and subjected to library preparation (see below). For RNA-seq in MEF cells, 3 million cells were seeded in 15 cm dishes in 20 ml growth medium and harvested two days later using TRIzol according to the manufacturer instructions.
For 80S footprinting and RNA-seq, libraries were prepared as follows: Samples were depleted of ribosomal RNA using the Illumina Ribo-Zero Gold kit. Poly-A mRNA was purified from total RNA using the NEB polyA Spin mRNA Isolation Kit. Poly-A mRNA was then fragmented using chemical cleavage in 50 mM NaHCO3 at pH 10, 95°C for 12 minutes. Then total RNA was processed in parallel with the depleted RNA from 80S ribosome fractions. For size selection, RNA was run on 15% Urea-Polyacrylamide gels and fragments from 25-35 nt were excised using reference ssRNA nucleotides of 25 and 35 basepairs run on a neighboring lane. RNA was extracted from the gel pieces and phosphorylated using T4 PNK. Deep sequencing libraries were prepared from these RNA fragments using the Bio-Scientific NEXTflex Small RNA-Seq Kit v3. DNA was amplified with 11 PCR cycles for the HeLa Ribo-seq samples and 9-14 cycles for the MEF samples. Deep-sequencing libraries were sequenced on the Illumina Next-Seq 550 system.

tag: library preparation

value: Nextflex small RNA

tag: rrna depletion

value: Ribo Zero Gold Illumina

tag: index sequence

value: GTGAAA


title: ChIP-Seq WT_Day6_BATF_10ug

tag: replicate group

value: WT

tag: tf

tag: corresponding input sample for peak calling


title: AW255_STM194


title: CD14+_ bottom 10% HLA-DRneg/low(Mo-MDSC)_healthy patient 1 [Sample 2]

description: mRNA

tag: tissue

tag: cell type

tag: disease state


title: CD14+_ top 10% HLA-DR+_healthy patient 1 [Sample 1]

description: mRNA


title: ATAC-Seq C2_WT_Irf4-floxed_Cre_P14

tag: sample group

value: in vivo Irf4 f/f without Cre

tag: primary stimulation

tag: restimulation


title: ATAC-Seq B2_WT_Batf-floxed_Cre_P14

tag: timepoint

tag: condition


title: GR12

city: La Plata

first: Guillermo

last: Giovambattista

state: Buenos Aires

address: Calle 60 y 118 S/N

department: Facultad de Ciencias Veterinarias

country: Argentina

institute: CONICET-UNLP

data_processing:
The NovaSeq Xp output files with base calls and qualities were converted into FASTQ file format and demultiplexed. Sequence reads were trimmed using fastp program v0.12.5.
Quality of sequencing data was checked and combined in one FASTQ file using FastQC v0.11.7.
All reads that passed quality control were mapped to the dog reference genome CanFam3.1 and the NCBI annotation release 105 with HISAT2 aligner v2.1.0.
The read abundance was calculated using the featureCounts algorithm as part of the Subread package v2.0.1.
DESeq2 package was used to read the featureCounts data. The count data were subjected to a regularized-logarithm transformation. DESeq2 v1.26.0 to assess differential expression between groups. DESeq2 applies a generalized linear model (GLM) to count data assuming a negative binomial distribution.
Genome_build: dog reference genome CanFam3.1
Supplementary_files_format_and_content: CVS file with a matrix table with normalized gene counts for every gene and every sample.

organism: Canis lupus familiaris

source_name: blood

extract_protocol:
RNA was isolated from RNAlater stored blood with the RiboPure™-Blood Kit (Ambion, Life Technologies, CA, USA).
From each sample 1 ug of high quality RNA (RNA integrity number (RIN) > 8) was used for non-stranded, paired-end cDNA library preparation (NEBNext Ultra II RNA Library Prep, Illumina).
Multiplexed total cDNA libraries were sequenced on one lane using the NovaSeq 6000 instrument with 2x150 bp paired-end sequencing cycles.

tag: strain

value: German Shepherd

value: Canine forms of osteoarthritis

value: blood


title: GR11


title: ATAC-Seq C1_WT_Irf4-floxed_Cre_P14


title: WRF55_ZT01

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

description: Shift work: Ad Libitum watered and food only at night while not working; euthanized ZT21

data_processing:
Libraries were sequenced on an Illumina NextSeq. Base calling and demultiplexing were performed with the accompanying software
Reads were aligned to rn6 transcriptome using Tophat2 using the following criteria: --read-realign-edit-dist 2 -g 1 --b2-sensitive
Gene expression was analyzed using Cufflinks with the following criteria: --library-type fr-firststrand
Genes where 18 of the 54 biological samples had a log2 (fpkm+1) value over 1 were kept for further processing.
Genome_build: rn6
Supplementary_files_format_and_content: FPKMs

organism: Rattus norvegicus

source_name: Heart

growth_protocol: Male Wistar rats around the age of 7-8 weeks underwent a shiftwork protocol for five weeks. Each animal was housed individually in a 12 L:12 D cycle (7am to 7pm) throughout the protocol.

extract_protocol:
Total RNA was extracted using TRIzol reagent and purified with an acid phenol-chloroform extraction
Sequencing libraries were constructed using NEB Utra Directional RNA Library Prep Kit from Illumina (New England BioLabs) following manufacturer’s instructions (n=54).

value: Wistar

tag: genotype

value: Wildtype

value: Heart

tag: treatment

value: Shift work:Ad Libitum watered and food only at night while not working; euthanized

tag: time


title: ATAC-Seq N2_Naive_WT_P14

value: in vivo WT Naive T Cells


title: AW269_STM418

tag: fibrosis stage

tag: pls risk prediction

value: Low


title: AW253_STM203

value: Intermediate


title: GR09


title: AW254_STM397


title: WRF54_ZT21

description: Shift work: Ad Libitum watered and food only at night while not working; euthanized ZT17


title: AW250_STM164


title: p-RPS6 selective Riosome footprints from HeLa cells

tag: library preparation

tag: rrna depletion

tag: index sequence

value: CGATGT


title: AW252_STM175


title: ATAC-Seq N1_Naive_WT_P14

tag: replicate group


title: ATAC-Seq F2_WT_P14

value: in vivo WT, with Cre

value: LCMV Arm challenge


title: GR08

tag: tissue


title: WRF52_ZT13

description: Shift work: Ad Libitum watered and food only at night while not working; euthanized ZT09


title: GR07

tag: disease state

value: control


title: WRF53_ZT17

description: Shift work: Ad Libitum watered and food only at night while not working; euthanized ZT13


title: AW249_STM445


title: WRF51_ZT09

description: Shift work: Ad Libitum watered and food only at night while not working; euthanized ZT05


title: AW248_STM163


title: ATAC-Seq F1_WT_P14

tag: sample group


title: GR06


title: WRF50_ZT05

description: Shift work: Ad Libitum watered and food only at night while not working; euthanized ZT01


title: ATAC-Seq E2_WT_iCre_P14

value: in vivo WT

tag: primary stimulation


title: GR05


title: GR10


title: ATAC-Seq E1_WT_iCre_P14

tag: restimulation


title: GR04


title: WRF46_ZT01


title: GR03


title: ATAC-Seq Dox72h_BATF_Rep2

tag: timepoint

value: Please see the fibroblast columns for details.

value: Yes

value: No


title: AW246_STM222


title: ATAC-Seq Dox72h_BATF_Rep1

tag: condition


title: AW244_STM463


title: WRF42_ZT13

tag: strain


title: WRF45_ZT21

tag: genotype


title: AW245_STM158


title: GR02

value: German Shepherd


title: WRF44_ZT17

tag: treatment


title: AW242_STM149


title: AW243_STM180


title: GR01

value: blood


title: AW247_STM453


title: ATAC-Seq Dox72h_BATF_IRF4_Runx3_2


title: WRF6_ZT21

value: Wistar

tag: time


title: ATAC-Seq Dox72h_BATF_IRF4_Runx3_1


title: ATAC-Seq Dox72h_BATF_IRF4_Runx3_Tbet_2


title: WRF62_ZT05

value: Wildtype


title: AW240_STM489

tag: fibrosis stage


title: AW241_STM396

tag: pls risk prediction


title: c.hidox.1  iWT-KRAS-MIA -PaCa-2 2.0 mg/mL doxycycline

city: New York

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

data_processing:
Bases were called with RTA (Illumina).
CASAVA (version 1.8.2) was used for converting BCL to fastq format, and for adaptor trimming.  .
Reads were mapped to the genome with Rsubread
Reads in each gene were counted with featureCounts
Genome_build: Grch38
Supplementary_files_format_and_content: txt file with raw counts for each gene

source_name: iWT-KRAS-MIA -PaCa-2

extract_protocol:
Extraction was performed with Qiagen's miRNeasy micro kit
The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent)..
Samples were only processed if their RIN>8.0
PolyAAA pulldown, amplification, and labeling was performed with the TruSeq mRNA kit.

treatment_protocol: Doxycycline was added to the cell growth medium

tag: cell line

value: iWT-KRAS-MIA -PaCa-2

value: 2.0 mg/mL doxycycline added.


title: c.hidox.3  iWT-KRAS-MIA -PaCa-2 2.0 mg/mL doxycycline


title: ATAC-Seq Dox72h_BATF_IRF4_Rep2


title: c.hidox.2  iWT-KRAS-MIA -PaCa-2 2.0 mg/mL doxycycline


title: WRF41_ZT09

value: Heart

value: Shift work:Ad Libitum watered and food only at night while not working; euthanized


title: AW239_STM192

value: Low


title: WRF5_ZT17


title: ATAC-Seq Dox72h_BATF_IRF4_Rep1


title: AW238_STM146


title: ATAC-Seq Dox72h_BATF_IRF4_Runx3_Tbet_1


title: ATAC-Seq Dox72h_BATF_IRF4_Tbet_Rep2


title: AW237_STM498


title: WRF4_ZT13


title: WRF3_ZT09


title: ATAC-Seq Dox72h_BATF_IRF4_Tbet_Rep1


title: WRF2_ZT05


title: AW236_STM229


title: a.ctrl.3   iWT-KRAS-MIA -PaCa-2 0mg/mL doxycycline

value: 0mg/mL doxycycline added.


title: ATAC-Seq Dox72h_BATF_Runx3_Rep2


title: WRF1_ZT01


title: AW235_STM151

value: Intermediate


title: ATAC-Seq Dox72h_BATF_Runx3_Rep1


title: W38_ZT21

description: Shift work: Ad Libitum watered and food ; euthanized ZT21

value: Shift work:Ad Libitum watered and food ; euthanized


title: a.ctrl .1  iWT-KRAS-MIA -PaCa-2 0mg/mL doxycycline


title: W37_ZT17

description: Shift work: Ad Libitum watered and food ; euthanized ZT17


title: AW234_STM380


title: b.lodox.2   iWT-KRAS-MIA -PaCa-2 0.5 mg/mL doxycycline

value: 0.5 mg/mL doxycycline added.


title: ATAC-Seq Dox72h_BATF_Runx3_Tbet_Rep1


title: W36_ZT13

description: Shift work: Ad Libitum watered and food ; euthanized ZT13


title: CC CC10- AEC2-3

city: Durham

first: Preetish

last: Kadur Lakshminarasimha Murthy

state: NC

address: 101 Science Dr

institute: Duke University

description: CC CC10- AEC2

data_processing:
ATAC-seq data were processed using the pipeline developed in (Koh et al., 2016) with default parameters. 75 bp PE reads were trimmed to 50 bp PE using FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) before analysing them. Reads were aligned to mm10 (mouse) or GRCh38 (human) genome using Bowtie 2 (Langmead and Salzberg, 2012). Duplicate and mitochondrial reads were removed. And peaks were called using MACS2 software. Peaks were annotated using HOMER (Heinz et al., 2010).
Genome_build: mm10/GRCh38
Supplementary_files_format_and_content: Peak file

source_name: lung

extract_protocol:
Mice were anaesthetised using Avertin. Skin and muscular layers were cut to expose the abdominal and thoracic cavities. Descending aorta was cut to exsanguinate and euthanise the animal. Cold PBS was perfused through the cardiac right ventricle to flush the blood out of the lungs. Lungs were then removed and inflated with 4% PFA and fixed overnight at 40C in PFA for histology. For isolation of live primary cells, lungs were instead inflated with lung/tumour dissociation buffer (Miltenyi Biotec), cut into small pieces and incubated at 370C for 30 minutes (normal lung) or 45 minutes (lung with neoplastic growth). A single cell suspension was obtained by mechanically dissociating using gentleMACS (Miltenyi Biotec) dissociator and passing the samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). To isolate AEC2 cells from CC mice, Lysotracker dye was used as described in (der Velden et al., 2013). Briefly, dissociated lung cells were resuspended in DMEM/F12 containing Lysotracker (1 µL dye in 14 mL medium) and incubated at 370C for 30 minutes. Human normal lung and cancer samples were stored on ice in DMEM/F12 medium supplemented with 2% FBS until dissociation. Samples were dissociated using human tumour dissociation kit (Miltenyi Biotec) following the manufacturer’s recommendation. A single cell suspension was obtained by passing the dissociated samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). Samples were resuspended in PBS supplemented with 10% FBS and incubated with anti-EpCAM antibodies for 10 minutes at room temperature. Samples were then washed once in PBS supplemented with 10% FBS. Primary cells were isolated by FACS using SONY SH800 sorter. Sytox dyes (Blue, Green, Red and AADvanced) were used to exclude dead cells.
Harvested primary cells were immediately used to prepare ATAC-seq libraries as described in (Buenrostro et al., 2013). Briefly, isolated cells were washed in PBS and resuspended in buffer containing transposase Tn5 and incubated at 370C for 30 minutes. Tagmented DNA was PCR amplified for 10-16 cycles. Mitochondrial DNA present in the libraries was cleaved using a CRISPR-Cas9 based method described in (Wu et al., 2016). sgRNA library targeting mitochondrial DNA was purchased from Addgene (#82480). In vitro transcription was performed to produce the gRNAs using MEGAshortscript Kit (Thermo Fisher Scientific). ATAC-seq libraries were treated with 10 µg Cas9 protein and 15 µg of sgRNA in a 40 µL reaction for 2 hours at 370C. The libraries were purified using Qiaquick PCR purification kit (Qiagen) and sequenced using Illumina Hi-Seq 2500 (50 bp paired end) or Next-Seq (75 bp paired end).

value: mixed

tag: cell type

value: lung epithelial cell


title: b.lodox.3   iWT-KRAS-MIA -PaCa-2 0.5 mg/mL doxycycline


title: CC CC10- AEC2-2

description: CC CC10- AEC2


title: AW226_STM161


title: AW225_STM218


title: ATAC-Seq Dox72h_BATF_Tbet_Rep2

value: Please see the fibroblast columns for details.

value: Yes


title: W35_ZT09

description: Shift work: Ad Libitum watered and food ; euthanized ZT09


title: W34_ZT05

description: Shift work: Ad Libitum watered and food ; euthanized ZT05


title: CC CC10- AEC2-1

description: CC CC10- AEC2


title: ATAC-Seq Dox72h_BATF_Tbet_Rep1

value: No


title: b.lodox.1   iWT-KRAS-MIA -PaCa-2 0.5 mg/mL doxycycline


title: CC Club-2

description: CC Club


title: W33_ZT01

description: Shift work: Ad Libitum watered and food ; euthanized ZT01


title: CC Club-1

description: CC Club


title: AW223_STM191


title: a.ctrl.2  iWT-KRAS-MIA -PaCa-2 0mg/mL doxycycline


title: AW224_STM368


title: ATAC-Seq Dox72h_IRF4_Rep1


title: ATAC-Seq Dox72h_BATF_Runx3_Tbet_Rep2


title: AW233_STM240


title: CC CC10+ AEC2-3

description: CC CC10+ AEC2


title: W9_ZT17


title: AW222_STM168


title: W11_ZT21


title: ATAC-Seq Dox72h_IRF4_Runx3_Rep1


title: ATAC-Seq Dox72h_IRF4_Runx3_Rep2


title: W5_ZT09


title: CC CC10+ AEC2-2

description: CC CC10+ AEC2


title: W7_ZT13


title: CC CC10+ AEC2-1

description: CC CC10+ AEC2


title: ATAC-Seq Dox72h_IRF4_Runx3_Tbet_Rep1


title: ATAC-Seq Dox72h_IRF4_Rep2


title: W3_ZT05


title: CK Week 22-3

description: CK Week 22


title: AW220_STM356


title: AW221_STM235


title: AW218_STM423


title: AW219_STM436


title: W1_ZT01


title: CK Week 22-2

description: CK Week 22


title: AW217_STM152


title: CK Week 22-1

description: CK Week 22


title: ATAC-Seq Dox72h_IRF4_Tbet_Rep1


title: AW216_STM150


title: W22_ZT21


title: CK Week 16-4

description: CK Week 16


title: ATAC-Seq Dox72h_NoTFs_Rep2


title: W21_ZT17


title: ATAC-Seq Dox72h_IRF4_Runx3_Tbet_Rep2


title: CK Week 16-3

description: CK Week 16


title: ATAC-Seq Dox72h_NoTFs_Rep1


title: AW215_STM494


title: W20_ZT13


title: W19_ZT09


title: AW214_STM451


title: ATAC-Seq Dox72h_Runx3_Rep1


title: AW213_STM238


title: W18_ZT05


title: CK Week 16-2

description: CK Week 16


title: ATAC-Seq Dox72h_IRF4_Tbet_Rep2


title: AW212_STM071


title: CK Week 16-1

description: CK Week 16


title: C38_ZT21

description: Ad Libitum feed and watered; euthanized ZT21

value: Ad Libitum feed and watered; euthanized


title: ATAC-Seq Dox72h_Runx3_Tbet_Rep2


title: CK Week 10-1

description: CK Week 10


title: ATAC-Seq Dox72h_Runx3_Tbet_Rep1


title: CK Week 4-2

description: CK Week 4


title: ATAC-Seq Dox72h_Runx3_Rep2


title: AW209_STM236


title: AW210_STM199


title: AW211_STM028

value: High


title: ATAC-Seq Dox72h_Tbet_Rep2


title: CK Week 10-2

description: CK Week 10


title: C37_ZT17

description: Ad Libitum feed and watered; euthanized ZT17

value: Wistar

value: Wildtype


title: CK Week 4-1

description: CK Week 4


title: ATAC-Seq Dox72h_Tbet_Rep1


title: AW208_STM154


title: SC AEC2-4

description: SC AEC2


title: C36_ZT13

description: Ad Libitum feed and watered; euthanized ZT13


title: AW207_STM138


title: ATAC-Seq NoDox_3T3_p23_2


title: ATAC-Seq NoDox_3T3_p23_1


title: W17_ZT01


title: C34_ZT05

description: Ad Libitum feed and watered; euthanized ZT05


title: SC AEC2-2

description: SC AEC2


title: SC AEC2-3

description: SC AEC2


title: SC AEC2-1

description: SC AEC2


title: ATAC-Seq NoDox_BATF_Rep1


title: SK Week 4-3

description: SK Week 4


title: C35_ZT09

description: Ad Libitum feed and watered; euthanized ZT09


title: AW205_STM186


title: C30_ZT21


title: ATAC-Seq NoDox_BATF_IRF4_Rep2


title: ATAC-Seq NoDox_BATF_Rep2


title: C29_ZT17


title: SK Week 4-2

description: SK Week 4


title: ATAC-Seq NoDox_BATF_IRF4_Rep1


title: ATAC-Seq NoDox_BATF_IRF4_Runx3_2


title: AW201_STM055


title: AW202_STM018


title: SK Week 4-1

description: SK Week 4


title: C28_ZT13


title: AW203_STM212


title: AW200_STM419


title: AW199_STM210


title: ATAC-Seq NoDox_BATF_IRF4_Runx3_1


title: C26_ZT05


title: C27_ZT09


title: C33_ZT01

description: Ad Libitum feed and watered; euthanized ZT01


title: AW204_STM232


title: ATAC-Seq NoDox_BATF_IRF4_Runx3_Tbet_2


title: CM2324

city: Stanford

first: Christopher

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

institute: Stanford University

data_processing:
Feature-barcode matrices were generated with cellranger count (expected cells: 8000)
Feature-barcode matrices were then merged with cellranger aggr (without depth normalization)
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger aggr filtered output: features, cells, and count matrix. Cloupe file contains depth-normalized data, whereas the count matrix contains non-normalized counts.

molecule: polyA RNA

source_name: lung tumor cells

growth_protocol: Lung tumors were initiated via intratracheal delivery of Lenti-Cre in 60 µL PBS. Lung tumors were developed for 16 weeks.

extract_protocol:
Microdissected lung tumors were dissociated with collagenase IV, dispase, and trypsin at 37 °C for 30 min. After dissociation, the samples were maintained on ice, in the presence of 2 mM EDTA and 1 U/mL DNase to prevent aggregation. For the sorting of viable cells, DAPI was used to exclude dead cells. FACSAria sorters (BD Biosciences) were used for cell sorting. Cells were loaded in each channel of Chromium Chip B (10X Genomics: 1000074) with a recovery target of 8,000 cells per sample, and emulsions were generated on the Chromium Controller (10X Genomics)
Libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 kit (10X Genomics: 1000075).

treatment_protocol: Mice were subjected to treatment with tamoxifen (4 mg doses in 200 µL corn oil) for two weeks prior to harvesting lung tumors.

tag: Sex

value: Female

tag: cohort

value: Non-Restored


title: AW198_STM234


title: CM2319

value: Restored


title: C25_ZT01

tag: tissue

value: Heart


title: AW197_STM110


title: ATAC-Seq NoDox_BATF_IRF4_Runx3_Tbet_1

tag: replicate group


title: C22_ZT21


title: CM2260


title: C21_ZT17


title: ATAC-Seq NoDox_BATF_IRF4_Tbet_Rep1

tag: sample group


title: C20_ZT13


title: AW196_STM060


title: ATAC-Seq NoDox_BATF_Runx3_Rep2

tag: primary stimulation


title: C19_ZT09


title: CM2328


title: AW195_STM157


title: ATAC-Seq NoDox_BATF_Runx3_Tbet_Rep2

tag: restimulation


title: AW193_STM226


title: AW192_STM100


title: C17_ZT01


title: ATAC-Seq NoDox_BATF_Runx3_Tbet_Rep1

tag: timepoint


title: ATAC-Seq NoDox_BATF_Tbet_Rep2

tag: condition


title: YCE1141 input MNase repeat 2

first: Zhiguo

last: Zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
Coverage for each base pair of the S. cerevisiae genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30°C in rich medium (1 % yeast extract, 2 % peptone) supplemented with 2 % Raffinose (YPRaff), 2 % Galactose (YPGal) or 2 % Glucose (YPD).  Cells were arrested in the G2-M phase of the cell cycle by treating an exponentially growing culture (at 7 x 106 cells per ml) with 5 μg / ml nocodazole (M1404, Sigma Aldrich) for 2 hours. Cells were arrested in the G1 phase of the cell cycle by treating an exponentially growing culture (at 7 x 106 cells per ml) with 5 μg / ml α-factor (synthesized by EZBiolab) for 2 hours.

extract_protocol:
ChIP in yeast was performed exactly as previously described (Yu et al., 2014).
ChIP-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center.

tag: strain

value: G1 + GAL + IAA

value: mutant spt5-3A

value: MNase

tag: chip antibody


title: YCE1141 H3K4me3 ChIP repeat 2

tag: genotype

tag: treatment


title: ATAC-Seq NoDox_BATF_Tbet_Rep1


title: AW189_STM215

tag: fibrosis stage

value: Intermediate


title: AW190_STM220

tag: pls risk prediction

value: Low


title: ATAC-Seq NoDox_BATF_IRF4_Tbet_Rep2


title: ATAC-Seq NoDox_BATF_Runx3_Rep1


title: ATAC-Seq NoDox_IRF4_Rep2


title: YCE1141 input sonication repeat 2

value: sonication


title: C18_ZT05

tag: time


title: ATAC-Seq NoDox_IRF4_Runx3_Rep2

value: Please see the fibroblast columns for details.


title: YCE1140 input MNase repeat 2

value: WT


title: AW194_STM147


title: ATAC-Seq NoDox_IRF4_Runx3_Rep1

value: No

value: Yes


title: ATAC-Seq NoDox_IRF4_Rep1


title: AW187_STM143


title: YCE1141 RNApolII ChIP repeat 2

value: CTD Ser5P


title: YCE1140 H3K4me3 ChIP repeat 2


title: AW185_STM098


title: AW186_STM119


title: AW184_STM182


title: YCE1140 input sonication repeat 2


title: YCE1140 RNApolII ChIP repeat 2


title: AW191_STM051


title: AW183_STM217


title: ATAC-Seq NoDox_IRF4_Runx3_Tbet_Rep1


title: YCE281 H3K4me3 ChIP repeat 2

value: Spt5 KO


title: ATAC-Seq NoDox_IRF4_Tbet_Rep2


title: YCE281 input MNase repeat 2


title: AW182_STM104


title: AW188_STM162


title: AW181_STM079


title: YCE281 RNApolII ChIP repeat 2


title: ATAC-Seq NoDox_Runx3_Rep2


title: ATAC-Seq NoDox_IRF4_Tbet_Rep1


title: AW180_STM116


title: ATAC-Seq NoDox_Runx3_Rep1


title: YCE281 input sonication repeat 2


title: ATAC-Seq NoDox_Runx3_Tbet_Rep2


title: ATAC-Seq NoDox_IRF4_Runx3_Tbet_Rep2


title: ATAC-Seq NoDox_Runx3_Tbet_Rep1


title: YCE1141 RNApolII ChIP repeat 1


title: AW177_STM122

value: High


title: YCE1141 input sonication repeat 1


title: AW176_STM053


title: ATAC-Seq NoDox_Tbet_Rep2


title: YCE1141 input MNase repeat 1


title: YCE1140 H3K4me3 ChIP repeat 1


title: ATAC-Seq NoDox_Tbet_Rep1


title: AW178_STM041


title: AW174_STM023


title: AW179_STM005


title: YCE1140 input MNase repeat 1


title: YCE1141 H3K4me3 ChIP repeat 1


title: ATAC-Seq BatfKO_day6_act_2

value: Batf KO,in vitro WT, 6 days post antiCD3/28 stimulation + PMA/ionomycin restimulation

value: anti-CD3, anti-CD28 and IL-2

value: PMA+ ionomycin for 3h


title: AW173_STM010


title: YCE1140 input sonication repeat 1


title: AW172_STM086


title: ATAC-Seq BatfKO_day6_act_3


title: ATAC-Seq BatfKO_day6_rest_1

value: Batf KO, in vitro WT, 6 days post antiCD3/28 stimulation


title: YCE281 H3K4me3 ChIP repeat 1

value: G1 + GAL + IAA


title: AW175_STM013


title: YCE281 input MNase repeat 1


title: AW171_STM052


title: ATAC-Seq BatfKO_day6_rest_3

value: Batf KO,in vitro WT, 6 days post antiCD3/28 stimulation


title: ATAC-Seq BatfKO_day6_rest_2


title: AW170_STM072


title: YCE281 RNApolII ChIP repeat 1


title: AW169_STM019


title: ATAC-Seq BatfKO_day6_act_1

value: Batf KO, in vitro WT, 6 days post antiCD3/28 stimulation + PMA/ionomycin restimulation


title: YCE281 input sonication repeat 1


title: AW167_STM139


title: ATAC-Seq WT_day6_act_1

value: in vitro WT, 6 days post antiCD3/28 stimulation + PMA/ionomycin restimulation


title: ATAC-Seq WT_day6_act_3


title: AW166_STM031

value: Intermediate


title: ATAC-Seq WT_day6_rest_1

value: in vitro WT, 6 days post antiCD3/28 stimulation


title: AW165_STM077


title: AW164_STM049

value: Low


title: AW163_STM054


title: ATAC-Seq WT_day6_rest_2


title: ATAC-Seq WT_day6_rest_3


title: Sol, Intralipos, 60mins

city: TOKYO

first: NOBUTAKA

last: KAMEI

address: 1-1-5 Sendagi, Bunkyo-ku,

country: Japan

institute: Nippon Medical School, Graduate School of Medicine

description:
Gene expression data from Sol treated by intralipos
brains of Male Wistar rats (8–10 weeks old)

hyb_protocol: The cDNA was hybridized using GeneChip Hybridization Oven 640 (Applied Biosystems, Waltham, Massachusetts, USA), washed and stained with GeneChip Fluidics Station 450 (Applied Biosystems),according to the manufacturer's instructions.

scan_protocol: Images were acquired with a GeneChip Scanner 3000 7G System (Applied Biosystems).

data_processing: Data were analyzed using the GeneChip Command Console Software ver. 3.2 and normalized with the GeneChip Expression Console Software ver. 1.3.0 (Applied Biosystems). The microarray data were analyzed using Transcriptome Viewer (Kurabo Industries. Osaka. Japan).

source_name: Sol, Intralipos, 60mins

label_protocol: Biotin-labelled cDNA was purified from 100 ng of total RNA using a GeneChip WT PLUS Reagent kit (Part# 902280 Applied Biosystems, Waltham, Massachusetts, USA), according to the manufacturer's instructions.

growth_protocol: rats were decapitated immediately after anesthesia, and unfixed brains were frozen in n-hexane at -80℃.

extract_protocol: RNA extraction was performed from tissue fragments using an RNeasy Micro kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions.

treatment_protocol: Brains were sliced using a cryostat at a thickness of 30 μm and mounted on membrane slides (PEN-membrane 2.0 μm; Leica, Heidelberg, Germany) followed by Nissl staining. Samples were microdissected using an LMD7000 (Leica Microsystems, Heidelberg, Germany) and frozen at -80℃.

tag: brain region

value: the solitary nucleus (Sol)

value: Intralipos


title: MVe, Intralipos, 60mins

description:
Gene expression data from MVe treated by intralipos
brains of Male Wistar rats (8–10 weeks old)

source_name: MVe, Intralipos, 60mins

value: the medial vestibular nucleus (MVe)


title: Retina Ptf1a-/- rep2

city: Ann Arbor

first: David

last: Turner

state: MI

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

data_processing:
fastq files generated with Illumina’s bcl2fastq v2.20.0.422
Insert sequences had adaptor sequences trimmed and inserts <18 nt or >30nt were removed
Sequences were  mapped to mature miRNA sequences in miRBase 22 using a custom Python script. Counts for sequences with equivalent mappings to multiple miRNA sequences were divided among the matches.
Read counts for miRNAs were normalized to input library size; the most frequent sequence for each mature miRNA was determined.
Genome_build: miRbase22
Supplementary_files_format_and_content: tab delimited text file with matrix of raw counts for all miRNAs and samples
Supplementary_files_format_and_content: tab delimited text file with matrix of counts per million input reads for all miRNAs and samples
Supplementary_files_format_and_content: tab delimited text file with matrix of most frequent sequence for each miRNA in each sample

source_name: retina

extract_protocol:
Total retina RNA was extracted using TRIzol, then denatured and separated on a 15% TBE urea gel. 18-30 nt small RNA was recovered from a gel slice.
Gel purified small RNA from 1 µg total RNA was used to prepare a small RNA library using a New England Biolabs Next Multiplex Small RNA Library Prep Kit according the manufacturer’s directions, with the following modification: after reverse transcription, the reaction was denatured, separated on a 10% TBE urea gel; a gel slice corresponding to 60 to 80 nt was isolated (based on size markers in an adjacent lane: low range ssRNA ladder, NEB). The reverse transcribed product in the gel slice was eluted, precipitated by adding 2-propanol, suspended in Tris-Hcl buffer, and then used in subsequent steps.

value: retina

tag: age

value: embryonic day E18.5


title: ATAC-Seq WT_day6_act_2


title: Retina Ptf1a-/- rep1


title: Total mRNA sequencing from p-RPS6 -/- MEF cells

source_name: MEF p-RPS6-/- Cells

tag: library preparation

value: Nextflex small RNA

tag: rrna depletion

value: Ribo Zero Gold Illumina

tag: index sequence

value: CAGATC


title: AW162_STM006


title: AW161_STM231


title: Total mRNA sequencing from WT MEF cells

source_name: MEF WT Cells

value: ACAGTG


title: AW160_STM259


title: Retina Ptf1a+/- rep1

tag: tissue


title: Total ribosome fooprints from p-RPS6 -/- MEF cells

value: AGTCAA


title: MHb, Intralipos, 60mins

description:
Gene expression data from MHb treated by intralipos
brains of Male Wistar rats (8–10 weeks old)

source_name: MHb, Intralipos, 60mins

value: the medial habenula (MHb)


title: AW159_STM272


title: AW158_STM121


title: AW157_STM069


title: Sol, Propofol, 60mins

description:
Gene expression data from Sol treated by propofol
brains of Male Wistar rats (8–10 weeks old)

source_name: Sol, Propofol, 60mins

value: Propofol


title: Total ribosome fooprints from WT MEF cells

value: GGCTAC


title: p-RPS6 selective Riosome footprints from WT MEF cells

value: ATGTCA


title: LHb, Intralipos, 60mins

description:
Gene expression data from LHb treated by intralipos
brains of Male Wistar rats (8–10 weeks old)

source_name: LHb, Intralipos, 60mins

value: the lateral habenula (LHb)


title: Retina Ptf1a+/- rep2


title: Retina P0 rep1

data_processing:
FASTQ files generated with Illumina’s bcl2fastq v2.17.1.14
Insert sequences had adaptor sequences trimmed and inserts <18 nt or >30nt were removed
Sequences were  mapped to mature miRNA sequences in miRBase 21 using a custom Python script. Unmapped sequences were discarded. Counts for sequences with equivalent mappings to multiple miRNA sequences were divided among the matches.
Read counts for miRNAs were normalized to input library size; the most frequent sequence for each mature miRNA was determined.
Genome_build: miRbase21
Supplementary_files_format_and_content: tab delimited text file with matrix of raw counts for all miRNAs and samples
Supplementary_files_format_and_content: tab delimited text file with matrix of counts per million input reads for all miRNAs and samples
Supplementary_files_format_and_content: tab delimited text file with matrix of most frequent sequence for each miRNA in each sample

extract_protocol:
Total retina RNA was extracted using TRIzol, then denatured and separated on a 15% TBE urea gel. 18-30 nt small RNA was recovered from a gel slice.
Gel purified small RNA from 1 µg total RNA was used to prepare a small RNA library using a  NEB Next Multiplex Small RNA Library Prep Kit (New England Biolabs) according the manufacturer’s directions, with the following modification: after reverse transcription, the reaction was denatured, separated on a 10% TBE urea gel; a gel slice corresponding to 60 to 80 nt was isolated (based on size markers in an adjacent lane: low range ssRNA ladder, NEB). The reverse transcribed product in the gel slice was eluted, precipitated by adding 2-propanol, suspended in Tris-Hcl buffer, and then used in subsequent steps.

value: postnatal day 0


title: IgG control rep1

description: UV-crosslinked protein-RNA

data_processing:
fastq files generated with Illumina’s CASAVA-1.8.2
Adapter sequences were trimmed, sequences <25nt were discarded, then mapped to mm10 with STAR, Sequences mapping to ChrM or rRNA sequences were removed. Multiple reads with identical sequence and length were considered duplicates and only a single read was retained.
T to C sequence substitutions relative to the genome were identified with Bambino. Reads with low base quality mismatches or mismatches near ends were filtered, so T to C substitution counts are conservative. T to C substitutions at same genomic position present in 2 or more Argonaute libraries and not in control libraries were considered crosslinks..
Reads with a deleted base at the position of a consistent T to C substitution were considered crosslinked reads. Consistent crosslinks within 15nt of a position with a greater number of reads with a consistent crosslink were removed, to create a set of predominant crosslinks, which were annotated with BEDTools using GENCODE VM16.
6 or 7nt miRNA seed matches with the 5’ base of the match within +/-15nt of a predominant crosslink site were identified, based on miRNAs expressed in P0 retinas, and miR-216a/b seed matches were identified.
Genome_build: mm10
Supplementary_files_format_and_content: bed file of predominant crosslink sites for Argonaute

source_name: retina explant

growth_protocol: P0 retinas were isolated and grown as explants on Corning Transwells with polyester membranes (pore size 0.4 µm), with the ganglion cell layer facing upwards in six-well plates, for 24 hours in high glucose DMEM supplemented with 20% horse serum and 0.1 mM 4-thiouridine

extract_protocol:
Crosslinked explants were lysed in low salt buffer. Lysates were sequentially treated with RNase-free DNase and micrococcal nuclease. EGTA was added to stop digestion. Lysates were cleared by centrifugation. Cleared lysates were immunoprecipitated with anti-Argonaute mAb or IgG, RNA was dephosphorylated, then phosphorylated with T4 Polynucleotide Kinase. Protein-RNA complexesb (100-150kd) were isolated by SDS-PAGE, digested with Proteinase K, and RNA recovered by acidic phenol/chloroform extraction and ethanol precipitation.
Libraries were prepared (input from 6 pooled retinas for each) using an IlluminaTruSeq Small RNA Library Preparation Kit according the manufacturer’s directions, with the following modification: after reverse transcription 80 to 150nt cDNA was gel purified and precipitated by with 2-propanol, then used for subsequent steps.

treatment_protocol: Live, intact retina explants were irradiated with 365 nm UV light (~300mJ/cm2) using a Stratalinker to crosslink RNA and proteins.

tag: par-clip antibody

value: mouse mAb IgG1 Isotype Control (CST 5415)


title: Argonaute rep5

description: UV-crosslinked protein-RNA

value: Anti-Ago Antibody 2A8 (Millipore MABE56)


title: IgG control rep2

description: UV-crosslinked protein-RNA


title: AW155_STM095

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: RNA was isolated using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.

value: High


title: AW156_STM038

value: Intermediate


title: AW154_STM118


title: AW153_STM169

value: Low


title: Retina P0 rep2

value: retina


title: Mve, O2, 60mins

description:
Gene expression data from MVe treated by O2
brains of Male Wistar rats (8–10 weeks old)

source_name: Mve, O2, 60mins

value: the medial vestibular nucleus (MVe)


title: LHb, Propofol, 60mins

description:
Gene expression data from LHb treated by propofol
brains of Male Wistar rats (8–10 weeks old)

source_name: LHb, Propofol, 60mins


title: MHb, Propofol, 60mins

description:
Gene expression data from MHb treated by propofol
brains of Male Wistar rats (8–10 weeks old)

source_name: MHb, Propofol, 60mins


title: Sol, Sevoflurane, 60mins

description:
Gene expression data from Sol treated by sevoflurane
brains of Male Wistar rats (8–10 weeks old)

source_name: Sol, Sevoflurane, 60mins

value: the solitary nucleus (Sol)

value: Sevoflurane


title: AW152_STM057


title: MHb, O2, 60mins

description:
Gene expression data from MHb treated by O2
brains of Male Wistar rats (8–10 weeks old)

source_name: MHb, O2, 60mins


title: Argonaute rep3

description: UV-crosslinked protein-RNA


title: HUc067post

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks.

tag: patient

value: liver biopsy

value: Follow-up


title: HUc066post

scan_protocol: Refer to the NanoString nCounter Assay System Manual.


title: HUc065post

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: HUc068post


title: HUc064post


title: Sol, O2, 60mins

description:
Gene expression data from Sol treated by O2
brains of Male Wistar rats (8–10 weeks old)

source_name: Sol, O2, 60mins


title: Argonaute rep2

description: UV-crosslinked protein-RNA


title: Mve, Sevoflurane, 60mins

description:
Gene expression data from MVe treated by sevoflurane
brains of Male Wistar rats (8–10 weeks old)

source_name: Mve, Sevoflurane, 60mins


title: Argonaute rep4

description: UV-crosslinked protein-RNA


title: Argonaute rep1

description: UV-crosslinked protein-RNA


title: HUc062post


title: AW151_STM068


title: RNA-Seq: keloid fibroblasts with nonspecific plasmid knock-down

city: Harbin

first: Yuhong

last: Wang

state: Heilongjiang

address: NO 23 Youzheng Street

institute: First Hospital of Harbin Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: keloids

growth_protocol: Fresh excised keloid samples were immediately punched into mini cube explants for further grinding into tiny pieces and primarily cultured. All fresh keloid mini explants were washed with phosphate-buffered saline (PBS; Cultilab, SP, Brazil), penicillin (100 Ul/ml; Gibco, Carlsbad, CA, USA) and streptomycin (100 µm/ml; Gibco). Mini explants were incubated in Dulbecco’s modified Eagle’s medium (DMEM; Cultilab) for surface adherence. Consistent culture was conducted in DMEM adding 15% fetal bovine serum (FBS; Cultilab), penicillin (100 UI/ml; Gibco) and streptomycin (100 µg/ml; Gibco).

extract_protocol:
Three anonymous patients affected with chronic keloids underwent keloid excision surgery. Keloid explants were collected from each patient under aseptic conditions. It was flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary cultured keloid fibroblasts (Passages 2–3) were used for siRNA interference using transfection approach. All siRNAs were designed and offered as commercial products from Sigma-Aldrich (Shanghai, China). Three 100 nM siRNA plasmids targeting HOXA11-AS were simultaneously transfected into two keloid fibroblasts (samples 1 and 2) respectively. Normal keloid fibroblasts were overtaken as a blank sample 0. Significantly reduced expres- sion of HOXAS-11 was validated using real-time PCR between HOXA11-AS-knockdown keloid fibroblasts and normal keloid fibroblasts. Simultaneously, plasmids harboring scram- bled nonspecific RNAs were transinfected as a positive control (sample 3). A blank plasmid harboring no siRNA was transfected as a negative control (sample 4).

tag: cell type

value: primary cultured keloid- derived fibroblasts

value: keloids

tag: disease state

value: three keloid patients

value: with nonspecific plasmid knock-down


title: MHb, Sevoflurane, 60mins

description:
Gene expression data from MHb treated by sevoflurane
brains of Male Wistar rats (8–10 weeks old)

source_name: MHb, Sevoflurane, 60mins

value: the medial habenula (MHb)


title: HUc063post


title: HUc061post


title: RNA-Seq: keloid fibroblasts with blank plasmid knock-down

value: with blank plasmid knock-down


title: CD11b+ Splenocytes in GM-conditioned state_ADT data

city: Seoul

first: Chae Gyu

last: Park

address: 50 Yonsei-ro, Seadaemun-gu

country: South Korea

institute: YONSEI UNIVERSITY

description:
single cell
Antibody derived tags
Total_ADT_count_matrix.txt
Total_cell_metadata.txt
MoMacDC_ADT_count_matrix.txt
MoMacDC_cell_metadata.txt

data_processing:
Library strategy: CITE-seq
CITE-seq data of the mRNA fraction and the ADT fraction were processed using the CellRanger-3.0.2 pipeline (10x Genomics) with a mouse reference genome (mm10) and the CITE-seq-Count-1.4.2, respectively.
The filtered gene expression matrix from the CellRanger and the ADT count matrix from the CITE-seq-Count were analyzed together by the ‘Seurat’ R package v3.6.0.
Before the downstream analysis, low quality cells with nFeature_RNA < 200, nFeature_RNA > 5,000, or mitocondrial gene expression > 15% were excluded.
For the remaining cells and genes, the UMI count matrix was normalized (for mRNA, log-normalized; for ADT, centered log-ratio (CLR) normalized) and scaled before use.
Genome_build: mm10
Supplementary_files_format_and_content: The "Total_*.txt" files are tab-deliminated text files (.txt) containing the 'RNA UMI count' or 'ADT UMI count' values for gene expression levels or 'Metadata' for a total of 11,631 cells.
Supplementary_files_format_and_content: The "MoMacDC_*.txt" files are tab-deliminated text files (.txt) containing the 'RNA UMI count' or 'ADT UMI count' values for gene expression levels or 'Metadata' only for 6,075 lineage-bundle cells.

molecule: other

extract_protocol:
CD11b+ splenocytes were collected by flow cytometric sorting.
Sequencing libraries for cDNA from RNAs were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit (v3). Following the CITE-seq protocol, ADT PCR additive primers were added to cDNA PCR and the ADT libraries were generated separately from the mRNAs. Constructed mRNA and ADT libraries were sequenced together on a HiSeq2500 system (Illumina) targeting 15,000 cDNA reads and 5,000 ADT reads per cell using the 100 base-pair paired end mode.

treatment_protocol: For GM sample, three once-daily injection of GM-CSF

tag: state

value: GM-conditioned state

value: CD11b+ Splenocytes


title: RNA-Seq: keloid fibroblasts with HOXA11-AS knock-down 2

value: with HOXA11-AS knock-down


title: RNA-Seq: keloid fibroblasts with HOXA11-AS knock-down


title: AW149_STM035

value: Intermediate


title: AW147_STM135


title: CD11b+ Splenocytes in steady state_ADT data

source_name: CD11b+ Splenocytes in steady state

value: steady state


title: AW148_STM117


title: RNA-Seq: keloid fibroblasts


title: CD11b+ Splenocytes in GM-conditioned state_RNA data

description:
single cell
Total_RNA_count_matrix.txt
Total_cell_metadata.txt
MoMacDC_RNA_count_matrix.txt
MoMacDC_cell_metadata.txt

data_processing:
CITE-seq data of the mRNA fraction and the ADT fraction were processed using the CellRanger-3.0.2 pipeline (10x Genomics) with a mouse reference genome (mm10) and the CITE-seq-Count-1.4.2, respectively.
The filtered gene expression matrix from the CellRanger and the ADT count matrix from the CITE-seq-Count were analyzed together by the ‘Seurat’ R package v3.6.0.
Before the downstream analysis, low quality cells with nFeature_RNA < 200, nFeature_RNA > 5,000, or mitocondrial gene expression > 15% were excluded.
For the remaining cells and genes, the UMI count matrix was normalized (for mRNA, log-normalized; for ADT, centered log-ratio (CLR) normalized) and scaled before use.
Genome_build: mm10
Supplementary_files_format_and_content: The "Total_*.txt" files are tab-deliminated text files (.txt) containing the 'RNA UMI count' or 'ADT UMI count' values for gene expression levels or 'Metadata' for a total of 11,631 cells.
Supplementary_files_format_and_content: The "MoMacDC_*.txt" files are tab-deliminated text files (.txt) containing the 'RNA UMI count' or 'ADT UMI count' values for gene expression levels or 'Metadata' only for 6,075 lineage-bundle cells.


title: HUc060post


title: HUc059post


title: AW146_STM125

value: Low


title: MVe, Propofol, 60mins

description:
Gene expression data from MVe treated by propofol
brains of Male Wistar rats (8–10 weeks old)

source_name: MVe, Propofol, 60mins

value: the medial vestibular nucleus (MVe)

value: Propofol


title: LHb, O2, 60mins

description:
Gene expression data from LHb treated by O2
brains of Male Wistar rats (8–10 weeks old)

source_name: LHb, O2, 60mins

value: the lateral habenula (LHb)


title: CD11b+ Splenocytes in steady state_RNA data


title: AW150_STM015


title: HUc058post

value: liver biopsy


title: AW145_STM159


title: Y3

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

institute: Indiana University

description:
ILMN_1174_genecounts.txt
Y3

data_processing:
For ribo-seq, reads were first aligned to rRNA followed by mapping to the rest of the mm10 reference genome using STAR aligner. Hg38 was used for human cell lines.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: text file, featureCounts

growth_protocol: HEK293T cells and PPP1R15A uORF mutant cells were cultured in Dulbecco’s Modified Eagle Medium with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin. All cell types were cultured at 37 °C with 5% CO2

extract_protocol:
For regular RNA seq, Kidneys were snap-frozen and RNA was extracted using Zymo Direct-zol RNA kit. For ribo-seq, polysome buffer (1 mL per one mouse kidney) consisted of 20 mM Tris pH 7.5 (140 µL of 1 M Tris 7.0 plus 60 µL of 1 M Tris 8.0 for 10 mL final buffer), 100 mM NaCl, 10 mM MgCl2, 1% Triton X-100, 0.1% sodium deoxycholate, DTT, 0.02 U/µL Turbo DNAse (ThermoFisher AM2238), 200 µg/mL cycloheximide, and Protease Inhibitor Cocktail Tablet.
for regular RNA seq, cDNA library preparation involved mRNA capture/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche). For ribo-seq, RNase I digested, size selected RNA fragments were treated with T4 PNK and adapter ligation was done using NEXTFLEX Small RNA-seq kit v3 (PerkinElmer NOVA-5132-05).

tag: timepoint


title: Smad4KO_3

city: Farmington

first: Linda

middle: S

last: Cauley

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

data_processing:
The data sets were analyzed with Tophat2 mapping (DNAnexus).
Expression levels were measured with Cuffilinks software (DNAnexus)
Differential expression analysis was done with Cuffdiff software (DNAnexus).
Genes with transcriptional changes over two folds (Log2 fold change >1 or <-1,p<0.05, false discovery rate<0.05) were selected for Ingenuity pathway analysis (Qiagen) and Gene set enrichment analysis
Supplementary_files_format_and_content: gtf file with FPKM values for each sample

source_name: spleen

extract_protocol:
RNAeasy Plus Kit (Qiagen)
Standard Illumina library construction protocols
RNA samples were sent to Otogenetics Corporation for RNA-Sequencing.

value: spleen

tag: strain

tag: cells

value: Early effector CD8 T cells

value: 6 days post infection

tag: genotype

value: Smad4 deficient


title: HUc057post

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

value: Follow-up


title: Y2

description:
ILMN_1174_genecounts.txt
Y2


title: Smad4KO_1


title: AW144_STM030

tag: fibrosis stage

tag: pls risk prediction


title: Y1

description:
ILMN_1174_genecounts.txt
Y1


title: HUc056post


title: AW143_STM211


title: HUc055post


title: S3

description:
ILMN_1174_genecounts.txt
S3

value: 0 h


title: S2

description:
ILMN_1174_genecounts.txt
S2


title: AW142_STM132


title: WT_3

tag: time

value: wild type


title: WT_2


title: Smad4KO_2


title: AW141_STM001

value: High


title: AW140_STM042


title: S1

description:
ILMN_1174_genecounts.txt
S1


title: WT_1


title: HUc053post


title: HUc054post


title: P3

description:
ILMN_1174_genecounts.txt
P3


title: KP_MIT

description: KP tumour

source_name: lung

extract_protocol:
Mouse KP cell lines were cultured in DMEM (Thermo Fisher) with 10% FBS and 1% Antibiotic-Antimycotic.
Mice were anaesthetised using Avertin. Skin and muscular layers were cut to expose the abdominal and thoracic cavities. Descending aorta was cut to exsanguinate and euthanise the animal. Cold PBS was perfused through the cardiac right ventricle to flush the blood out of the lungs. Lungs were then removed and inflated with 4% PFA and fixed overnight at 40C in PFA for histology. For isolation of live primary cells, lungs were instead inflated with lung/tumour dissociation buffer (Miltenyi Biotec), cut into small pieces and incubated at 370C for 30 minutes (normal lung) or 45 minutes (lung with neoplastic growth). A single cell suspension was obtained by mechanically dissociating using gentleMACS (Miltenyi Biotec) dissociator and passing the samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). To isolate AEC2 cells from CC mice, Lysotracker dye was used as described in (der Velden et al., 2013). Briefly, dissociated lung cells were resuspended in DMEM/F12 containing Lysotracker (1 µL dye in 14 mL medium) and incubated at 370C for 30 minutes. Human normal lung and cancer samples were stored on ice in DMEM/F12 medium supplemented with 2% FBS until dissociation. Samples were dissociated using human tumour dissociation kit (Miltenyi Biotec) following the manufacturer’s recommendation. A single cell suspension was obtained by passing the dissociated samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). Samples were resuspended in PBS supplemented with 10% FBS and incubated with anti-EpCAM antibodies for 10 minutes at room temperature. Samples were then washed once in PBS supplemented with 10% FBS. Primary cells were isolated by FACS using SONY SH800 sorter. Sytox dyes (Blue, Green, Red and AADvanced) were used to exclude dead cells.
Harvested primary cells were immediately used to prepare ATAC-seq libraries as described in (Buenrostro et al., 2013). Briefly, isolated cells were washed in PBS and resuspended in buffer containing transposase Tn5 and incubated at 370C for 30 minutes. Tagmented DNA was PCR amplified for 10-16 cycles. Mitochondrial DNA present in the libraries was cleaved using a CRISPR-Cas9 based method described in (Wu et al., 2016). sgRNA library targeting mitochondrial DNA was purchased from Addgene (#82480). In vitro transcription was performed to produce the gRNAs using MEGAshortscript Kit (Thermo Fisher Scientific). ATAC-seq libraries were treated with 10 µg Cas9 protein and 15 µg of sgRNA in a 40 µL reaction for 2 hours at 370C. The libraries were purified using Qiaquick PCR purification kit (Qiagen) and sequenced using Illumina Hi-Seq 2500 (50 bp paired end) or Next-Seq (75 bp paired end).

value: lung epithelial cell


title: HUc052post


title: LHb, Sevoflurane, 60mins

description:
Gene expression data from LHb treated by sevoflurane
brains of Male Wistar rats (8–10 weeks old)

source_name: LHb, Sevoflurane, 60mins

tag: brain region

tag: treatment

value: Sevoflurane


title: P2

description:
ILMN_1174_genecounts.txt
P2


title: KP_779

description: KP tumour


title: HUc050post


title: AW139_STM134

value: Intermediate


title: AW138_STM188


title: SPC_FosL1_Kras4w_tumour_tdTom+GF-2

value: mixed


title: P1

description:
ILMN_1174_genecounts.txt
P1


title: AW136_STM185


title: YCE1140 RNApolII ChIP repeat 1

tag: condition

value: G1 + GAL + IAA

value: WT

value: sonication

tag: chip antibody

value: CTD Ser5P


title: HC-9

description:
ILMN_1133_genecounts.txt
HC-9

tag: tissue


title: Intestine Lgr5 Kras Week 25-2

description: Intestine Lgr5 Kras Week 25

source_name: Intestine


title: AW137_STM213


title: HUc047post

value: liver biopsy


title: HC-8

description:
ILMN_1133_genecounts.txt
HC-8


title: HUc048post


title: AW134_STM197

value: Low


title: HUc051post


title: HC-6

description:
ILMN_1133_genecounts.txt
HC-6


title: Intestine Lgr5 Ctrl Week 25-2

description: Intestine Lgr5 Ctrl Week 25


title: Intestine Lgr5 Kras Week 25-1

description: Intestine Lgr5 Kras Week 25


title: HC-5

description:
ILMN_1133_genecounts.txt
HC-5


title: AW132_STM219


title: AW131_STM174


title: HUc046post


title: HC-4

description:
ILMN_1133_genecounts.txt
HC-4


title: HUc044post


title: HUc049post


title: AW130_STM189


title: HUc043post


title: Intestine Lgr5 Ctrl Week 25-1

description: Intestine Lgr5 Ctrl Week 25


title: Intestine Lgr5 Kras Week 17

description: Intestine Lgr5 Kras Week 17


title: HC-3

description:
ILMN_1133_genecounts.txt
HC-3


title: Intestine Lgr5 Ctrl Week 17

description: Intestine Lgr5 Ctrl Week 17


title: HUc042post


title: AW135_STM209


title: SPC_FosL1_Kras4w_tumour_tdTom+GF-1


title: AW128_STM462


title: HC-2

description:
ILMN_1133_genecounts.txt
HC-2


title: Intestine Lgr5 Kras Week 5

description: Intestine Lgr5 Kras Week 5


title: Intestine Lgr5 Ctrl Week 5

description: Intestine Lgr5 Ctrl Week 5


title: HC-1

description:
ILMN_1133_genecounts.txt
HC-1


title: HC-7

description:
ILMN_1133_genecounts.txt
HC-7


title: HC-12

description:
ILMN_1133_genecounts.txt
HC-12


title: HUc040post


title: AW129_STM376


title: Intestine Lgr5 Kras-2

description: Intestine Lgr5 Kras


title: AW127_STM389


title: HUc041post


title: HUc045post


title: AW125_STM345


title: AW124_STM398


title: HC-11

description:
ILMN_1133_genecounts.txt
HC-11


title: HUc039post


title: Intestine Lgr5 Ctrl-2

description: Intestine Lgr5 Ctrl


title: Intestine Lgr5 Kras-1

description: Intestine Lgr5 Kras


title: AW123_STM366


title: HUc037post


title: AW122_STM020


title: HC-10

description:
ILMN_1133_genecounts.txt
HC-10


title: Intestine Lgr5 Ctrl-1

description: Intestine Lgr5 Ctrl


title: AW121_STM357


title: HUc035post


title: CK Tumour Excised Week 22-2

description: CK Tumour Excised Week 22


title: GTFB-PDX1009, Olaparib treated, mouse no. 827

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

data_processing:
Hisat2 (version 2.1.0) (Used to map reads to human genome GRCh37)
bedtools (Used to assemble transcripts)
edgeR (Used to identify differenentially expressed genes )
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: Excel File containing counts and TPMs for all samples

growth_protocol: 5 million human HGSOC ascites cells were injected by intraperitoneal route into NSG mice and allowed to develop to 7 days prior to treatment. The ascites cells are from GTFB-PDX1009, a BRCA-wildtype HGSOC sample.

extract_protocol:
RNeasy plus kit (Qiagen)
RNAlibraries were prepared for sequencing using TruSEQ RNA Sample Prep v4 using standard Illumina protocols.
per Novogene protocol for PE150 Illumina NGS

treatment_protocol: 7 days after injection, mice were injected IP once daily with vehicle control or 50 mg/kg olaparib for 21 days. Following treatment, diesease was allowed to develop/recur for 2 months. Mice were then sacrificed and necropsied. Ascites were collected for analysis.

value: GTFB-PDX1009 (BRCA-wildtype human high-grade serous ovarian cancer)

value: Olaparib

value: ascites cells


title: GTFB-PDX1009, Olaparib treated, mouse no. 878


title: GTFB-PDX1009, Vehicle control, mouse no. 834

value: control


title: GTFB-PDX1009, Vehicle control, mouse no. 846


title: Treated by Adenovirus encoding Cre recombinase (Ad-Cre), biological rep3

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

data_processing:
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
The reads were aligned to NCBI GRCm38 using tophat v.2.1.1
FPKMs were generated using Cufflinks v. 2.2.1
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: Mus musculus sequence GRCm38
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples.

source_name: Mesenchymal stem cells from p75 floxed mice (p75fl/fl) calvarial tissue

growth_protocol: Calvarial bones were dissected from p75 floxed embryos at postnatal day 1-5. Frontal and parietal bones were subjected to six sequential enzymatic digestions with a mixture containing 1 mg/mL collagenase type I (Worthington Biochemical Corporation, Lakewood, NJ) and 1 mg/mL collagenase type II (Worthington Biochemical Corporation). Cell fractions (from sequential digestions 3-6) were collected and filtered at 40 μm and centrifuged. Cells were resuspended in αMEM (Gibco) containing 15% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was extract from cells by Trizol (Life technologies corporation, Gaitherburg, MD, USA).
TruSeq Stranded Total RNA LT Sample Prep Kit (Human Mouse Rat)/TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

treatment_protocol: For p75 deletion, cells were stimulated with an adenovirus encoding either Cre Recombinase (Ad-Cre, 1045-HT, Vector Biosystems, Malvern, PA) or GFP (Ad-GFP, 1060-HT, Vector Biosystems). Cells were resuspended in Trizol (Life technologies corporation, Gaitherburg, MD, USA) for RNA isolation.

value: Cre-treated


title: CK Tumour Excised Week 22-1

description: CK Tumour Excised Week 22


title: Dataset2_Day 15 continued replicate 3

city: Zurich

first: Moritz

last: Schaefer

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description:
replicate 3
Brunello2_D15-Cont3

data_processing:
Library strategy: CRISPR Screen
FastQ files were obtained as provided by the sequencing facility
The MAGeCK-VISPR pipeline (v0.5.6) was employed to map R1-reads to sgRNA-library and for all downstream analyses
Genome_build: Brunello library

source_name: HEK293-hACE2 cells

extract_protocol:
DNA STAT-60 Kit
Genomic DNA was extracted from each sample (detailed extraction methods are described in supplemental methods). The sgRNA regions were then amplified and indexed for Illumina sequencing using a one-step PCR method and primers specific to the LentiCRISPRv2-based Brunello libraries. Primers and indices used for the generation of amplicon libraries are listed in Table S1. Brunello  DNA samples were amplified in ten 100 µl reactions using the NEBNext High-Fidelity 2X Master Mix Kit (New England Biolabs), 0.5 µM of forward and reverse primers and 10 µg of DNA template per reaction with the following program: initial denaturation at 98°C for 3 min, 24 cycles of denaturation at 98°C for 10 s, annealing 60°C for 15 s and extension 72°C for 25 s, and final extension at 72°C for 2 min. 256 bp amplicons were quantified on a 2% agarose gel stained with SYBR Safe (Invitrogen), using the Gel Doc quantification software (Bio-Rad).
Amplicons were first pooled in an equimolar fashion and then the pools were gel-extracted using the PureLink Quick Gel Extraction Kit (Thermo Fisher Scientific). The sequencing was carried out at the Interdisciplinary Center for Biotechnology Research (ICBR; University of Florida) using a NovaSeq 6000 sequencer (Illumina). The Brunello amplicons were sequenced using the S4 2X150 cycles Kit (Illumina)

treatment_protocol: human HEK293T-hACE2 cells (Genecopoeia) were transduced with the Brunello sgRNA library. For each screen, 1.2x108 cells were transduced with lentivirus-packaged sgRNA library at MOI 0.3 in the presence of 8 μg/ml polybrene (Sigma) to achieve ~500-fold overrepresentation of each sgRNA. After 48 h, 0.6 µg/ml puromycin (Gibco) was added to eliminate non-transduced cells and cultures were expanded in Matrigel-coated (Corning) T300 flasks. Control replicates were collected at this time to determine input library composition and additional replicates were infected with SARS-CoV-2 or OC43 at the indicated MOIs. Cells surviving initial infections were collected when they had expanded to confluency. A portion of each replicate was stored in DNA/RNA Shield (Zymo Research) at -80°C for genomic DNA extraction and the remaining cells were reseeded and reinfected at the indicated MOIs.

tag: virus

value: uninfected

tag: single or double infected

tag: moi


title: AW116_STM434

city: Dallas


title: AW119_STM372

value: High


title: AW120_STM387


title: HUc113pre

tag: patient

value: Baseline


title: HUc038post

value: Follow-up


title: Dataset2_Day 15 continued replicate 2

description:
replicate 2
Brunello2_D15-Cont2


title: HUc112pre


title: Treated by Adenovirus encoding Cre recombinase (Ad-Cre), biological rep2

tag: cell type

value: Mesenchymal stem cells from p75 floxed mice (p75fl/fl) calvarial tissue


title: Treated by Adenovirus encoding Cre recombinase (Ad-Cre), biological rep1


title: HUc111pre


title: AW115_STM358


title: Treated by control Adenovirus (Ad-GFP), biological rep3

value: control Adenovirus (Ad-GFP)


title: AW114_STM465

value: Intermediate


title: HUc110pre


title: HUc036post


title: Dataset2_Day 15 continued replicate 1

description:
replicate 1
Brunello2_D15-Cont1


title: Dataset2_Day 10 continued replicate 3

description:
replicate 3
Brunello2_D10-Cont3


title: HUc109pre


title: HUc034post


title: Treated by control Adenovirus (Ad-GFP), biological rep2

value: WT


title: AW112_STM105


title: Dataset2_Day 10 continued replicate 2

description:
replicate 2
Brunello2_D10-Cont2


title: Treated by control Adenovirus (Ad-GFP), biological rep1


title: AW111_STM325


title: Dataset2_Day 0 replicate 3

description:
replicate 3
Brunello2_BrT0puro3


title: HUc107pre


title: Dataset2_Day 10 continued replicate 1

description:
replicate 1
Brunello2_D10-Cont1


title: HUc108pre


title: HUc106pre


title: Dataset2_Day 0 replicate 1

description:
replicate 1
Brunello2_BrT0puro1


title: Dataset2_Day 0 replicate 2

description:
replicate 2
Brunello2_BrT0puro2


title: HUc105pre


title: Dataset2_SARS-CoV2 single-infected replicate 3

description:
replicate 3
Brunello2_BrCov-ST3

value: single-infected

value: MOI 0.3


title: ZR1337

data_processing:
Reads were aligned to mm10 via 2-pass mapping with the STAR aligner (v2.6.1d).
Estimates of gene expression were generated using RSEM (v1.2.30) with standard input parameters.
The differentially expressed genes between different tumor genotypes were called by DESeq2 (v1.26.0) using transcript abundance estimates imported via tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Median of ratios normalized (DESeq2) counts across all samples; Differential expression analysis output from DESeq2; RSEM gene-level outputs for each library, which can be imported into R with tximport.

source_name: Neoplastic cells isolated from lung tumors by FACS

growth_protocol: Lung tumors were initiated via intratracheal delivery of Lenti-sgRNA/Cre (sgNeo1/sgNT/sgNeo2/Cre (sgInert), Lenti-sgLkb1/Cre (sgLkb1), or Lenti-sgCebpa/sgCebpb/sgCebpd/Cre (sgCebpa/b/d)) in 60 µL PBS. Lung tumors were developed for 17 weeks.

extract_protocol:
Microdissected lung tumors were dissociated with collagenase IV, dispase, and trypsin at 37 °C for 30 min. After dissociation, the samples were maintained on ice, in the presence of 2 mM EDTA and 1 U/mL DNase to prevent aggregation. For the sorting of neoplastic cells, the dissociated cells were stained with antibodies against CD45 (BioLegened, 103112), CD31 (BioLegend, 303116), F4/80 (BioLegend, 123116), and Ter119 (BioLegend, 116212) to exclude hematopoietic and endothelial cells (lineage-positive (Lin+) cells). DAPI was used to exclude dead cells. FACSAria sorters (BD Biosciences) were used for cell sorting.RNA was purified using RNA/DNA Allprep kit (Qiagen, 80284). RNA quality was assessed using the RNA6000 PicoAssay for the Agilent 2100 Bioanalyzer.
Two to ten nanograms of total RNA served as input for the preparation of RNA-Seq libraries using the Trio RNA-Seq, Mouse rRNA kit (Tecan Genomics: 0507-32). Libraries were constructed per the manufacturer’s instructions. Purified libraries were assessed using the Agilent High Sensitivity DNA kit (Agilent Technologies: 5067-4626).

tag: Sex

value: Male

tag: label


title: ZR1524


title: ZR1532 [C/EBP Bulk RNA-seq]

value: Female


title: HUc104pre

value: liver biopsy


title: AW107_STM045


title: AW109_STM432


title: HUc102pre


title: HUc103pre


title: AW108_STM365


title: AW99_STM456


title: AW113_STM382

value: Low


title: MT1205_AGG3

value: Lenti-sgCebpa/sgCebpb/sgCebpd/Cre


title: Dataset2_SARS-CoV2 single-infected replicate 2

description:
replicate 2
Brunello2_BrCov-ST2


title: AW110_STM367


title: Dataset2_SARS-CoV2 single-infected replicate 1

description:
replicate 1
Brunello2_BrCov-ST1


title: MT1205_AGG2


title: ZR1327