title: 203715550092_R03C01


title: AE1_Control_rep2

status: Public on Dec 10 2021

type: SRA

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: KAPA RNA Stranded PolyA

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 98
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 98 transcript annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

molecule: polyA RNA

organism: Mus musculus

source_name: alveolar epithelial cell type 1

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from polyA-enriched mRNA using the KAPA Stranded mRNA-Seq Kit and were further amplified for sequencing.

treatment_protocol: LPS inhalation (5ml of 2mg/ml). The primary lung ECs were freshly isolated using Liberase and DNase-I digestion. The cells were sorted directly into Trizol (Ambion, #15596018)

tag: strain

tag: age

value: 6 to 12 weeks

tag: Sex

value: Male

tag: tissue

value: Lung

tag: cell type

value: alveolar epithelial


title: 203715550003_R03C01

type: genomic

city: Rochester

first: Julie

last: Cunningham

state: MN

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

country: USA

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data were normalized separately for the two platforms, and batch correction across the two platforms were performed via COMBAT

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Fresh Frozen Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA extraction

tag: gender

value: Female

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch

value: epic


title: 203715550002_R03C01


title: SS9ZB4OA-SUR

type: RNA

city: Barcelona

first: Fernando

last: Salvador Gómez

address: Balmes 89, 3º 7

country: Spain

institute: SOLTI

description: A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA). Data were log2 transformed and normalized using the housekeeping genes.

hyb_protocol: NOT PROVIDED

scan_protocol: NOT PROVIDED

data_processing: Data were normalized using 5 housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0, and SF3A1), and log2 transformed

label: NOT PROVIDED

molecule: total RNA

source_name: Breast tumor

label_protocol: NOT PROVIDED

extract_protocol: At baseline, a section of the formalin-fixed paraffin-embedded (FFPE) breast tissue was examined with haematoxylin and eosin (H&E) staining to confirm the presence of invasive tumor cells and to determine the minimum tumor surface area. For samples obtained at Cycle 2 Day 1, those without invasive tumor cells were also profiled. For RNA purification (High Pure FFPET RNA isolation kit, Roche, Indianapolis, IN, USA), at least 1–5 10 μm FFPE slides were used for each tumor specimen, and macrodissection was performed (when needed) to avoid contamination with normal breast tissues. A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA).

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: 203715550016_R03C01


title: AE1_Control_rep1

description: KAPA RNA Stranded PolyA


title: 203715540052_R04C01


title: T103E9MR-2W


title: ETA3KUIB-SUR


title: 203715550001_R03C01


title: 203715540074_R03C01


title: BSC Fracture-2 rep1

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.3a) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

source_name: Bone stromal cells

extract_protocol:
For fracture healing model, we used 10-week-old female mice for the fracture experiments. Mice were anesthetized by using a ketamine hydrochloride/xylazine mixture (80 /12 mg/kg body weight, i.p.) the left leg was fractured with three-point bending. It was stabilized with an intramedullary nail (hollow needle 23G) as described previously. Carprofen (4 mg/kg intra muscular) was given as an analgesic and further on at 24-hour intervals when required. Mice were sacrificed by cervical dislocation after post-fracture surgery day at 14 and 12 weeks wild-type female were used as control.
Single cell suspension was subjected to droplets based scRNA-seq. Single cells were encapsulated into emulsion droplets using Chromium controller (10X genomics). The scRNA seq libraries were prepared using the chromium single cells 3’ regent kit (V3) (10X genomics, cat#PN-10000075) according to the manufactures protocol. scRNAseq library were evaluated and quantified by Agilent Bioanalyzer using High sensitivity DNA kit (cat#5067-4626) and Qubit (ThermoFisher Scientific, Cat# Q32851). Individual libraries were diluted to 4nM and pooled for sequencing. Pooled library was sequenced by using High Output kit (150 cycle) (Illumina cat#TG-160-2002) with Next500 sequencer (Illumina).

value: Bone

value: Bone stromal cells


title: 203715540057_R03C01


title: BSC Fracture-1 rep2


title: BSC Fracture-2 rep2


title: 203715540119_R03C01


title: 203715540097_R03C01


title: 6NG1D6S9-SCR

value: No

value: Negative


title: 203715540052_R03C01


title: BSC Fracture-1 rep1


title: 203715540051_R03C01


title: 203715550003_R02C01


title: BSC Control-2 rep2


title: 203715550092_R02C01


title: 203715550016_R02C01


title: ETA3KUIB-2W


title: ETA3KUIB-SCR


title: 203715550001_R02C01


title: 203715540119_R02C01


title: BSC Control-1 rep2


title: SS9ZB4OA-SCR


title: BSC Control-2 rep1


title: BSC Control-1 rep1


title: UX38NFCY-SCR


title: T103E9MR-SCR


title: WT Input DNA

city: Münster

first: Dong

last: Han

address: Röntgenstraße 20

department: Cell and developmental biology

institute: Max Planck Institute for Molecular Biomedicine

library_source: genomic

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data
Sequence reads were aligned to the mm10 mouse reference genome using Map with Bowtie for Illumina with default parameters except suppress all alignments for a read if more than 1 reportable alignments exist.
Peak calling was performed using MACS  with the following parameters: do not build the shifting model, shift size 100.
The Wig files generated before were converted into bigWig files for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: mouse embryonic stem cells

growth_protocol: ESCs were culture on gelatin-coated dishes in ESCs medium: Konckout DMEM medium supplemented with 10% KSR, 10% FCS, 1% Glutamax, 1% NEAA, 1% penicillin-streptomycin, 1% b-mercaptoethanol, and 20 ng/ml human recombinant LIF.

extract_protocol:
Cells were lysed in lysis buffer 1 (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM 0.5 M EDTA, 10% glycerol, 0.5% IGEPAL CA630, 0.25% Triton X-100) containing protease inhibitor cocktail (Sigma) for 30 min at 4°C and washed in lysis buffer 2 (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Chromatin was sheared using Diagenode Bioruptor (high power, 40 cycles of 30 s on and 30 s off) equipped with a water-cooling system (4°C) in 1 mL of sonication buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.5% SDS) per 1 ´ 10^7 cells.
ChIP seq sequencing libraries were prepared according to the instruction of KAPA Hyper Prep Kit (Roche).

value: Mixture of C57BL/6, C3H and CD1

value: mouse embryonic stem cells

tag: genotype

value: WT

tag: chip antibody

value: none (input)


title: 203717910020_R01C01


title: L80A Input DNA

value: L80A Oct4


title: 203715540051_R02C01


title: 203715540052_R02C01


title: 203715550003_R01C01


title: GQAYGK8I-SCR


title: WWULABG5-SUR


title: 203715550092_R01C01


title: 203715550002_R01C01


title: 203715540119_R01C01


title: 203715550001_R01C01


title: 203715550002_R02C01


title: 203715550016_R01C01


title: ATACSeq_WT Oct4_ESCs


title: WWULABG5-SCR


title: 203715540097_R01C01


title: EKCIFI7K-SUR


title: H3K4me3_ChIPSeq_L80A Oct4_ESCs

value: Rabbit anti-H3K4me3 (ab8580, Abcam)


title: 203715540052_R01C01


title: EKCIFI7K-2W


title: 203715540074_R01C01


title: H3K4me3_ChIPSeq_WT Oct4_ESCs


title: 203715540057_R01C01


title: EKCIFI7K-SCR


title: 203715540051_R01C01


title: GQAYGK8I-2W


title: 203715540036_R08C01


title: 203715540025_R08C01


title: 203715540029_R08C01


title: WT_Oct4_ChIPSeq_1

value: goat anti-Oct4 (sc-8628, Santa Cruz)


title: 203715540024_R08C01


title: WDGTY0UP-SUR


title: 203711910070_R08C01


title: ATACSeq_L80A Oct4_ESCs


title: WDGTY0UP-2W


title: KO_GC-Tfh_4

city: Hamilton

first: Brendan

middle: McNie

last: Jeffrey

state: MT

address: 903 South 4th Street

department: BCBB

institute: NIH

data_processing:
Raw paired-end FASTQ  reads for each sample were quality trimmed using Trimmomatic tool, version 0.3 using the following settings: PE ILLUMINCLIP:Truseq3-PE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36.
Quality trimmed reads were aligned to Ensembl Mus musculus genome assembly GRCm38.94 using STAR alignment tool version 2.5.3.
STAR alignment was run including –quantMode TranscriptSam flag to generate read counts per gene using Ensembl GRCm38.94 annotation to define gene features.
Sample gene counts were analyzed for differential expression using the Bioconductor package DESeq2.
Genome_build: GRCm38.94
Supplementary_files_format_and_content: raw counts

source_name: transferred SMARTA cells

growth_protocol: Naïve WT or KO SMARTA cells (CD4+CD62L+CD44-) were isolated from donors and transferred into WT B6J recipients.

extract_protocol:
On day 8 post-infection, splenocytes were sorted into Th1, pre-Tfh, and GC Tfh populations based on CXCR5 and PD-1 gating, then stored in Trizol at -80C. Total RNA was purified using the Qiagen RNEasy kit.
Library samples were prepared with 1 ug total RNA per sample, using the TruSeq RNA Library Preparation Kit v2, Set A and Set B (Illumina #RS-122-2001 and RS-122-2002) following manufacturer instructions, and sequenced on an Illumina NextSeq 500 using a NextSeq 500 High Output v2 kit (150 cycles) (Illumina #FC-404-2005).

treatment_protocol: One day post-adoptive transfer, recipients were infected with 2e5 pfu LCMV Armstrong.

value: spleen


title: 203711910027_R08C01


title: KO_pre-Tfh_4


title: 203711910055_R08C01


title: WDGTY0UP-SCR


title: 203711910012_R08C01


title: XVDKFB5R-SUR


title: 203711910011_R08C01


title: XVDKFB5R-2W


title: 203715540050_R07C01


title: KO_Th1_4


title: 203715540036_R07C01


title: WT_GC-Tfh_4


title: L80A_Oct4_ChIPSeq_1


title: XVDKFB5R-SCR


title: WT_pre-Tfh_4


title: 203715540025_R07C01


title: 203715540029_R07C01


title: 203715540024_R07C01


title: 203711910055_R07C01


title: 203711910070_R07C01


title: 203711910056_R07C01


title: 8FKRMT1P-SCR


title: 8FKRMT1P-2W


title: 203711910027_R07C01


title: 203711910056_R08C01


title: WT_Th1_4


title: 203711910030_R07C01


title: 203711910011_R07C01


title: KO_GC-Tfh_3


title: H31V8MRO-2W


title: J0DPFV8F-SCR


title: 203711910012_R07C01


title: H31V8MRO-SCR


title: 203715540050_R06C01


title: KO_Th1_3


title: KO_pre-Tfh_3


title: WT_GC-Tfh_3


title: 203715540029_R06C01


title: ODY1DV9D-SCR

value: Yes


title: 203715540025_R06C01

value: Female


title: WLP7PGV0-2W


title: 203711910070_R06C01

value: Ovarian Clear Cell Carcinoma (OCCC)


title: 203715540024_R06C01

value: epic


title: WT_Th1_3


title: 203711910056_R06C01


title: 203711910030_R06C01


title: KO_GC-Tfh_2


title: 203711910027_R06C01


title: WLP7PGV0-SCR


title: 203711910055_R06C01


title: 203711910012_R06C01


title: 203711910011_R06C01


title: JMIGCBAX-2W

value: N/A; no information


title: 203715540050_R05C01


title: KO_Th1_2


title: JMIGCBAX-SCR


title: 203715540036_R05C01


title: WT_GC-Tfh_2


title: 203715540024_R05C01


title: KJ189SGD-2W


title: 203711910055_R05C01


title: 8T68MG9B-2W


title: 203711910070_R05C01


title: 203711910056_R05C01


title: WT_pre-Tfh_3


title: KO_pre-Tfh_2


title: WT_Th1_2


title: 203711910030_R05C01


title: 203711910027_R05C01


title: KO_GC-Tfh_1


title: 60TBVIU5-SCR


title: 8T68MG9B-SCR


title: KO_pre-Tfh_1


title: 203715540050_R04C01


title: 203715540029_R04C01


title: 203715540036_R04C01


title: 203715540025_R04C01


title: 01BXNEBL-SCR


title: WT_GC-Tfh_1


title: WT_pre-Tfh_2


title: 203711910070_R04C01


title: 7PP3WXMZ-SUR


title: 203711910056_R04C01


title: 203711910030_R04C01


title: WT_pre-Tfh_1


title: 203711910012_R04C01


title: 203711910055_R04C01


title: WT_Th1_1


title: 60TBVIU5-SUR


title: 203711910011_R04C01


title: 203711910012_R05C01


title: 7PP3WXMZ-SCR


title: L6RQSTFA-SUR


title: 203715540024_R03C01


title: 01BXNEBL-2W


title: Control siRNA/LPS [DK21070_06]

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

description:
DK21070_06
3' mRNA-Seq

data_processing:
Basecalls performed using bcl2fastq ver2.17.
3' mRNA-Seq reads were aligned to the GRCh38 genome assembly using STAR v2.7.6a.
Reads per million (RPM) values were calculated using samtools v1.11 and htseq-count v0.12.4.
Genome_build: GRCh38
Supplementary_files_format_and_content: DK20171_DK21070_rpm.txt: Tab-delimited text file includes RPM values for every gene and every sample.
Supplementary_files_format_and_content: DK20171_DK21070_raw_counts.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: lung microvascular endothelial cell

extract_protocol:
Total RNA was extracted with isogen reagent (Nippon Gene, Tokyo, Japan) according to the manufacturer's protocol.
Libraries were prepared according to the manufacturer's instructions accompanying the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). Briefly, an oligodT primer containing an Illumina-compatible sequence at its 5’ end is hybridized to the RNA and reverse transcription is performed. Then, RNA Removal and Second Strand Synthesis were conducted. The libraries were amplified by 12 cycles of polymerase chain reaction (PCR). The purified libraries were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

value: lung microvascular endothelial cells

value: female

tag: race

value: Hispanic

tag: sirna

value: Control

tag: treatment

value: LPS


title: siRNA2 CD26/LPS [DK21070_08]

description:
DK21070_08
3' mRNA-Seq

tag: age


title: 203715540024_R04C01


title: 203715540036_R03C01


title: 203711910056_R03C01


title: 203711910070_R03C01


title: L6RQSTFA-2W


title: KO_Th1_1


title: siRNA2 CD26/PBS [DK21070_04]

description:
DK21070_04
3' mRNA-Seq

tag: Sex

value: PBS


title: 203711910055_R03C01


title: 203711910030_R03C01


title: 7PP3WXMZ-2W


title: UX38NFCY-2W


title: 203711910012_R03C01


title: 203711910011_R03C01


title: Control siRNA/PBS [DK21070_02]

description:
DK21070_02
3' mRNA-Seq


title: 203715540050_R02C01


title: 203715540029_R02C01


title: Control siRNA/LPS [DK20171_22]

description:
DK20171_22
3' mRNA-Seq


title: 203715540036_R02C01


title: 203715540025_R02C01


title: 203715540024_R02C01


title: N81I09ZB-SCR

value: No

value: Negative


title: UX38NFCY-SUR


title: 203711910056_R02C01


title: siRNA2 CD26/PBS [DK20171_20]

description:
DK20171_20
3' mRNA-Seq


title: 4LETAZ9E-2W


title: 203711910027_R02C01


title: 203711910055_R02C01


title: 4LETAZ9E-SCR


title: 4LETAZ9E-SUR


title: 203711910012_R02C01


title: EOINGU0Q-SUR


title: 203711910011_R02C01


title: siRNA2 CD26/LPS [DK20171_16]

description:
DK20171_16
3' mRNA-Seq

value: male

value: Caucasian


title: siRNA2 CD26/PBS [DK20171_12]

description:
DK20171_12
3' mRNA-Seq


title: 203715540050_R01C01


title: 203715540036_R01C01


title: siRNA2 CD26/LPS [DK20171_24]

description:
DK20171_24
3' mRNA-Seq


title: N81I09ZB-2W


title: 203715540029_R01C01


title: EOINGU0Q-2W


title: 203711910070_R02C01


title: EOINGU0Q-SCR


title: 203715540025_R01C01


title: Control siRNA/PBS [DK20171_18]

description:
DK20171_18
3' mRNA-Seq


title: siRNA2 CD26/LPS [DK20171_08]

description:
DK20171_08
3' mRNA-Seq


title: 203711910055_R01C01


title: 203711910056_R01C01


title: 203711910027_R01C01


title: 203711910030_R01C01


title: 203711910030_R02C01


title: Control siRNA/LPS [DK20171_14]

description:
DK20171_14
3' mRNA-Seq


title: siRNA2 CD26/PBS [DK20171_04]

description:
DK20171_04
3' mRNA-Seq


title: 203715540024_R01C01


title: 203711910012_R01C01


title: 813F3PFJ-2W


title: Control siRNA/LPS [DK20171_06]

description:
DK20171_06
3' mRNA-Seq


title: 203711910070_R01C01


title: Father Ind.5 rep2

city: Nantes

first: Alice

last: Mollé

address: 30 bd Jean Monnet

country: France

institute: University of Nantes

data_processing:
Single-end reads were mapped to the hg19 genome by the BWA algorithm and duplicate reads (read-pairs mapping to the same genomic location) were collapsed. Reads mapped to non-canonical and mitochondrial chromosomes were also removed. For each sample, ChIP-seq peaks were detected using MACS2 standard parameters, and peaks were selected only if they are present in both duplicates
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files are generated using MACS2

source_name: Peripheral blood mononuclear cell

extract_protocol:
Cells were lysed and chromatin was fragmented with Micrococcal nuclease (MNase) and incubuated with 2 mg of anti-H3K27ac (39133, Active Motif) for immunoprecipitation
Libraries were prepared as follows. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by double-sided SPRI size selection . The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were send to a sequencing platform core facility and sequenced on  a Next-seq 500 (Illumina).

tag: disease state

value: Healthy

tag: family

value: Ind.5 Father

value: Peripheral blood mononuclear cell


title: Control siRNA/PBS [DK20171_10]

description:
DK20171_10
3' mRNA-Seq

tag: cell type


title: 12NHJR2F-2W


title: 4ZS39E9D-SCR


title: 12NHJR2F-SUR


title: 813F3PFJ-SUR


title: 813F3PFJ-SCR


title: 12NHJR2F-SCR


title: BG8VHU9U-2W


title: Control siRNA/PBS [DK20171_02]

description:
DK20171_02
3' mRNA-Seq


title: Father Ind.5 rep1


title: Mother Ind.1 rep2

value: Ind.1 Mother


title: Ind.5 rep2

value: BAP1 variants


title: Ind.5 rep1


title: BG8VHU9U-SCR


title: Father Ind.1 rep2

value: Ind.1 Father


title: Mother Ind.1 rep1


title: D2LHRT9L-SUR

value: N/A; no information


title: D2LHRT9L-2W


title: Father Ind.1 rep1


title: Ind.1 rep2


title: 8T68MG9B-SUR


title: D2LHRT9L-SCR

value: Positive


title: L6RQSTFA-SCR


title: Ind.1 rep1


title: 31RJISH4-2W


title: BLISS_Dox_R2_merged

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1
barcodes used as follows: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
reads were aligned with Bowtie2 v2.3.4.1 to hg19
reads were filtered with bedtools intersect v2.26.0
reads were counted for specific regions using the R package exomeCopy v1.18.0
density plots were generated using the R package metagene2 v3.10
Genome_build: hg19
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: SH-EP-MYCNER shEXOSC10

growth_protocol: SH-EP-MYCNER cells stably expressing a Dox-inducible shRNA against EXOSC10 were grown in RPMI-1640 (Thermo Fisher Scientific), supplemented with 10% fetal calf serum (Capricorn Scientific) and 1% penicillin/streptomycin (Sigma Aldrich).

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol. Barcodes used as follows: EtOH: CATCACGC, 4-OHT: GTCGTTCC, Dox: TGATGATC, Dox_4-OHT: ACGACATC

treatment_protocol: Cells were treated with Dox (1 µg/ml) and/or 4-OHT (100 nM) for 96 h

tag: treatment (etoh or 4-oht)

value: EtOH

value: Dox (1 microg/ml)


title: 31RJISH4-SCR


title: HaCaT_24h_RASPtreated_miRNA_RASPb

city: Patras

first: Katerina

last: Grafanaki

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

data_processing:
Small RNA-Seq data were exported in FASTQ files and quality checked with FastQC.
Reads were aligned on miRBase Release 21 with Bowtie2 and read counts were computed with SAMtools IdxStats. Reads that did not align on miRBase miRNAs were subsequently aligned on the whole human genome [Homo sapiens: hg38 GRCh38] with Bowtie2 and read counts were computed with htseq-count.
Aligned reads on miRNAs were combined and RPKM values were computed. In addition, Log2fold changes and p-values of treated vs untreated were computed.
We considered as differentially expressed miRNAs those at the 5% ends of the normal distribution and added as an additional filtering criterion to have at least 5 aligned reads at every experiment.
Genome_build: Homo sapiens: hg38 GRCh38

source_name: HaCaT cell line

growth_protocol: HaCaT cell line was obtained by ATCC

extract_protocol:
Cells were immediately lysed and small RNA fractions were extracted and isolated using PureLink RNA mini Kit and mirVana miRNA Isolation Kit (Ambion)
Ion Total RNA-Seq Kit v2 protocol for small RNA sequencing

treatment_protocol: RASP treatment

value: RASP


title: SWHXBUBZ-SUR


title: HaCaT_24h_RASPtreated_miRNA_RASPa


title: BLISS_4-OHT_R2_merged


title: SWHXBUBZ-2W


title: BLISS_EtOH_R2_merged


title: HaCaT_24h_DMSOtreated_miRNA_Controlb

value: DMSO


title: HaCaT_24h_DMSOtreated_miRNA_Controla


title: BLISS_Dox_4-OHT_R2_merged


title: SWHXBUBZ-SCR


title: ChIPRX_FANCD2_shEXOSC10_IgG

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.2.7. and normalized to the sample with the spike in control (mm10) except for MYCN ChIPseq, which was read normalized
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: SH-EP-MYCNER cells stably expressing Dox-inducible shRNAs against EXOSC10, TCEA1 or DCP1A were grown in RPMI-1640 (Thermo Fisher Scientific), supplemented with 10% fetal calf serum (Capricorn Scientific) and 1% penicillin/streptomycin (Sigma Aldrich).

extract_protocol:
Cells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

treatment_protocol: For shRNA experiments, cells were treated for 72 h with Dox (1 µg/ml) before adding 4-OHT (200 nM) for 4 h. For the ATM inhibition 4sU, cells were treated for 4 h with 4-OHT (200 nM) and/or KU-60019 ATM inhibitor (100 nM). For all 4sU experiments, 4sU (500 µM) was added in the last 20 min of treatment.

tag: treatment (etoh ordox)

tag: exosc10 protein (wild type (wt) or mutant (mut))

tag: treatment (dmso or ku-60019)

tag: treatment (dmso or aphidicolin)

tag: label

tag: antibody

value: Rabbit IgG, Sigma-Aldrich, I5006


title: ChIPRX_FANCD2_shEXOSC10_Dox_4-OHT

value: Recombinant Anti-FANCD2 antibody, Abcam, ab221932


title: 2B_IPSC_Slo9IPSK7

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

data_processing:
Trimming was perfromed using Adapter Removal v2, using defaul parameters
Alignment on GRCH38 genome assembly  was performed using STAR and RSEM
differential expression was obtained using limma voom protocol, using TMM and CPM normalizations
Genome_build: GRCH38
Supplementary_files_format_and_content: Processed count files  were obtained using RSEM.

source_name: induced pluripotent stem cells dreived from fibroblasts - 2B_IPSC

extract_protocol:
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories). The RNA quality index was higher than 8.5 in all samples.
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.

value: induced pluripotent stem cells

tag: batch

value: Batch 1

tag: disease status

value: PD


title: 2B_NPC_Slo12NP7

source_name: neural progenitor cells derived from human fibroblasts - 2B_NPC

value: neural progenitor cells


title: 2K_IPSC_Slo15IPSK8

source_name: induced pluripotent stem cells dreived from fibroblasts - 2K_IPSC

value: healthy


title: RVTYGB9J-SUR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: RVTYGB9J-2W

tag: age


title: 2K_NPC_Slo18

source_name: neural progenitor cells derived from human fibroblasts - 2K_NPC


title: 1B_NPC_Slo6NP16

source_name: neural progenitor cells derived from human fibroblasts - 1B_NPC


title: ChIPRX_FANCD2_shEXOSC10_Dox


title: 1K_NPC_Slo24NP15

source_name: neural progenitor cells derived from human fibroblasts - 1K_NPC


title: 1B_IPSC_Slo3IPSK16

source_name: induced pluripotent stem cells dreived from fibroblasts - 1B_IPSC


title: RVTYGB9J-SCR

value: No

value: Negative


title: ChIPRX_FANCD2_shEXOSC10_4-OHT


title: 1K_IPSC_Slo21IPSK15

source_name: induced pluripotent stem cells dreived from fibroblasts - 1K_IPSC


title: BTF8KCLO-SUR


title: 2B_NPC_Slo11NP7


title: ChIPRX_FANCD2_shEXOSC10_EtOH


title: 2B_IPSC_Slo8IPSK7


title: 1B_NoA, control after - 1B_noA_a

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

description: staring sample: 3 ml whole blood in freeze EDTA-coated tubes

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R package: missMethyl 1.26.1

extract_protocol: Gentra(r) Puregene(r) Blood kit (Qiagen, ref. 158467) used in a P2 laboratory with authorization from OFEV number A203065.

tag: subject

tag: diagnosis

value: control

tag: tissue

value: blood DNA

tag: timepoint

value: control after


title: Patient12 before acupuncture - 12_b

value: Burnout

value: before acupuncture


title: Patient7 after acupuncture - 7_a

value: after acupuncture


title: Patient11 after acunpuncture - 11_a

value: after acunpuncture


title: 2K_IPSC_Slo14IPSK8

tag: cell type


title: 2K_NPC_Slo17NP8


title: Patient3 after acupuncture - 3_a


title: Patient11 before acupuncture - 11_b


title: BTF8KCLO-SCR

value: Positive


title: Patient1 before acupuncture - 1_b


title: Patient9 after acupuncture - 9_a


title: Patient13 before acupuncture - 13_b


title: Patient8 after acupuncture - 8_a


title: Patient4 before acupuncture - 4_b


title: 1K_NPC_Slo23NP15


title: Patient4 after acupuncture - 4_a


title: Patient2 after acupuncture - 2_a


title: Patient7 before acupuncture - 7_b


title: ChIPRX_IgG_R2

source_name: SH-EP-MYCNER

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

tag: exosc10 protein (wild type (wt) or mutant (mut))

tag: treatment (dmso or ku-60019)

value: Rabbit IgG, Sigma-Aldrich, I5006


title: TZNVU4CE-2W

source_name: Breast tumor

value: N/A; no information


title: Patient13 after acupuncture - 13_a


title: Patient9 before acupuncture - 9_b


title: 1B_IPSC_Slo2IPSK16

value: induced pluripotent stem cells

tag: batch


title: ChIPRX_FANCD2_APH_R2

tag: treatment (dmso or aphidicolin)

value: Aphidicolin (APH) (400 nM)

tag: label

tag: antibody

value: Recombinant Anti-FANCD2 antibody, Abcam, ab221932


title: 1K_IPSC_Slo20IPSK15

value: Batch 1

tag: disease status


title: Patient10 before acupuncture - 10_b


title: 2B_NPC_Slo10NP7

value: neural progenitor cells

value: PD


title: TZNVU4CE-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

value: Yes

tag: er

value: Negative


title: Patient12 after acupuncture - 12_a

tag: subject

tag: diagnosis

value: blood DNA


title: Patient3 before acupuncture - 3_b

tag: tissue

tag: timepoint


title: ChIPRX_FANCD2_DMSO_R2

tag: treatment (etoh or 4-oht)

value: DMSO


title: 2K_NPC_Slo16NP8

tag: cell type

value: healthy


title: ChIPRX_FANCD2_shEXOSC10_Input

tag: treatment (etoh ordox)

tag: exosc10 protein (wild type (wt) or mutant (mut))


title: Patient8 before acupuncture - 8_b

value: Burnout

value: before acupuncture


title: Patient10 after acupuncture - 10_a

value: after acupuncture


title: 2K_IPSC_Slo13IPSK8

tag: batch


title: 1B_NPC_Slo4NP16


title: 2B_IPSC_Slo7IPSK7


title: ChIPRX_totalRNAPII_shEXOSC10_Dox_4-OHT_R2

value: Dox (1 microg/ml)

tag: treatment (dmso or ku-60019)

tag: treatment (dmso or aphidicolin)

value: Pol II antibody (A-10), Santa Cruz Biotechnology, sc-17798


title: ChIPRX_FANCD2_Input_R2

tag: label

tag: antibody


title: 82SDROMV-SUR

tag: cellularity

value: N/A; no information

tag: age

tag: pr


title: XSD5Z32C-2W

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er


title: 1K_NPC_Slo22NP15

tag: disease status


title: 1K_IPSC_Slo19

value: induced pluripotent stem cells


title: 1B_NoA, control before  - 1B_noA_b

tag: subject

tag: diagnosis

value: control

tag: tissue

tag: timepoint

value: control before


title: Patient1 after acupuncture - 1_a


title: RA2SPMa

hyb_protocol: 2 μg labeled aRNA hybridization was performed using Ambion Amplification/hybridization kit and samples were applied to microarrays in 42oC for 15 min enclosed in OneArray chips chambers. After hybridization, slides were washed.

scan_protocol: Scanned on a ProScanArray scanner, Serial No.: 61982

data_processing:
LOWESS normalized. Easy quant protocol was used.
Normalized log2 ratio (Cy5/Cy3) representing test/reference

label_protocol: 1 µg of total RNA per sample was primed with 1 µl of 100 µM T7 oligo(dT) primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), and aRNA was transcribed in vitro using T7 RNA polymerase (NEB). Control samples were labeled with Cy3-label and experimental samples with Cy5-label.

extract_protocol: Cells were immediately lysed and total RNA fractions was extracted and isolated using PureLink RNA mini Kit (Ambion)

tag: treatment

value: RASP


title: Patient2 before acupuncture - 2_b


title: ChIPRX_totalRNAPII_shEXOSC10_4-OHT_R2

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

value: EtOH

tag: exosc10 protein (wild type (wt) or mutant (mut))


title: XSD5Z32C-SCR

value: No

value: Positive


title: ChIPRX_totalRNAPII_shEXOSC10_Dox_R2

tag: treatment (dmso or ku-60019)

tag: treatment (dmso or aphidicolin)

tag: label


title: EOHJF3NI-SUR

tag: cellularity

tag: age


title: EOHJF3NI-2W

tag: tumor infiltrating lymphocytes (tils)

tag: pr


title: Pst DB29-infiltrated; Rep 3

city: Sherbrooke

first: Peter

last: Moffett

address: 2500 boulevard de l'universite, Departement de Biologie

department: Biologie

institute: Universite de Sherbrooke

description:
Leaves were infiltrated with Pst DB29 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 18

data_processing:
Illumina bcl2fastq software used for basecalling and using FastQC (v.0.11.2)
Sequenced reads were trimmed for adaptor sequence with the Cutadapt software, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using RNA STAR (Galaxy Version 2.7.8a+galaxy0) with parameters --runThreadN 12 --runMode genomeGenerate \        --genomeDir star_index --genomeFastaFiles ref/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa uncompressed \        --sjdbGTFfile ref/Arabidopsis_thaliana.TAIR10.36.gtf.gz --sjdbOverhang 41
Aligned reads were counted by using featureCounts (Galaxy Version 2.0.1+galaxy1)
DESeq2 (Galaxy Version 2.11.40.6+galaxy2) was used to determine diffentially-expressed genes from count tables
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing count tables produced with featureCounts (Galaxy Version 2.0.1+galaxy1)

organism: Arabidopsis thaliana

source_name: Leaf tissue

growth_protocol: Arabidopsis plants were grown on Promix soil (Premier Tech Inc.; Rivière-Du-Loup, QC, CANADA) for 4 weeks at 21 degrees Celsius, 50-60% relative humidity levels under 12 hours light/dark regime.

extract_protocol:
Infected leaves were removed, flash frozen in liquid nitrogen, and RNA was harvested using QIAzol reagent.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (Cat#E7760S) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: 4-weeks-old Arabidopsis leaves were either infiltrated with MgCl2 (10 mM) or bacterial strains (1 x 10e6 CFU/mL). Samples were harvested 36 hours post-infiltration.

tag: ecotype

tag: infiltration method

value: Syringe-infiltrated

value: leaf

value: Pst DB29


title: ChIPRX_totalRNAPII_shEXOSC10_EtOH_R2

tag: antibody


title: BTF8KCLO-2W

tag: pcrb

tag: er


title: Pst DB29-infiltrated; Rep 2

description:
Leaves were infiltrated with Pst DB29 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 17

tag: tissue


title: 1B_IPSC_Slo1IPSK16

tag: cell type

tag: batch

value: Batch 1

tag: disease status

value: PD


title: ChIPRX_totalRNAPII_shEXOSC10_input_R2

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

tag: exosc10 protein (wild type (wt) or mutant (mut))


title: Pst DB29-infiltrated; Rep 1

description:
Leaves were infiltrated with Pst DB29 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 16

tag: treatment


title: RA2SPMb


title: Pst DC3000 Δhopm1/avre1-infiltrated; Rep 2

description:
Leaves were infiltrated with Pst DC3000 Δhopm1/avre1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 14

value: Pst DC3000 delta-hopm1/avre1


title: Pst DC3000 Δhopm1/avre1-infiltrated; Rep 1

description:
Leaves were infiltrated with Pst DC3000 Δhopm1/avre1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 13


title: Pst DC3000 Δavre1-infiltrated; Rep 3

description:
Leaves were infiltrated with Pst DC3000 Δavre1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 12

value: Pst DC3000 delta-avre1


title: 81E7Z2UF-SUR

tag: cellularity


title: Pst DC3000 Δavre1-infiltrated; Rep 2

description:
Leaves were infiltrated with Pst DC3000 Δavre1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 11


title: ChIPRX_pSer2RNAPII_shEXOSC10_Dox_4-OHT_R2

value: Dox (1 microg/ml)

tag: treatment (dmso or ku-60019)

tag: treatment (dmso or aphidicolin)

tag: label

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, ab5095


title: ChIPRX_pSer2RNAPII_shEXOSC10_Dox_R2


title: Pst DC3000 Δhopm1/avre1-infiltrated; Rep 3

description:
Leaves were infiltrated with Pst DC3000 Δhopm1/avre1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 15

tag: ecotype


title: ChIPRX_pSer2RNAPII_shEXOSC10_4-OHT_R2


title: Pst DC3000 Δhopm1-infiltrated; Rep 2

description:
Leaves were infiltrated with Pst DC3000 Δhopm1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 8

tag: infiltration method

value: Pst DC3000 delta-hopm1


title: Pst DC3000-infiltrated; Rep 3

description:
Leaves were infiltrated with Pst DC3000 wild-type (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 6

value: Pst DC3000 wild-type


title: 04TOUUJH-2W

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: age

tag: pr


title: Pst DC3000 Δhopm1-infiltrated; Rep 1

description:
Leaves were infiltrated with Pst DC3000 Δhopm1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 7

tag: tissue


title: Pst DC3000-infiltrated; Rep 2

description:
Leaves were infiltrated with Pst DC3000 wild-type (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 5


title: Pst DC3000 Δhopm1-infiltrated; Rep 3

description:
Leaves were infiltrated with Pst DC3000 Δhopm1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 9


title: 04TOUUJH-SCR

tag: pcrb

tag: er

value: Negative


title: S82FMZ5S-SUR


title: Pst DC3000-infiltrated; Rep 1

description:
Leaves were infiltrated with Pst DC3000 wild-type (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 4


title: S82FMZ5S-2W


title: EOHJF3NI-SCR


title: SALI_KO_S3

city: Oxford

first: Altar

middle: Mert

last: Munis

state: Oxfordshire

address: L4 Academic, John Radcliffe Hospital

country: United Kingdom

institute: University of Oxford

description:
P200321_SALI_v_H441_in_KO_DE_results.txt
P200321_KO_v_WT_SALI_DE_results.txt

data_processing:
Ilumina NextSeq500 RTA system used for basecalling
Reads were aligned to the human reference genome (GRCh37) using HISAT2 and duplicate reads removed using the Picard ‘MarkDuplicates’ tool.
Reads mapping uniquely to Ensembl-annotated genes were summarized using featureCounts.
Genes with very low expression were excluded based on the following heuristic: to be retained a gene needed to be expressed at the equivalent of 10 reads or more (after normalizing for library size) in at least as many samples as the smallest experimental group considered (in this case, usually four). Multiple testing correction was performed by using edgeR's default Benjamini-Hochburg method for controlling the false discovery rate.
Genome_build: GRCh37
Supplementary_files_format_and_content: normalized full differential gene expression summary for all four groups of samples

source_name: Pulmonary Cell Line

growth_protocol: wild type and SFTPB KO H441 cells were grown in submerged or SALI culture conditions

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to manufacturer's instructions.
cDNA was prepared using the NEBNext poly-A mRNA magnetic isolation module. Multiplexed cDNA library was prepared using the NEBNext Ultra II DNA Prep kit for Illumina according to manufacturer’s instructions.

tag: culture condition

value: SALI

tag: genotype

value: SFTPB KO

tag: cell type

value: Lung adenocarcinoma


title: Mock-infiltrated; Rep 3

description:
Leaves were infiltrated with MgCl2 (10 mM) and harvested 36 hours post-infiltration.
Sample 3


title: SALI_KO_S2


title: Mock-infiltrated; Rep 2

description:
Leaves were infiltrated with MgCl2 (10 mM) and harvested 36 hours post-infiltration.
Sample 2


title: Pst DC3000 Δavre1-infiltrated; Rep 1

description:
Leaves were infiltrated with Pst DC3000 Δavre1 (1x10e6 CFU/ml) and harvested 36 hours post-infiltration.
Sample 10


title: Mock-infiltrated; Rep 1

description:
Leaves were infiltrated with MgCl2 (10 mM) and harvested 36 hours post-infiltration.
Sample 1


title: S82FMZ5S-SCR

description: A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA). Data were log2 transformed and normalized using the housekeeping genes.

value: No

value: Positive


title: m6a_mo3_input

city: Columbus

first: Federica

last: Accornero

state: OH

address: 473 W 12th Ave.

institute: Ohio State University Medical Center

data_processing:
Library strategy: MeRIP-seq
Sequencing alignment, hisat2 v2.2.0.
Read count matrix formation, htseq v2.0.
Peak calling, exomePeak2 v1.2. FDR <0.05 and peak enrichment > 4.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq read counts (.txt).
Supplementary_files_format_and_content: exomePeak2 output (.xlsx).

source_name: mouse plantaris tissue

extract_protocol:
Trizol isolation after sample collection (either total RNA or IP RNA).
m6A samples were constructed using NEB Illumina kit. m6A samples were used for meRIP-seq analysis.
ribo samples were constructed using the DNBseq preparation method (BGI). ribo samples were used for Ribotag-seq analysis.

treatment_protocol: Muscle overload (mo) was attained using bilateral synergistic ablation of the soleus and gastrocnemius.

value: wildtype

value: plantaris

tag: muscle state

value: muscle overload

tag: rna isolation

value: total RNA


title: m6a_mo2_ip

value: m6A IP RNA


title: SALI_KO_S1


title: m6a_mo3_ip


title: ChIPRX_pSer2RNAPII_shEXOSC10_EtOH_R2

tag: treatment (etoh or 4-oht)

value: EtOH

tag: treatment (etoh ordox)

tag: exosc10 protein (wild type (wt) or mutant (mut))

tag: antibody


title: SALI_S6

description:
P200321_SALI_v_H441_in_WT_DE_results.txt
P200321_KO_v_WT_SALI_DE_results.txt

value: wild type


title: SALI_KO_S4


title: SALI_S5


title: KR0O0XTF-2W

tag: cellularity


title: m6a_mo1_ip


title: m6a_mo2_input


title: KR0O0XTF-SUR


title: SALI_S4


title: 04TOUUJH-SUR


title: m6a_base3_ip

value: normal


title: m6a_base3_input


title: m6a_mo1_input


title: KR0O0XTF-SCR


title: m6a_base2_ip


title: LLP4HO7N-SUR


title: LLP4HO7N-2W


title: SALI_S3


title: SALI_S2


title: m6a_base1_ip


title: m6a_base1_input


title: LLP4HO7N-SCR


title: mouse-cerebellum granule cell-KDYthdf2-rep2

city: Shenzhen

first: Lixin

last: Yang

address: 1088 Xueyuan Avenue, Shenzhen

department: brain institute

country: China

institute: Southern Universith of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: Cerebellum

growth_protocol: Dissociated granule cells were cultured in Neurobasal A-medium with B27 supplement , GlutaMAX-1, and Penicillin-Streptomycin.

extract_protocol:
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

treatment_protocol: Cultured granule cells were infected with lentiviral shYthdf2 or shCtrl.

value: mouse-cerebellum granule cell

tag: strain

value: Cerebellum

value: post natal day 8


title: mouse-cerebellum granule cell-KDYthdf2-rep3


title: H441_KO_S5

description:
P200321_SALI_v_H441_in_KO_DE_results.txt
P200321_KO_v_WT_H441_DE_results.txt

value: submerged


title: mouse-cerebellum granule cell-KDYthdf2-rep1


title: mouse-cerebellum granule cell-WT-rep3

value: Wildtype


title: 1NKMP88G-SUR

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)


title: SALI_S1

value: SALI

value: Lung adenocarcinoma


title: mouse-cerebellum granule cell-WT-rep1

tag: age


title: 1NKMP88G-2W

tag: pr


title: H441_KO_S4

value: SFTPB KO


title: mouse-cerebellum granule cell-WT-rep2

tag: tissue


title: ECGTYFA8-SUR

tag: pcrb


title: H441_KO_S3


title: H441_KO_S2


title: 1YV0TJ3P-SUR

tag: er


title: m6a_base2_input

value: wildtype


title: H441_KO_S1

tag: culture condition


title: 1B_NPC_Slo5NP16

value: neural progenitor cells

tag: batch

value: Batch 1

tag: disease status

value: PD


title: H441_S4

description:
P200321_SALI_v_H441_in_WT_DE_results.txt
P200321_KO_v_WT_H441_DE_results.txt

tag: genotype

tag: cell type


title: Lane8_additionalLines

city: Chicago

first: Katherine

last: Rhodes

state: IL

address: 5841 South Maryland Avenue, MC 6092

department: Genetic Medicine

institute: University of Chicago

description:
cell_metadata_additionalLines.txt
cell_counts_additionalLines.mtx

data_processing:
Transcripts were aligned to GRCh38 using CellRanger (Zheng et al. 2017).
Demuxlet (Kang et al. 2018) was used to demultiplex the pooled single cell data, and assign each cell a probability that the cell was a doublet as well as a maximum likelihood donor (cell line) assignment
Cells were filtered to include only singlets called by Demuxlet (Kang et al. 2018), , cells containing between 3%-15% mitochondrial reads, and cells expressing more than 1,000 genes
Genome_build: GRCh38
Supplementary_files_format_and_content: cell_counts.mtx contains a genesxcells matrix with raw UMI counts for each cell (in the MatrixMarket format)
Supplementary_files_format_and_content: genes.tsv contains the gene names corresponding to the counts matrix (row names for cell_counts.mtx)
Supplementary_files_format_and_content: barcodes.tsv contains the barcodes corresponding to the count matrix (column names for cell_counts.mtx)
Supplementary_files_format_and_content: cell_metadata.txt contains metadata fror each cells. Rows are cells, columns are nCount_RNA (total UMI counts for each cells), nFeature_RNA (total genes per cell), individual, CollectionDate_10xLane(collection date and 10x lane number corresponding to a particular library), and Seurat Cluster assignments at resolution 0.15.

source_name: iPSC-derived embryoid bodies

growth_protocol: Feeder-free iPSC cultures were maintained on Matrigel Growth Factor Reduced Matrix with Essential 8 Medium and Penicillin/Streptomycin.

extract_protocol:
We harvested and dissociated EBs 21 days after formation. We collected scRNA-seq data using the 10X Genomics V3.1 kit.
Libraries were generated using the 10X Genomics V3.1 kit. Libraries were sequenced using paired-end 100 base pair sequencing on the NovaSeq 6000.

treatment_protocol: We formed EBs using a modified version of the STEMCELL Aggrewell400 protocol. After 24 hours, we replaced half of the spent media with fresh Aggrewell EB Formation Medium. 48 hours after seeding the Aggrewell plate, we harvested EBs and moved them to an ultra-low attachment 6-well plate in E6 media. We maintained EBs in culture for an additional 19 days, replacing media with fresh E6 every 48 hours.

tag: cell line

tag: 10x lane


title: 1YV0TJ3P-2W

data_processing: Data were normalized using 5 housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0, and SF3A1), and log2 transformed

extract_protocol: At baseline, a section of the formalin-fixed paraffin-embedded (FFPE) breast tissue was examined with haematoxylin and eosin (H&E) staining to confirm the presence of invasive tumor cells and to determine the minimum tumor surface area. For samples obtained at Cycle 2 Day 1, those without invasive tumor cells were also profiled. For RNA purification (High Pure FFPET RNA isolation kit, Roche, Indianapolis, IN, USA), at least 1–5 10 μm FFPE slides were used for each tumor specimen, and macrodissection was performed (when needed) to avoid contamination with normal breast tissues. A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA).


title: Lane7_additionalLines


title: Lane6_additionalLines


title: 1YV0TJ3P-SCR

value: No

value: Positive

value: Negative


title: H441_S3

value: wild type


title: IFP87SCY-SUR


title: Lane4_additionalLines


title: H441_S2


title: Lane3_additionalLines


title: Lane1_additionalLines


title: Lane2_additionalLines


title: HD3

city: Beijing

first: Zhong

last: Cao

state: CHINA

address: Tsinghua University

department: Automation

institute: Tsinghua University

data_processing:
The Cell Rnager software pipeline (version 6.0.0) provided by 10X Genomics was used to process Chromium single cell data. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrices.
Genome_build: GRCh38(version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Peripheral blood mononuclear cell

extract_protocol:
Single cells were suspended in PBS containing 0.04% BSA.
Single-cell RNA-seq libraries were constructed using Single Cell 5’ Library and Gel Bead Kit, Single Cell V(D)J Enrichment Kit, Human T Cell(1000005) and Single Cell V(D)J Enrichment Kit, Human B Cell (1000016). The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

tag: Sex

value: female

tag: disease state

value: Health donors

value: Peripheral blood mononuclear cell


title: IFP87SCY-2W

tag: cellularity


title: IFP87SCY-SCR


title: ECGTYFA8-2W


title: HD1


title: H441_S1

value: submerged


title: HD2


title: ASS-ILD5

value: Patient with ASS-ILD


title: SG.NK.CD49a+#4

city: Boston

first: Liang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Whole Tissue

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 6 Weeks Old

tag: exclusion markers

tag: genetic background

tag: phenotype markers

tag: separation method

value: FACSAria

value: Male


title: Patient12P4

city: Amsterdam

first: Lennart

last: Kester

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: single cell RNA seq data

data_processing:
single cell mRNA sequencing data was processed using STAR in STARsolo mode, reads were aligned to the hg38 reference genome. Raw counts were further analysed using Seurat
Genome_build: hg38
Supplementary_files_format_and_content: csv format, gene expression counts per single cell

source_name: Human breast tumor

extract_protocol:
Following pathological examination, tumor material was kept on ice in DMEM/F12 + GlutaMAX (GIBCO, Invitrogen Life Technologies), 1% HEPES, 1% penicillin-streptomycin from that point onwards. Tumors were mechanically dissociated using sterile scalpels and enzymatically digested with 25 μg/ml DNase I (Roche) and 15 Wünsch units TH Liberase /ml (Roche) diluted in PBS at 37 ⁰C for 35 minutes, followed by mashing through a 70 µm filter (BD Falcon) while adding DMEM/F12 + GlutaMAX (GIBCO, Invitrogen Life Technologies), 1% Hepes, 1% Penicillin-Streptomycin. Tumor cells were blocked in 80% FACS buffer (5 mM EDTA in PBS supplemented with 5% fetal calf serum / 20% serum mix (50/50 normal goat serum (monx10961, Monosan) and FcγII/III receptor blocking serum 2.4G2 (kind gift from L. Boon, Bioceros, The Netherlands)) for 10 minutes on ice before labeling with EpCAM PE (1B7, eBioscience), CD14-FITC (MɸP-9, bdBiosciences) labeled antibodies for 40 minutes on ice. DAPI was added as a cell death marker, and cells were sorted either on a FACS AriaII Special Ordered Research Product (BD Biosciences), on a FACS Jazz (BD biosciences), or on a FACS Fusion (BD biosciences). A broad FSC SSC gate was followed by a gate excluding doublets, after which the DAPI negative cells were selected. These DAPI negative cells were sorted into 384-well plates and further processed for single cell sequencing. To obtain enough cancer cells and macrophages, additionally EpCAM positive and CD14 positive cells were selected and index-sorted into 384-well plates and further processed for single cell sequencing. For 3 out of 10 patients, only EpCAM positive and CD14 positive cells were isolated and sequenced.
Single-cell mRNA sequencing was performed using Sort-seq as described in Muraro et al. (Cell Systems 2016). Briefly, cells were sorted into 384 well plates containing a lysis buffer and barcoded RT primer containing a T7 promoter. Reverse transcripion and second strand synthesis were performed individually for each single cell. Afterwards cells were pooled and IVT was performed.
Libraries were prepped according to the Illumina small RNA protocol. Single-cell libraries were sequenced on an Illumina NextSeq500 with 75bp paired end reads.

tag: molecular subtype

value: Triple negative

tag: t stage

tag: n stage

tag: m stage

tag: neoadjuvant treatment

value: yes

tag: bc set


title: SG.NK.CD49a+#1

tag: age


title: SG.NK.CD49a-#2


title: SG.NK.CD49a+#2


title: SG.NK.CD49a+#3


title: Patient12P3

description: single cell RNA seq data


title: Patient12P1

description: single cell RNA seq data


title: Lane5_additionalLines


title: LO3PCAQD-2W

city: Barcelona

first: Fernando

last: Salvador Gómez

address: Balmes 89, 3º 7

institute: SOLTI

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: LO3PCAQD-SCR


title: SV70_all_TGFb2

city: Suita

first: Nobuhiko

last: Shiraki

state: Osaka

address: 2-2 Yamadaoka,

department: Ophthalmology

institute: Osaka University

data_processing:
Illumina Casava 1.8.2 software was used for base calling.
The sequenced reads (30M reads, single-end 100bp) were mapped to the human reference genome sequence (hg19) using TopHat v2.0.12.
Fragments per kilobase of exons per million mapped fragments (FPKMs) were calculated using Cufflinks v2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM
Supplementary_files_format_and_content: count

source_name: Human: Immortalised human microglia-SV40 cells

growth_protocol: The hiPSC line 201B7 was obtained from the RIKEN Bio Resource Centre. The cells were cultured in StemFit medium on LN511E8-coated (0.5 μg/cm2) dishes. SEAMs were generated as described (Hayashi et al., 2017; Hayashi et al., 2016). The hiPS or hES cells were seeded on LN511E8-coated dishes at a density of 300–600 cells/cm2, after which they were cultured in StemFit medium for 10 days. The culture medium was then changed to differentiation medium (DM; Glasgow modified Eagle’s medium (Life Technologies) supplemented with 10% knockout serum replacement (KSR; Life Technologies), 1 mM sodium pyruvate (Life Technologies), 0.1 mM non-essential amino acids (Life Technologies), 2 mM L-glutamine (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), and 55 μM monothioglycerol (Wako, Osaka, Japan) (Hayashi et al., 2017).   Immortalised human microglia-SV40 cells were purchased from Applied Biological Materials Inc. These had been immortalised by serial passaging and transduction with recombinant lentiviruses carrying SV40 Large T antigen (Applied Biomedical Materials: abm, Richmond, QC, Canada). The cells were grown in Prigrow II media (abm) containing 10% foetal bovine serum (FBS) and 1% penicillin-streptomycin solution (abm) in T25 flasks coated with Applied Cell Extracellular Matrix (abm) and seeded at a density of 35,00040,000 cells/cm2. DMEM-F12 medium was supplemented with 10% FBS in T25 flasks coated with poly-D-lysine (1.3 μg/cm2) (Sigma-Aldrich, MO,6USA).

extract_protocol:
Total RNA was extracted from the cells using a miRNeasy mini kit (Qiagen) according to the manufacturer’s protocol.Full-length cDNA was generated using a SMART-Seq HT kit (TaKaRa Bio, Mountain View, CA, USA) according to the manufacturer’s instructions.
The sequencing library was prepared using a Nextera DNA library preparation kit (Illumina, San Diego, CA, USA) according to SMARTer kit instructions. Sequencing was performed on an Illumina NovaSeq 6000 sequencer (Illumina) in the 100-base single-end mode. Illumina Casava 1.8.2 software was used for base calling. The sequenced reads (30M reads, single-end 100bp) were mapped to the human reference genome sequence (hg19) using TopHat v2.0.12. Fragments per kilobase of exons per million mapped fragments (FPKMs) were calculated using Cufflinks v2.1.1.

treatment_protocol: Samples were obtained from the cells sorted by FACS and cultured for 24 h with stimulating medium for the microglia.

tag: cell line

value: Immortalised human microglia-SV40 cells

tag: treatment


title: ASS-ILD4

tag: Sex

tag: disease state

tag: tissue


title: ASS-ILD1


title: Patient12P2

description: single cell RNA seq data


title: ASS-ILD3


title: Patient11P3

description: single cell RNA seq data


title: LO3PCAQD-SUR

tag: cellularity


title: SV70_all_LPS_IFN

value: LPS and IFNgemma


title: SV70_all_nostress

value: untreated


title: ECGTYFA8-SCR

value: No

value: Positive


title: 1NKMP88G-SCR

value: Negative


title: Y9VFMO0U-SUR


title: Patient11P2

description: single cell RNA seq data

tag: molecular subtype


title: Patient11P1

description: single cell RNA seq data

tag: t stage


title: ASS-ILD2

value: female


title: SEAM_FACs_TGFb1

source_name: hiPS SEAM cells CD11b cells

value: iPS cell line


title: SEAM_FACs_TGFb2


title: ZWZZI8N1-SUR


title: SEAM_FACs_LPS_IFN


title: SEAM_FACs_nostress


title: SEAM_FACs_LPS

value: LPS


title: ZWZZI8N1-2W


title: Case4_PD1_nega_Treg_cells

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

data_processing:
Low quality bases and adapter sequences were removed from raw Fastq read sequences by Trim Galore v 0.6.5. Then, reads mapped to rRNA genes were removed using bowite2 v 2.4.1. The filtered Fastq sequence reads were then aligned to the human genome (hg38) using STAR v 2.7.3a.
Genome_build: hg38
Supplementary_files_format_and_content: The expression level of each gene was calculated from the mapped read counts using Strigtie v2.1.2 and prepDE.py.

source_name: tumor infiltrating lymphocytes

extract_protocol:
PD-1+, PD-1- CD8+ T cells and CD45RA-CD25highCD4+ T cells (eTreg cells) were sorted from three surgically resected NSCLC samples. Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.
cDNA was prepared from the isolated RNA using a SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio). The RNA-seq libraries were prepared using the amplified cDNA and a Nextera XT DNA Sample Preparation Kit (Illumina).
The prepared RNA-seq libraries underwent next-generation sequencing of 100 bp from both ends (paired-end reads) with a Novaseq 6000 platform (Illumina).

tag: histology of cancer

value: NSCLC

tag: cell type

value: PD1-Treg T cells


title: ZWZZI8N1-SCR


title: Case2_PD1_nega_Treg_cells


title: Case3_PD1_nega_Treg_cells


title: SV70_all_LPS


title: Case1_PD1_nega_Treg_cells


title: Patient9P4

description: single cell RNA seq data

value: ER/PR positive

tag: n stage

tag: m stage

tag: neoadjuvant treatment

value: no


title: Patient9P3

description: single cell RNA seq data

tag: bc set


title: 849CO2AJ-SUR

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age


title: Case2_PD1_posi_Treg_cells

value: PD1+Treg T cells


title: Case4_PD1_posi_Treg_cells


title: Case1_PD1_posi_Treg_cells

value: PD1+Treg cells


title: 849CO2AJ-SCR

tag: er

tag: pr


title: Patient10P4

description: single cell RNA seq data

value: yes


title: 21IEZ00P-SUR

value: N/A; no information


title: Case3_PD1_nega_CD8_posi_T_cells

value: PD1-CD8+ T cells


title: Case4_PD1_nega_CD8_posi_T_cells


title: Case2_PD1_nega_CD8_posi_T_cells


title: Patient9P1

description: single cell RNA seq data


title: Case3_PD1_posi_CD8_posi_T_cells

value: PD1+CD8+ T cells


title: Case1_PD1_nega_CD8_posi_T_cells


title: Case4_PD1_posi_CD8_posi_T_cells


title: 21IEZ00P-2W


title: Patient8P4

description: single cell RNA seq data

value: ER positive


title: Case2_PD1_posi_CD8_posi_T_cells


title: Patient8P3

description: single cell RNA seq data


title: Patient9P5

description: single cell RNA seq data


title: XNQVEVQF-2W


title: Case3_PD1_posi_Treg_cells


title: Patient9P2

description: single cell RNA seq data


title: XNQVEVQF-SCR

value: Yes


title: Case1_PD1_posi_CD8_posi_T_cells


title: HT280neg_Single cell

city: San Francisco

first: Jaymin

middle: J

last: Kathiriya

state: CA

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

data_processing:
Reads were aligned to hg19 human genome and quantified using Cell Ranger Single-Cell Software. The matrix outputs were generated with barcodes (cell IDs), genes (gene names).
Genome_build: hg19
Supplementary_files_format_and_content: 10X genomics cellranger output

source_name: Distal lung epithelium

extract_protocol:
Single cells were isolated via flow cytometry based on Epcam and HTII-280 from an unidentified donor lung tissue
Libraries were constructed using the Chromium Single-Cell 3' library kit (10X Genomics)

value: lung


title: Patient7P4

description: single cell RNA seq data


title: BCPNHF1C-SUR


title: 849CO2AJ-2W


title: Patient8P2

description: single cell RNA seq data


title: Patient8P1

description: single cell RNA seq data


title: 21IEZ00P-SCR

value: No

value: Positive

value: Negative


title: Trunc CAR in pCAR_stimulated_replicate4

city: London

first: John

last: Maher

address: Great Maze Pond

institute: King's College London

hyb_protocol: For hybridisation 85ng RNA was used with the CAR-T Characterization Panel (XT-CSO-CART1) at 65C for 23 hours. This was followed by sample processing with the NanoString nCounter® Sprint Profiler (NanoString Technologies, Seattle, WA, USA) following the manufacturer's instructions.

scan_protocol: Sample scanning was performed with the Sprint profiler following the manufacturer's instructions.

data_processing: Raw data (RCC files) were used directly as input for the open source R package, NanoStringNorm for backgorund correction and between-sample normalization.

source_name: Human T-cells expressing 34BB/CTr CAR, 24h stimulated on T47D CSF1R cells

label_protocol: Labelled probes were provided by NanoString.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human blood by density gradient centrifugation, activated with 5μg/mL phytohemagglutinin-L in RPMI supplemented with GlutaMax and 5% human serum for 48h, after which 100U/mL IL-2 was added for a further 24h. The activated T-cells were then transduced with retrovirus encoding  the CAR constructs and a chimeric cytokine receptor which enabled expansion in IL-4. The T-cells were expaned for a further 7 days in the presence of 30 ng/mL IL-4 prior to antigen-specific stimulation.

extract_protocol: Total RNA was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: CAR-T cells were labelled using the CellTrace CFSE Cell Proliferation Kit (ThermoFisher Scientific) according to the manufacturer's protocol and were stimulated on a confluent T47D or T47D CSF1R monolayer. After 24h stimulation, live (DAPI-), CFSE+ T-cells were flow sorted subsequently lysed for RNA isolation.

tag: stimulation

value: T47D CSF1R cells (stimulated)

tag: car type

value: 2nd generation

tag: chimeric co-stimulatory receptor (ccr)

tag: car targeting moiety

tag: ccr targeting moiety

tag: car endodomain

value: none (truncated)

tag: ccr endodomain


title: Trunc CAR in pCAR_stimulated_replicate3


title: Trunc CAR in pCAR_stimulated_replicate1


title: Trunc CAR in pCAR_stimulated_replicate2


title: BCPNHF1C-SCR

tag: cellularity


title: BCPNHF1C-2W


title: Trunc CAR in pCAR_unstimulated_replicate3

source_name: Human T-cells expressing 34BB/CTr CAR, 24h stimulated on T47D cells

value: T47D cells (control)


title: Patient7P2

description: single cell RNA seq data

tag: molecular subtype

value: ER/PR positive

tag: t stage

tag: n stage

value: no


title: Trunc CAR in pCAR_unstimulated_replicate4


title: Patient6P3

description: single cell RNA seq data

value: in situ

tag: m stage

tag: neoadjuvant treatment

tag: bc set


title: Patient6P1

description: single cell RNA seq data


title: Trunc CAR in pCAR_unstimulated_replicate1


title: Patient7P3

description: single cell RNA seq data


title: V3ZJ8AFD-SUR

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age


title: 1G CAR/ Dual CCR_stimulated_replicate3

source_name: Human T-cells expressing 3428BB/CZ CAR, 24h stimulated on T47D CSF1R cells

tag: stimulation

value: 1st generation


title: Trunc CAR in pCAR_unstimulated_replicate2

tag: car type


title: 1G CAR/ Dual CCR_unstimulated_replicate3

source_name: Human T-cells expressing 3428BB/CZ CAR, 24h stimulated on T47D cells

tag: chimeric co-stimulatory receptor (ccr)


title: 1G CAR/ Dual CCR_stimulated_replicate1

tag: car targeting moiety


title: 1G CAR/ Dual CCR_unstimulated_replicate4

tag: ccr targeting moiety


title: 7SWLE1F1-2W

source_name: Breast tumor

value: N/A; no information

tag: er

tag: pr


title: Patient6P2

description: single cell RNA seq data


title: 1G CAR/ Dual CCR_stimulated_replicate4

tag: car endodomain

tag: ccr endodomain


title: 1G CAR/ Dual CCR_unstimulated_replicate1


title: pCAR-M/34_stimulated_replicate2

source_name: Human T-cells expressing p34BB/C CAR, 24h stimulated on T47D CSF1R cells


title: 1G CAR/ Dual CCR_stimulated_replicate2


title: LBN13RDH-SUR

tag: cellularity


title: 7SWLE1F1-SCR


title: THGLGU2M-SUR


title: pCAR-M/34_stimulated_replicate1


title: pCAR-M/34_stimulated_replicate3


title: pCAR-M/34_stimulated_replicate4


title: Patient5P3

description: single cell RNA seq data

tag: molecular subtype

tag: t stage

tag: n stage

value: yes


title: Patient5P2

description: single cell RNA seq data

tag: m stage

tag: neoadjuvant treatment

tag: bc set


title: 1G CAR/ Dual CCR_unstimulated_replicate2


title: THGLGU2M-SCR

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age


title: THGLGU2M-2W


title: Patient4P3

description: single cell RNA seq data


title: pCAR-M/34_unstimulated_replicate3

source_name: Human T-cells expressing p34BB/C CAR, 24h stimulated on T47D cells

tag: stimulation

tag: car type

tag: chimeric co-stimulatory receptor (ccr)


title: Patient5P1

description: single cell RNA seq data


title: LBN13RDH-SCR

tag: er


title: pCAR-M/34_unstimulated_replicate2

tag: car targeting moiety

tag: ccr targeting moiety


title: pCAR-M/34_unstimulated_replicate4

tag: car endodomain

tag: ccr endodomain


title: Y9VFMO0U-2W

tag: cellularity

tag: pr


title: LBN13RDH-2W


title: SP_1314

first: WEN-CHING

last: CHAN

department: Biological Sciences Division

institute: The University of Chicago

description: 1314 side population sorted

data_processing:
Illumina Casava1.7 software used for basecalling.
All RNA-seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations.
Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM (Fragments Per Kilobase Million) tables.
Using 4 as the fold change cutoff, DEGs (Differentially expressed genes) were detected using both Tuxedo suite (FPKM-based method) and featureCounts-DESeq (v1.30.0), edgeR (v3.20.7) (read count-based method) with default configurations.
Genes detected by at least more than one method were collected to create a high-confidence DEG lists.
Genome_build: GRCz10
Supplementary_files_format_and_content: Count tables were generated using featureCount (v1.28.1) based on Ensembl annotation (GRCz10).

organism: Danio rerio

source_name: ALL tumor

extract_protocol:
Tumors were removed, sorted by FACS,and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: ALL


title: nonSP_1314

description: 1314 Non-side population sorted


title: pCAR-M/34_unstimulated_replicate1


title: SP_1279

description: 1279 side population sorted


title: Y9VFMO0U-SCR


title: 3G-M_stimulated_replicate4

source_name: Human T-cells expressing C-3 CAR, 24h stimulated on T47D CSF1R cells

value: 3rd generation


title: Patient4P1

description: single cell RNA seq data

tag: molecular subtype

tag: t stage

tag: n stage

tag: m stage

tag: neoadjuvant treatment


title: nonSP_1279

description: 1279 Non-side population sorted


title: 3G-M_stimulated_replicate3

tag: stimulation


title: nonSP_1404

description: 1404 Non-side population sorted


title: 3G-M_stimulated_replicate2

tag: car type


title: Patient3P2

description: single cell RNA seq data

value: ER positive

tag: bc set


title: 7OLR1T6F-2W

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age

tag: er


title: Patient3P1

description: single cell RNA seq data


title: Patient2P4

description: single cell RNA seq data


title: Patient4P2

description: single cell RNA seq data


title: 3G-M_stimulated_replicate1

tag: chimeric co-stimulatory receptor (ccr)

tag: car targeting moiety

tag: ccr targeting moiety

tag: car endodomain

tag: ccr endodomain


title: 7OLR1T6F-SCR

tag: cellularity

tag: pr


title: SP_1404

description: 1404 side population sorted

tag: strain

tag: tissue


title: Patient2P3

description: single cell RNA seq data

tag: molecular subtype

tag: t stage

tag: n stage

tag: m stage

tag: neoadjuvant treatment


title: Patient2P2L4

description: single cell RNA seq data

tag: bc set


title: 3G-M_unstimulated_replicate3

source_name: Human T-cells expressing C-3 CAR, 24h stimulated on T47D cells

tag: stimulation

tag: car type


title: Patient3P3

description: single cell RNA seq data


title: Patient2P2L2

description: single cell RNA seq data


title: Patient2P2L3

description: single cell RNA seq data


title: 7OLR1T6F-SUR

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age

tag: er


title: 3G-M_unstimulated_replicate2

tag: chimeric co-stimulatory receptor (ccr)

tag: car targeting moiety

tag: ccr targeting moiety

tag: car endodomain

tag: ccr endodomain


title: 3G-M_unstimulated_replicate1


title: TDKUZX35-SUR

tag: cellularity

tag: pr


title: QU6VKUUX-SCR


title: 3G-M_unstimulated_replicate4


title: 7SWLE1F1-SUR


title: 2G-M (41BB)_stimulated_replicate4

source_name: Human T-cells expressing C2BB CAR, 24h stimulated on T47D CSF1R cells


title: Patient2P2L1

description: single cell RNA seq data

tag: molecular subtype

tag: t stage

tag: n stage


title: 2G-M (41BB)_stimulated_replicate1


title: 2G-M (41BB)_stimulated_replicate3


title: Patient1P2L4

description: single cell RNA seq data

value: Triple negative

tag: m stage

tag: neoadjuvant treatment

tag: bc set


title: intestine_mice_I/R_7

city: Dalian

first: Xiaofeng

last: Tian

address: Zhongshan Road NO.467

department: General Surgery

institute: The Second Hospital of Dalian Medical University

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences, the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: The small intestine tissue, ischemia/reperfusion, 4h

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: The fresh intestinal tissue was immersed in 4% paraformaldehyde.

extract_protocol: The total RNA from intestinal tissue was extracted by TRIzol reagent.

tag: tissue

value: small intestine

tag: treatment

value: ischemia/reperfusion

tag: strain background


title: intestine_mice_I/R_9

tag: age


title: TDKUZX35-2W

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er


title: QU6VKUUX-SUR


title: 2G-M (41BB)_stimulated_replicate2

tag: stimulation

tag: car type

tag: chimeric co-stimulatory receptor (ccr)

value: No

tag: car targeting moiety

tag: ccr targeting moiety

tag: car endodomain


title: TDKUZX35-SCR

tag: cellularity

value: Yes

value: Positive

tag: pr

value: Negative


title: HNKE30J8-2W


title: Patient1P2L2

description: single cell RNA seq data

source_name: Human breast tumor

tag: molecular subtype

tag: t stage

tag: n stage

tag: m stage

tag: neoadjuvant treatment


title: QU6VKUUX-2W

tag: age


title: ARH77 Btz replicate 2

city: Stanford

first: Ian

middle: Daniel

last: Ferguson

address: 265 Campus Dr

department: Cancer Biology PhD program

institute: Stanford University

data_processing:
HISAT v2.0.4
Bowtie v2.2.5
RSEM v1.2.12
Supplementary_files_format_and_content: FPKM (Fragments Per Kilobase of transcript per Million) values for Samples 1-20 with gene names, NCBI Reference Sequence IDs, Entrez Gene IDs

source_name: ARH77 B-lymphoblastoid cell line

growth_protocol: All cells were grown in RPMI-1640 medium supplemented with 10% FBS, PenStrep, and 2mM glutamine. Proteasome-inhibitor resistant cell lines were grown in 90nM Bortezomib or 90nM Carfilzomib.

extract_protocol:
RNA extraction from flash frozen cell pellets (5e6 cells) was peformed by BGI (Beijing Genomics Institute)
Libraries were constructed by BGI.
BGISEQ-500 platform, RNA QC done with Agilent 2100 Bio analyzer and Agilent RNA 6000 Nano kit

tag: cell type

value: B-lymphoblastoid cell line

tag: cell line


title: intestine_mice_sham_2

source_name: The small intestine tissue, sham

tag: tissue

tag: treatment

value: sham

tag: strain background


title: ARH77 WT replicate 1

treatment_protocol: Proteasome-inhibitor resistant cell lines were grown in 90nM Bortezomib or 90nM Carfilzomib.


title: Patient1P2L3

description: single cell RNA seq data

tag: bc set


title: intestine_mice_I/R_6


title: ARH77 Btz replicate 1


title: intestine_mice_sham_3


title: ARH77 WT replicate 2


title: 2G-M (41BB)_unstimulated_replicate4

source_name: Human T-cells expressing C2BB CAR, 24h stimulated on T47D cells

tag: stimulation

value: T47D cells (control)

tag: car type

value: 2nd generation

tag: chimeric co-stimulatory receptor (ccr)

tag: car targeting moiety

tag: ccr endodomain


title: Patient1P1L4

description: single cell RNA seq data

tag: molecular subtype


title: HNKE30J8-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: 2G-M (41BB)_unstimulated_replicate2

tag: ccr targeting moiety

tag: car endodomain


title: 2G-M (41BB)_unstimulated_replicate3


title: PCF653CE-2W

tag: age


title: PCF653CE-SUR


title: RPMI Btz replicate 2

source_name: RPMI myeloma cell line

tag: cell type

value: multiple myeloma cell line

tag: cell line

value: RPMI-BtzR


title: Patient1P1L2

description: single cell RNA seq data

tag: t stage

tag: n stage

tag: m stage

tag: neoadjuvant treatment

value: yes

tag: bc set


title: RPMI WT replicate 2

value: RPMI-WT


title: Patient1P2L1

description: single cell RNA seq data


title: Patient1P1L3

description: single cell RNA seq data


title: Patient1P1L1

description: single cell RNA seq data


title: K07G8R7C-SUR

value: N/A; no information


title: PCF653CE-SCR


title: RPMI WT replicate 1


title: 2G-M (41BB)_unstimulated_replicate1

tag: stimulation

tag: car type

tag: chimeric co-stimulatory receptor (ccr)

tag: car targeting moiety

tag: ccr endodomain


title: 2G-M (CD28)_stimulated_replicate3

source_name: Human T-cells expressing C-2 CAR, 24h stimulated on T47D CSF1R cells

value: T47D CSF1R cells (stimulated)


title: 2G-M (CD28)_stimulated_replicate4


title: K07G8R7C-2W

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er


title: L363 Cfz replicate 2

source_name: L363 myeloma cell line


title: Adult chondrocytes

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Raw sequencing reads were processed using Partek Flow Analysis Software (build version 10.0.21.0210). Briefly, raw reads were checked for their quality, trimmed and reads with an average base quality score per position>30 were considered for alignment. Trimmed reads were aligned to the human genome version hg38-Gencode Genes- release 30 using STAR -2.6.1d with default parameters. Reads with alignment percentage >75% were deduplicated based on their unique molecular identifiers (UMIs). Reads mapping to the same chromosomal location with duplicate UMIs were removed. Thereafter ‘Knee’ plot was constructed using the cumulative fraction of reads/UMIs for all barcodes. Barcodes below the cut-off defined by the location of the knee were assigned as true cell barcodes and quantified. Further noise filtration was done by removing cells having >3% mitochondrial counts and total read counts >24,000. Genes not expressed in any cell were also removed as an additional clean-up step. Cleaned-up reads were normalized using counts per million (CPM) method followed by log-transformation generating count matrices for each sample. Samples were batch-corrected on the basis of expressed genes and mitochondrial reads percent. Count matrices were used to visualize and explore the samples in further details by generating tSNE plots, a non-linear dimensional reduction technique. This algorithm learns the underlying manifold of the data and places similar cells together in a low-dimensional space.
Genome_build: hg38-Gencode Genes- release 30
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows

source_name: Chondrocytes from 19years old

extract_protocol:
Single cell samples were prepared using Single Cell 3/ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics) according to the manufacturer’s protocol. Briefly samples were FACS sorted using DAPI to select live cells followed by resuspension in 0.04% BSA-PBS. Nearly 1200cells/µl were added to each well of the chip with a target cell recovery estimate of 8000 cells. Thereafter Gel bead-in Emulsions (GEMs) were generated using GemCode Single-Cell Instrument. GEMs were reverse transcribed, droplets were broken and single stranded cDNA was isolated. cDNAs were cleaned up with DynaBeads and amplified. Finally, cDNAs were ligated with adapters, post-ligation products were amplified, cleaned-up with SPRIselect and purified libraries were sequenced on NextSeq500.
Single Cell 3/ Library & Gel Bead Kit v2

value: chondrocytes

tag: age

value: 19 years old


title: Juvenile chondrocytes

source_name: Chondrocytes from 5years old

tag: cell type

value: 5 years old


title: RPMI Btz replicate 1

tag: cell line


title: K07G8R7C-SCR

source_name: Breast tumor

value: No

tag: pr


title: L363 Cfz replicate 1


title: NBPFW8WC-SUR


title: 2G-M (CD28)_stimulated_replicate2

tag: ccr targeting moiety

tag: car endodomain


title: Embryonic chondroprogenitor

source_name: Chondrocytes from 7weeks old fetus

value: 7 weeks old fetus


title: Fetal chondrocytes

source_name: Chondrocytes from 17weeks old fetus

value: 17 weeks old fetus


title: NBPFW8WC-2W


title: hBM-MSC-M

source_name: Human bone marrow derived mesenchymal stem cells on membrane

value: Human bone marrow


title: NBPFW8WC-SCR

value: Positive

value: Negative


title: L363 WT replicate 2


title: L363 Btz replicate 1


title: hESDC-M2

source_name: Embryonic stem-cell derived chondrocyte on membrane

value: Embryonic stem cells


title: L363 WT replicate 1


title: V3ZJ8AFD-2W


title: hESDC-M1


title: 2G-M (CD28)_unstimulated_replicate3

source_name: Human T-cells expressing C-2 CAR, 24h stimulated on T47D cells

value: T47D cells (control)

value: 2nd generation


title: 2G-M (CD28)_unstimulated_replicate2


title: 2G-M (CD28)_unstimulated_replicate4


title: QKGAPYPL-SUR


title: 2G-M (CD28)_unstimulated_replicate1


title: 2G-M (CD28)_stimulated_replicate1


title: ESI-017

source_name: Embryonic stem cell, ESI-017 line


title: AMO1 Cfz replicate 1

source_name: AMO1 myeloma cell line

value: multiple myeloma cell line


title: L363 Btz replicate 2


title: ChIPRX_totalRNAPII_shEXOSC10_input

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

institute: University of Wuerzburg

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.2.7. and normalized to the sample with the spike in control (mm10) except for MYCN ChIPseq, which was read normalized
For 4sU-seq, reads were mapped to hg19 with  Bowtie2, reads mapping to rRNA,exons and blacklist regions were removed, and then normalized based on read depth, except for no chase 4sUseq, which was normalized to spike in control (mm10)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

source_name: SH-EP-MYCNER shEXOSC10

extract_protocol:
Cells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

tag: treatment (etoh or 4-oht)

tag: treatment (etoh or dox)

tag: exosc10 protein (wild type (wt) or mutant (mut))

tag: treatment (dmso or ku-60019)

tag: label

tag: antibody


title: 5L05HHLV-SUR


title: 5L05HHLV-2W


title: V3ZJ8AFD-SCR


title: ChIPRX_totalRNAPII_shEXOSC10_Dox_4-OHT

value: Dox (1 µg/ml)

value: Pol II antibody (A-10), Santa Cruz Biotechnology, sc-17798


title: 5L05HHLV-SCR


title: AMO1 Btz replicate 1


title: AMO1 WT replicate 2


title: HNKE30J8-SUR

value: N/A; no information


title: AMO1 Cfz replicate 2


title: AMO1 WT replicate 1


title: JUNBMHG7-SUR


title: ChIPRX_totalRNAPII_shEXOSC10_EtOH

value: EtOH


title: ChIPRX_totalRNAPII_shEXOSC10_Dox


title: JUNBMHG7-2W


title: ChIPRX_totalRNAPII_EXOSC10wt-mut_input

source_name: SH-EP-MYCNER


title: AMO1 Btz replicate 2


title: ChIPRX_totalRNAPII_EXOSC10wt_4-OHT

value: wild-type EXOSC10


title: JUNBMHG7-SCR


title: ChIPRX_totalRNAPII_EXOSC10wt_EtOH


title: 9RQPT10U-SUR


title: intestine_mice_sham_1

source_name: The small intestine tissue, sham

tag: tissue

value: small intestine

tag: treatment

value: sham

tag: strain background


title: ChIPRX_totalRNAPII_shEXOSC10_4-OHT


title: 9RQPT10U-2W

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: ChIPRX_totalRNAPII_EXOSC10mut_4-OHT

value: mutant EXOSC10


title: screen2_Dox_4-OHT_rep3

data_processing:
Following sequencing, base calling was done with Illumina’s FASTQ Generation software v2.19, high quality PF-clusters (according to the CASAVA filter) were selected for further analyses. The overall sequencing quality was determined with the software FastQC.
For shRNA screen analysis, fastq files for screen 1 and screen 2 were separately mapped to a custom generated reference database containing the guide-stem sequences of all shRNA sequences that were used in the shRNA screen. Mapping was done using Bowtie v1.1.2 not allowing any mismatches.
Reads per reference database entry (= unique shRNA sequences) were counted. Rawcounts for all replicates and conditions were combined in a count-table, separately for screen1 and screen2. Size-normalization of all samples was done based on the sample with the smallest overall count-sum in each screening dataset.
Averages were calculated for the size-normalized counts of all replicates per condition. Based on these average-values, fold changes (FCs) and log2FCs were calculated to determine enrichment or depletion of individual shRNAs between different conditions. Additinaly, the median of the effect-strengths (log2FC) of all five shRNAs per target gene was determined.
Supplementary_files_format_and_content: For both screens, a count matrix was generated that contains an identifyer (unique for each shRNA-sequence used in the sceen) and the normalized counts for all represented shRNAs in each screened condition.

growth_protocol: SH-EP-MYCNER cells stably expressing the Dox-inducible shRNA library were grown in RPMI-1640 (Thermo Fisher Scientific), supplemented with 10% fetal calf serum (Capricorn Scientific) and 1% penicillin/streptomycin (Sigma Aldrich).

extract_protocol:
Genomic DNA was extracted using a Phenol-Chloroform extraction preceded by shearing of DNA and followed by an ethanol based purification of the DNA.
To retrieve shRNA sequences, custom PCR-primers were used that specifically bind to pLT3GEPIR vector sequences flanking the guide-stem of the shRNA hairpin sequence. A PCR was done with the genomic DNA as template to amplify the required sequences. PCR products were gel-purified and in a subsequent PCR the index-sequences for multiplexed NGsequencing were added using the primers of the Kit NEBNext Multiplex Oligos for Illumina. Finally libraries were quantified and the size was determinded using the Fragment Analyzer (Thermo Fisher Scientific).
shRNA screen

treatment_protocol: Following 96 h puromycin selection, the cells were treated with Dox and/or 4-OHT continuously for 10 population doublings.

tag: shRNA

value: custom shRNA library pool


title: 9RQPT10U-SCR

value: No

tag: age

tag: er


title: AKQ9V8LR-2W

tag: pr


title: ChIPRX_totalRNAPII_EXOSC10mut_EtOH


title: AKQ9V8LR-SUR


title: IDO1-O/E U87 IDO1-siRNA Expt 3 Duplicate 2

first: Matthew

middle: J.

last: Schipma

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: RNA expression value derived from Transcriptome Analysis Console software

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

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

data_processing: Data analysis was performed using the Affymetrix software, Transcriptome Analysis Console (TAC) version 4.0

label: biotin

source_name: human glioblastoma

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

growth_protocol: U87 cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 100 units/ml penicillin as well as 100 ug/ml strepmycin. The IDO1-O/E U87 cells were cultured using the same medium with additional puromycin (1ug/ml) to maintain IDO1 overexpression. Both cell lines are cultured at 37 oC with 5% CO2.

extract_protocol: After the incubation, cells were lysed using RNA Lysis Buffer from the PureLink RNA Mini Kit (Thermo Fisher Scientific, catalog# 12183020)

treatment_protocol: Cells were transfected with 20 nM siRNA using either Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific, catalog# 13778030) or jetPRIME siRNA transfection reagent (Polyplus-transfection) according to the product manual, followed by 100 ng/ml human IFNg treatment (Shenandoah Biotechnology, SKU# 100-77-100ug).

value: brain

tag: Sex

value: male


title: IDO1-O/E U87 IDO1-siRNA Expt 3 Duplicate 1


title: CEAE51OS-SUR


title: IDO1-O/E U87 NT Expt 3 Duplicate 2


title: IDO1-O/E U87 NT Expt 3 Duplicate 1


title: AKQ9V8LR-SCR

value: Positive

value: Negative


title: U87 IFNg + IDO1-siRNA Expt 3 Duplicate 1


title: screen2_Dox_4-OHT_rep1

tag: treatment (etoh or 4-oht)


title: U87 IFNg + IDO1-siRNA Expt 3 Duplicate 2


title: CEAE51OS-2W


title: Patient7P1

description: single cell RNA seq data

source_name: Human breast tumor

tag: molecular subtype

value: ER/PR positive

tag: t stage

tag: n stage

tag: m stage

tag: neoadjuvant treatment

value: no

tag: bc set


title: screen2_Dox_rep2

tag: treatment (etoh or dox)


title: CEAE51OS-SCR


title: U87 IDO1-siRNA Expt 3 Duplicate 2

tag: tissue


title: screen2_Dox_rep1


title: screen2_Dox_4-OHT_rep2


title: U87 IDO1-siRNA Expt 3 Duplicate 1


title: 204094670179_R02C01

first: Olivia

last: Okereke

state: MASSACHUSETTS

address: One bowdoin square, room no. 745

institute: Massachusetts General Hospital

description: Additional sample characteristics of  baseline and follow-up (values: 1=yes, 0=No) were added to reflect baseline sample and 2-year follow-up sample respectively.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadArray technology (Methyl850K chip) using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN Reader using standard recommended Illumina scanner setting

data_processing: Minfi bioconductor package

label: Cy5 and Cy70

source_name: blood

extract_protocol: Genomic DNA was extracted from peripheral blood leukocytes (buffy-coat cryotubes had been stored in the vapor phase of liquid nitrogen freezers at ≤−130°C for later use) using the QIAamp® DNA Blood Mini Kit (Qiagen Inc., Valencia, CA), and PicoGreen DNA quantitation was performed using a Molecular Devices 96-well spectrophotometer.

value: peripheral blood leucocytes

tag: gender

tag: disease status

value: Control

tag: race /ethnicity

value: Black

tag: baseline

tag: follow-up


title: 204094670179_R06C01

label: Cy5 and Cy74

value: Case

tag: age

value: Non-Hispanic white


title: BOD95CFL-2W

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: screen2_T0_rep3

tag: treatment (etoh or 4-oht)

tag: shRNA


title: screen2_Dox_rep3

value: EtOH

value: Dox (1 µg/ml)


title: U87 IFNg Expt 3 Duplicatet 1

tag: Sex


title: U87 IFNg Expt 3 Duplicatet 2


title: U87 NT Expt 3 Duplicate 1


title: 204094670179_R03C01

label: Cy5 and Cy71

value: female


title: screen2_T0_rep2

value: custom shRNA library pool


title: 204094670179_R01C01

label: Cy5 and Cy69


title: screen2_T0_rep1


title: IDO1-O/E U87 IDO1-siRNA Expt 2 Duplicate 2


title: 204094670093_R08C01

label: Cy5 and Cy68


title: U87 NT Expt 3 Duplicate 2


title: BOD95CFL-SCR

value: No


title: MVV2GLYR-2W


title: screen2_4-OHT_rep2


title: 204094670093_R04C01

label: Cy5 and Cy64


title: YHZKQK6A-SUR


title: screen2_4-OHT_rep3


title: 204088190012_R07C01

label: Cy5 and Cy59


title: 204094670179_R05C01

label: Cy5 and Cy73


title: 204094670093_R03C01

label: Cy5 and Cy63


title: 204094670093_R07C01

label: Cy5 and Cy67


title: MVV2GLYR-SCR


title: YHZKQK6A-SCR


title: YHZKQK6A-2W


title: screen2_4-OHT_rep1


title: 204088190012_R06C01

label: Cy5 and Cy58


title: 204094670093_R01C01

label: Cy5 and Cy61


title: 204088190012_R08C01

label: Cy5 and Cy60


title: IDO1-O/E U87 IDO1-siRNA Expt 2 Duplicate 1

value: brain


title: OIRUCBMN-SUR


title: 204094670179_R04C01

label: Cy5 and Cy72


title: screen2_EtOH_rep1


title: IDO1-O/E U87 NT Expt 2 Duplicate 1

value: male


title: screen2_EtOH_rep2


title: IDO1-O/E U87 NT Expt 2 Duplicate 2


title: OG2ME6GY-SUR

label: NOT PROVIDED


title: OIRUCBMN-2W


title: U87 IFNg + IDO1-siRNA Expt 2 Duplicate 2


title: 204094670093_R02C01

label: Cy5 and Cy62


title: 204088190012_R03C01

label: Cy5 and Cy55


title: screen2_EtOH_rep3


title: screen1_Dox_4-OHT_rep2


title: OIRUCBMN-SCR

value: Positive


title: U87 IDO1-siRNA Expt 2 Duplicate 2

label: biotin


title: screen1_Dox_4-OHT_rep3


title: U87 IDO1-siRNA Expt 2 Duplicate 1


title: 204088190012_R05C01

label: Cy5 and Cy57


title: OG2ME6GY-2W


title: screen1_Dox_4-OHT_rep1


title: U87 IFNg + IDO1-siRNA Expt 2 Duplicate 1


title: 204088150165_R06C01

label: Cy5 and Cy50


title: screen1_Dox_rep2


title: screen1_Dox_rep1


title: MXOGTQ7A-2W


title: MXOGTQ7A-SUR


title: MXOGTQ7A-SCR

value: Negative


title: U87 IFNg Expt 2 Duplicatet 1


title: 204088190012_R04C01

label: Cy5 and Cy56


title: screen1_Dox_rep3


title: 204088190012_R01C01

label: Cy5 and Cy53


title: U87 IFNg Expt 2 Duplicatet 2


title: screen1_T0_rep3


title: IDO1-O/E U87 IDO1-siRNA Expt 1 Duplicate 2


title: GRTIPRG8-SCR


title: 204088190012_R02C01

label: Cy5 and Cy54


title: screen1_T0_rep2


title: 204088150165_R04C01

label: Cy5 and Cy48


title: U87 NT Expt 2 Duplicate 1


title: screen1_T0_rep1


title: U87 NT Expt 2 Duplicate 2


title: IDO1-O/E U87 IDO1-siRNA Expt 1 Duplicate 1


title: QKGAPYPL-2W


title: IDO1-O/E U87 NT Expt 1 Duplicate 2


title: 204088150165_R05C01

label: Cy5 and Cy49


title: 204088150164_R08C01

label: Cy5 and Cy44


title: 204088150165_R02C01

label: Cy5 and Cy46


title: OG2ME6GY-SCR


title: 204088150165_R03C01

label: Cy5 and Cy47


title: IDO1-O/E U87 NT Expt 1 Duplicate 1


title: U87 IFNg + IDO1-siRNA Expt 1 Duplicate 1


title: JKET02IV-SUR


title: QKGAPYPL-SCR


title: 204088150165_R01C01

label: Cy5 and Cy45


title: screen1_4-OHT_rep2


title: U87 IFNg + IDO1-siRNA Expt 1 Duplicate 2


title: screen1_4-OHT_rep1


title: JKET02IV-2W


title: screen1_4-OHT_rep3


title: 204088150164_R07C01

label: Cy5 and Cy43


title: screen1_EtOH_rep3


title: screen1_EtOH_rep2


title: screen1_EtOH_rep1


title: U87 IDO1-siRNA Expt 1 Duplicate 2


title: 43BNQ9CW-SUR


title: JKET02IV-SCR


title: 204088150164_R05C01

label: Cy5 and Cy41


title: U87 IDO1-siRNA Expt 1 Duplicate 1


title: 43BNQ9CW-SCR

label: NOT PROVIDED