title: S140_week_4-TB Subjects-140805_I284_FCC4MJAACXX_L4_RHUMjlxTAAKVRAAPEI-202


title: S140_week_24-TB Subjects-140805_I284_FCC4MJAACXX_L4_RHUMjlxTAAKWRAAPEI-203

status: Public on Nov 01 2017

type: SRA

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

library_source: transcriptomic

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome STAR_2.3.1d
Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome
Gene counts were calculated by usingHTSEQ to map the read counts to the gene names
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome (number of reads mapped to the splice junctions in all samples)
Supplementary_files_format_and_content: tab delimited file including the raw gene counts for all the detected genes in the genome

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: tissue

value: blood

tag: subject

tag: disease state

value: TB Subjects

tag: treatmentresult

value: Definite Cure

tag: time

tag: timetonegativity

tag: mgit

tag: xpert

tag: tgrv


title: S140_week_24-TB Subjects-140805_I284_FCC4MJAACXX_L6_RHUMjlxTAAKWRAAPEI-203


title: S140_DX-TB Subjects-140805_I284_FCC4MJAACXX_L2_RHUMjlxTAAKTRAAPEI-227

value: DX


title: S140_day_7-TB Subjects-140805_I284_FCC4MJAACXX_L3_RHUMjlxTAAKURAAPEI-201


title: S13_week_4-TB Subjects-140726_I232_FCC4NA4ACXX_L2_RHUMjlxTAAATRAAPEI-204


title: S141_week_4-TB Subjects-140805_I284_FCC4MJAACXX_L8_RHUMjlxTAAKZRAAPEI-206


title: S13_DX-TB Subjects-140726_I232_FCC4NA4ACXX_L3_RHUMjlxTAAARRAAPEI-202


title: S13_week_4-TB Subjects-140724_I269_FCC4N24ACXX_L6_RHUMjlxTAAATRAAPEI-204


title: S13_day_7-TB Subjects-140726_I232_FCC4NA4ACXX_L2_RHUMjlxTAAASRAAPEI-203


title: S13_day_7-TB Subjects-140724_I269_FCC4N24ACXX_L6_RHUMjlxTAAASRAAPEI-203


title: S13_DX-TB Subjects-140724_I269_FCC4N24ACXX_L7_RHUMjlxTAAARRAAPEI-202


title: S139_week_4-TB Subjects-140804_I270_FCC4RL0ACXX_L6_RHUMjlxTAAKRRAAPEI-223


title: S13_week_24-TB Subjects-140726_I232_FCC4NA4ACXX_L2_RHUMjlxTAAAURAAPEI-205


title: S139_week_24-TB Subjects-140805_I284_FCC4MJAACXX_L2_RHUMjlxTAAKSRAAPEI-225


title: S13_week_24-TB Subjects-140724_I269_FCC4N24ACXX_L6_RHUMjlxTAAAURAAPEI-205


title: S139_week_4-TB Subjects-140804_I270_FCC4RL0ACXX_L7_RHUMjlxTAAKRRAAPEI-223


title: S139_week_24-TB Subjects-140805_I284_FCC4MJAACXX_L3_RHUMjlxTAAKSRAAPEI-225


title: S138_week_24-TB Subjects-140804_I270_FCC4RL0ACXX_L7_RHUMjlxTAAKORAAPEI-220


title: S139_day_7-TB Subjects-140804_I270_FCC4RL0ACXX_L7_RHUMjlxTAAKQRAAPEI-222


title: S138_week_4-TB Subjects-140804_I270_FCC4RL0ACXX_L4_RHUMjlxTAAKNRAAPEI-219


title: S139_day_7-TB Subjects-140804_I270_FCC4RL0ACXX_L6_RHUMjlxTAAKQRAAPEI-222


title: S138_week_4-TB Subjects-140804_I270_FCC4RL0ACXX_L3_RHUMjlxTAAKNRAAPEI-219


title: S138_DX-TB Subjects-140804_I270_FCC4RL0ACXX_L3_RHUMjlxTAAKLRAAPEI-216


title: S140_day_7-TB Subjects-140805_I284_FCC4MJAACXX_L2_RHUMjlxTAAKURAAPEI-201


title: S138_DX-TB Subjects-140804_I270_FCC4RL0ACXX_L4_RHUMjlxTAAKLRAAPEI-216


title: S138_week_24-TB Subjects-140804_I270_FCC4RL0ACXX_L6_RHUMjlxTAAKORAAPEI-220


title: S140_DX-TB Subjects-140805_I284_FCC4MJAACXX_L3_RHUMjlxTAAKTRAAPEI-227


title: S138_day_7-TB Subjects-140804_I270_FCC4RL0ACXX_L4_RHUMjlxTAAKMRAAPEI-218


title: S137_week_4-TB Subjects-140804_I270_FCC4RL0ACXX_L1_RHUMjlxTAAKJRAAPEI-214


title: S137_week_4-TB Subjects-140804_I270_FCC4RL0ACXX_L2_RHUMjlxTAAKJRAAPEI-214


title: S137_week_24-TB Subjects-140804_I270_FCC4RL0ACXX_L3_RHUMjlxTAAKKRAAPEI-215


title: S136_week_24-TB Subjects-140804_I270_FCC4RL0ACXX_L1_RHUMjlxTAAKGRAAPEI-211

value: Probable Cure


title: S136_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L7_RHUMjlxTAAKFRAAPEI-210


title: S136_week_24-TB Subjects-140804_I270_FCC4RL0ACXX_L2_RHUMjlxTAAKGRAAPEI-211


title: S137_day_7-TB Subjects-140804_I270_FCC4RL0ACXX_L1_RHUMjlxTAAKIRAAPEI-213


title: S139_DX-TB Subjects-140804_I270_FCC4RL0ACXX_L7_RHUMjlxTAAKPRAAPEI-221


title: S137_DX-TB Subjects-140804_I270_FCC4RL0ACXX_L2_RHUMjlxTAAKHRAAPEI-212


title: S136_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L8_RHUMjlxTAAKFRAAPEI-210


title: S135_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L8_RHUMjlxTAAKCRAAPEI-207


title: S139_DX-TB Subjects-140804_I270_FCC4RL0ACXX_L6_RHUMjlxTAAKPRAAPEI-221


title: S137_day_7-TB Subjects-140804_I270_FCC4RL0ACXX_L2_RHUMjlxTAAKIRAAPEI-213


title: S136_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L7_RHUMjlxTAAKERAAPEI-209


title: S135_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L7_RHUMjlxTAAKCRAAPEI-207


title: S136_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L8_RHUMjlxTAAKERAAPEI-209


title: S135_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L8_RHUMjlxTAAKDRAAPEI-208


title: S135_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L7_RHUMjlxTAAKDRAAPEI-208


title: S135_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L6_RHUMjlxTAAKARAAPEI-205


title: S135_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L6_RHUMjlxTAAKBRAAPEI-206


title: S135_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L4_RHUMjlxTAAKBRAAPEI-206


title: S134_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L6_RHUMjlxTAAJZRAAPEI-204


title: S134_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L4_RHUMjlxTAAJYRAAPEI-203


title: S138_day_7-TB Subjects-140804_I270_FCC4RL0ACXX_L3_RHUMjlxTAAKMRAAPEI-218


title: S134_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L4_RHUMjlxTAAJZRAAPEI-204


title: S137_week_24-TB Subjects-140804_I270_FCC4RL0ACXX_L4_RHUMjlxTAAKKRAAPEI-215


title: S137_DX-TB Subjects-140804_I270_FCC4RL0ACXX_L1_RHUMjlxTAAKHRAAPEI-212


title: S133_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L3_RHUMjlxTAAJWRAAPEI-201


title: S133_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L2_RHUMjlxTAAJXRAAPEI-202


title: S133_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L2_RHUMjlxTAAJWRAAPEI-201


title: S133_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L3_RHUMjlxTAAJXRAAPEI-202


title: S133_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L3_RHUMjlxTAAJURAAPEI-225


title: S133_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L2_RHUMjlxTAAJURAAPEI-225


title: S132_week_4-TB Subjects-140731_I269_FCC4RC2ACXX_L1_RHUMjlxTAAJSRAAPEI-222


title: S133_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L3_RHUMjlxTAAJVRAAPEI-227


title: S132_week_24-TB Subjects-140731_I269_FCC4RC2ACXX_L1_RHUMjlxTAAJTRAAPEI-223


title: S132_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L1_RHUMjlxTAAJQRAAPEI-220


title: S132_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L1_RHUMjlxTAAJRRAAPEI-221


title: S132_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L8_RHUMjlxTAAJSRAAPEI-222


title: S132_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L8_RHUMjlxTAAJRRAAPEI-221


title: S133_day_7-TB Subjects-140731_I269_FCC4RC2ACXX_L2_RHUMjlxTAAJVRAAPEI-227


title: S132_DX-TB Subjects-140731_I269_FCC4N1JACXX_L8_RHUMjlxTAAJQRAAPEI-220


title: S135_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L4_RHUMjlxTAAKARAAPEI-205


title: S132_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L8_RHUMjlxTAAJTRAAPEI-223


title: S131_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L6_RHUMjlxTAAJORAAPEI-218


title: S131_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L7_RHUMjlxTAAJPRAAPEI-219


title: S131_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L7_RHUMjlxTAAJORAAPEI-218


title: S131_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L6_RHUMjlxTAAJPRAAPEI-219


title: S134_DX-TB Subjects-140731_I269_FCC4RC2ACXX_L6_RHUMjlxTAAJYRAAPEI-203


title: S131_DX-TB Subjects-140731_I269_FCC4N1JACXX_L7_RHUMjlxTAAJMRAAPEI-215


title: S131_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L7_RHUMjlxTAAJNRAAPEI-216


title: S130_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L3_RHUMjlxTAAJKRAAPEI-213


title: S130_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L4_RHUMjlxTAAJKRAAPEI-213


title: S131_DX-TB Subjects-140731_I269_FCC4N1JACXX_L6_RHUMjlxTAAJMRAAPEI-215


title: S130_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L4_RHUMjlxTAAJLRAAPEI-214


title: S130_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L3_RHUMjlxTAAJLRAAPEI-214


title: S131_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L6_RHUMjlxTAAJNRAAPEI-216


title: S130_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L4_RHUMjlxTAAJJRAAPEI-212


title: S130_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L3_RHUMjlxTAAJJRAAPEI-212


title: S129_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L2_RHUMjlxTAAJHRAAPEI-210


title: S129_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L4_RHUMjlxTAAJIRAAPEI-211


title: S129_DX-TB Subjects-140731_I269_FCC4N1JACXX_L2_RHUMjlxTAAJFRAAPEI-208


title: S129_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L3_RHUMjlxTAAJIRAAPEI-211


title: S129_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L1_RHUMjlxTAAJGRAAPEI-209


title: S129_day_7-TB Subjects-140731_I269_FCC4N1JACXX_L2_RHUMjlxTAAJGRAAPEI-209


title: S129_DX-TB Subjects-140731_I269_FCC4N1JACXX_L1_RHUMjlxTAAJFRAAPEI-208


title: S128_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L2_RHUMjlxTAAJERAAPEI-207

value: Possible Cure


title: S128_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L8_RHUMjlxTAAJDRAAPEI-206


title: S128_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L8_RHUMjlxTAAJDRAAPEI-206


title: S126_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L7_RHUMjlxTAAIZRAAPEI-202


title: S126_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L8_RHUMjlxTAAJARAAPEI-203


title: S128_DX-TB Subjects-140801_I162_FCC4MHCACXX_L8_RHUMjlxTAAJBRAAPEI-204


title: S128_DX-TB Subjects-140802_I232_FCC4N8BACXX_L8_RHUMjlxTAAJBRAAPEI-204


title: S128_week_24-TB Subjects-140731_I269_FCC4N1JACXX_L1_RHUMjlxTAAJERAAPEI-207


title: S126_DX-TB Subjects-140802_I232_FCC4N8BACXX_L7_RHUMjlxTAAIXRAAPEI-227


title: S128_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L8_RHUMjlxTAAJCRAAPEI-205


title: S126_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L7_RHUMjlxTAAIZRAAPEI-202


title: S126_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L8_RHUMjlxTAAJARAAPEI-203


title: S128_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L8_RHUMjlxTAAJCRAAPEI-205


title: S125_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L7_RHUMjlxTAAIWRAAPEI-225


title: S125_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L7_RHUMjlxTAAIWRAAPEI-225


title: S125_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L6_RHUMjlxTAAIVRAAPEI-223


title: S125_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L6_RHUMjlxTAAIVRAAPEI-223


title: S126_DX-TB Subjects-140801_I162_FCC4MHCACXX_L7_RHUMjlxTAAIXRAAPEI-227


title: S126_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L7_RHUMjlxTAAIYRAAPEI-201


title: S126_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L7_RHUMjlxTAAIYRAAPEI-201


title: S125_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L6_RHUMjlxTAAIURAAPEI-222


title: S129_week_4-TB Subjects-140731_I269_FCC4N1JACXX_L1_RHUMjlxTAAJHRAAPEI-210


title: S124_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L6_RHUMjlxTAAISRAAPEI-220


title: S125_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L6_RHUMjlxTAAIURAAPEI-222


title: S124_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L6_RHUMjlxTAAITRAAPEI-221


title: S124_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L6_RHUMjlxTAAISRAAPEI-220


title: S124_DX-TB Subjects-140802_I232_FCC4N8BACXX_L4_RHUMjlxTAAIQRAAPEI-218


title: S124_DX-TB Subjects-140801_I162_FCC4MHCACXX_L4_RHUMjlxTAAIQRAAPEI-218


title: S124_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L4_RHUMjlxTAAIRRAAPEI-219


title: S124_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L4_RHUMjlxTAAIRRAAPEI-219


title: S123_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L4_RHUMjlxTAAIORAAPEI-215


title: S123_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L4_RHUMjlxTAAIPRAAPEI-216


title: S123_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L4_RHUMjlxTAAIORAAPEI-215


title: S123_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L4_RHUMjlxTAAIPRAAPEI-216


title: S123_DX-TB Subjects-140802_I232_FCC4N8BACXX_L3_RHUMjlxTAAINRAAPEI-214


title: S112_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L3_RHUMjlxTAAILRAAPEI-212


title: S123_DX-TB Subjects-140801_I162_FCC4MHCACXX_L3_RHUMjlxTAAINRAAPEI-214


title: S112_DX-TB Subjects-140802_I232_FCC4N8BACXX_L2_RHUMjlxTAAIJRAAPEI-210


title: S112_DX-TB Subjects-140801_I162_FCC4MHCACXX_L2_RHUMjlxTAAIJRAAPEI-210


title: S112_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L3_RHUMjlxTAAIMRAAPEI-213


title: S111_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L2_RHUMjlxTAAIHRAAPEI-208


title: S112_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L3_RHUMjlxTAAIKRAAPEI-211


title: S112_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L3_RHUMjlxTAAIKRAAPEI-211


title: S111_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L2_RHUMjlxTAAIHRAAPEI-208


title: S111_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L2_RHUMjlxTAAIIRAAPEI-209


title: S111_DX-TB Subjects-140801_I162_FCC4MHCACXX_L1_RHUMjlxTAAIFRAAPEI-206


title: S124_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L6_RHUMjlxTAAITRAAPEI-221


title: S111_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L2_RHUMjlxTAAIGRAAPEI-207


title: S111_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L2_RHUMjlxTAAIGRAAPEI-207


title: S111_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L2_RHUMjlxTAAIIRAAPEI-209


title: S10_DX-Healthy Controls-140817_I162_FCC4MT4ACXX_L2_RHUMjlxTAAQPRAAPEI-208

value: Healthy Controls


title: S108_week_4-TB Subjects-140802_I232_FCC4N8BACXX_L1_RHUMjlxTAAIDRAAPEI-204


title: S108_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L1_RHUMjlxTAAIDRAAPEI-204


title: S108_week_24-TB Subjects-140801_I162_FCC4MHCACXX_L1_RHUMjlxTAAIERAAPEI-205


title: S108_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L1_RHUMjlxTAAIERAAPEI-205


title: S108_DX-TB Subjects-140801_I162_FCC4T6AACXX_L8_RHUMjlxTAAIBRAAPEI-202


title: S108_DX-TB Subjects-140730_I284_FCC4N7JACXX_L8_RHUMjlxTAAIBRAAPEI-202


title: S108_day_7-TB Subjects-140802_I232_FCC4N8BACXX_L1_RHUMjlxTAAICRAAPEI-203


title: S106_week_4-TB Subjects-140801_I162_FCC4T6AACXX_L8_RHUMjlxTAAIARAAPEI-201


title: S108_day_7-TB Subjects-140801_I162_FCC4MHCACXX_L1_RHUMjlxTAAICRAAPEI-203


title: S106_DX-TB Subjects-140730_I284_FCC4N7JACXX_L8_RHUMjlxTAAHYRAAPEI-225


title: S106_week_4-TB Subjects-140730_I284_FCC4N7JACXX_L8_RHUMjlxTAAIARAAPEI-201


title: S111_DX-TB Subjects-140802_I232_FCC4N8BACXX_L1_RHUMjlxTAAIFRAAPEI-206


title: S106_day_7-TB Subjects-140801_I162_FCC4T6AACXX_L8_RHUMjlxTAAHZRAAPEI-227


title: S112_week_4-TB Subjects-140801_I162_FCC4MHCACXX_L3_RHUMjlxTAAILRAAPEI-212


title: S105_DX-TB Subjects-140730_I284_FCC4N7JACXX_L7_RHUMjlxTAAHURAAPEI-220


title: S105_week_4-TB Subjects-140730_I284_FCC4N7JACXX_L7_RHUMjlxTAAHWRAAPEI-222


title: S105_week_24-TB Subjects-140801_I162_FCC4T6AACXX_L7_RHUMjlxTAAHXRAAPEI-223


title: S104_week_4-TB Subjects-140801_I162_FCC4T6AACXX_L6_RHUMjlxTAAHSRAAPEI-218


title: S10_DX-Healthy Controls-140817_I162_FCC4MT4ACXX_L3_RHUMjlxTAAQPRAAPEI-208


title: S104_week_24-TB Subjects-140730_I284_FCC4N7JACXX_L6_RHUMjlxTAAHTRAAPEI-219


title: S105_DX-TB Subjects-140801_I162_FCC4T6AACXX_L7_RHUMjlxTAAHURAAPEI-220


title: S105_week_24-TB Subjects-140730_I284_FCC4N7JACXX_L7_RHUMjlxTAAHXRAAPEI-223


title: S104_DX-TB Subjects-140730_I284_FCC4N7JACXX_L6_RHUMjlxTAAHQRAAPEI-215


title: S106_day_7-TB Subjects-140730_I284_FCC4N7JACXX_L8_RHUMjlxTAAHZRAAPEI-227


title: S105_day_7-TB Subjects-140801_I162_FCC4T6AACXX_L7_RHUMjlxTAAHVRAAPEI-221


title: S105_day_7-TB Subjects-140730_I284_FCC4N7JACXX_L7_RHUMjlxTAAHVRAAPEI-221


title: S106_DX-TB Subjects-140801_I162_FCC4T6AACXX_L8_RHUMjlxTAAHYRAAPEI-225


title: S104_week_24-TB Subjects-140801_I162_FCC4T6AACXX_L6_RHUMjlxTAAHTRAAPEI-219


title: S112_week_24-TB Subjects-140802_I232_FCC4N8BACXX_L3_RHUMjlxTAAIMRAAPEI-213


title: S103_week_4-TB Subjects-140801_I162_FCC4T6AACXX_L4_RHUMjlxTAAHORAAPEI-213


title: S103_DX-TB Subjects-140801_I162_FCC4T6AACXX_L4_RHUMjlxTAAHMRAAPEI-211


title: S103_week_24-TB Subjects-140730_I284_FCC4N7JACXX_L4_RHUMjlxTAAHPRAAPEI-214


title: S105_week_4-TB Subjects-140801_I162_FCC4T6AACXX_L7_RHUMjlxTAAHWRAAPEI-222


title: S103_day_7-TB Subjects-140801_I162_FCC4T6AACXX_L4_RHUMjlxTAAHNRAAPEI-212


title: S103_day_7-TB Subjects-140730_I284_FCC4N7JACXX_L4_RHUMjlxTAAHNRAAPEI-212


title: S102_week_4-TB Subjects-140801_I162_FCC4T6AACXX_L3_RHUMjlxTAAHKRAAPEI-209


title: S104_week_4-TB Subjects-140730_I284_FCC4N7JACXX_L6_RHUMjlxTAAHSRAAPEI-218


title: S102_week_4-TB Subjects-140730_I284_FCC4N7JACXX_L3_RHUMjlxTAAHKRAAPEI-209


title: S104_DX-TB Subjects-140801_I162_FCC4T6AACXX_L6_RHUMjlxTAAHQRAAPEI-215


title: S104_day_7-TB Subjects-140730_I284_FCC4N7JACXX_L6_RHUMjlxTAAHRRAAPEI-216


title: S103_week_4-TB Subjects-140730_I284_FCC4N7JACXX_L4_RHUMjlxTAAHORAAPEI-213


title: S104_day_7-TB Subjects-140801_I162_FCC4T6AACXX_L6_RHUMjlxTAAHRRAAPEI-216


title: S102_DX-TB Subjects-140805_I272_FCC4MTNACXX_L8_RHUMjlxTAAHIRABPEI-207


title: S101_week_24-TB Subjects-140805_I284_FCC4MJAACXX_L1_RHUMjlxTAAHHRABPEI-206


title: S102_DX-TB Subjects-140805_I284_FCC4MJAACXX_L1_RHUMjlxTAAHIRABPEI-207


title: S102_week_24-TB Subjects-140801_I162_FCC4T6AACXX_L3_RHUMjlxTAAHLRAAPEI-210


title: S102_week_24-TB Subjects-140730_I284_FCC4N7JACXX_L3_RHUMjlxTAAHLRAAPEI-210


title: S101_week_24-TB Subjects-140805_I272_FCC4MTNACXX_L8_RHUMjlxTAAHHRABPEI-206


title: S101_DX-TB Subjects-140805_I272_FCC4MTNACXX_L7_RHUMjlxTAAHERABPEI-203


title: S102_day_7-TB Subjects-140805_I284_FCC4MJAACXX_L2_RHUMjlxTAAHJRABPEI-208


title: S103_week_24-TB Subjects-140801_I162_FCC4T6AACXX_L4_RHUMjlxTAAHPRAAPEI-214


title: S100_week_4-TB Subjects-140815_I175_FCC4MVKACXX_L8_RHUMjlxTAAHCRBAPEI-201


title: S101_week_4-TB Subjects-140805_I272_FCC4MTNACXX_L8_RHUMjlxTAAHGRABPEI-205


title: S100_week_24-TB Subjects-140805_I272_FCC4MTNACXX_L7_RHUMjlxTAAHDRABPEI-202


title: S100_week_24-TB Subjects-140805_I272_FCC4MTNACXX_L6_RHUMjlxTAAHDRABPEI-202


title: S101_day_7-TB Subjects-140805_I272_FCC4MTNACXX_L8_RHUMjlxTAAHFRABPEI-204


title: S100_week_4-TB Subjects-140815_I175_FCC4MVKACXX_L7_RHUMjlxTAAHCRBAPEI-201


title: S101_day_7-TB Subjects-140805_I284_FCC4MJAACXX_L1_RHUMjlxTAAHFRABPEI-204


title: S100_DX-TB Subjects-140805_I272_FCC4MTNACXX_L6_RHUMjlxTAAHARABPEI-225


title: S102_day_7-TB Subjects-140805_I284_FCC4MJAACXX_L3_RHUMjlxTAAHJRABPEI-208


title: S100_DX-TB Subjects-140805_I272_FCC4MTNACXX_L7_RHUMjlxTAAHARABPEI-225


title: S100_day_7-TB Subjects-140805_I272_FCC4MTNACXX_L7_RHUMjlxTAAHBRABPEI-227


title: S100_day_7-TB Subjects-140805_I272_FCC4MTNACXX_L6_RHUMjlxTAAHBRABPEI-227


title: S103_DX-TB Subjects-140730_I284_FCC4N7JACXX_L4_RHUMjlxTAAHMRAAPEI-211


title: S101_DX-TB Subjects-140805_I272_FCC4MTNACXX_L6_RHUMjlxTAAHERABPEI-203


title: 22Rv1_FBS

city: New York

first: Shipra

last: Shukla

state: NY

address: 417 East 68th Street

institute: MSKCC

data_processing:
The sequenced reads from fastq files were mapped to hg19 using STAR and and downstream processing was done usig cuffquant
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
RNA was harvested using Trizol reagent and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

tag: treatment

value: FBS


title: 22Rv1_DHT

value: DHT


title: No treatment rep2

city: Kuopio

first: Suvi

last: Kuosmanen

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

data_processing:
RNA-seq libraries were sequenced on Illumina HiSeq 2000
RNA-seq data was mapped using TopHat2  with underlying Bowtie2
Samtools were used for CountTable
Genome_build: hg19
Supplementary_files_format_and_content: comma-separeted values text file includes raw counts for all samples

source_name: Vascular endothelial cells

extract_protocol:
Standard RNA extraction protocol
RNA library preparation is described in the publication

value: HUVEC

value: non-treated


title: S101_week_4-TB Subjects-140805_I284_FCC4MJAACXX_L1_RHUMjlxTAAHGRABPEI-205


title: No treatment rep1


title: Inhibitor rep2

value: miR-93-5p inhibitor


title: Inhibitor rep1


title: Inhibitor rep3


title: Control Inhibitor rep2

value: miR-93-5p inhibitor control


title: Control Inhibitor rep1


title: Mimic rep3

value: miR-93-5p mimic


title: Mimic rep2


title: Mimic control rep1

value: miR-93-5p mimic control


title: Mock rep2

value: mock


title: 22Rv1_Dox_INPUT

library_source: genomic

data_processing:
The sequenced reads from fastq files were mapped to hg19 using Bowtie 1.0
Peaks were called using MACS2. Downstream analysis were performed using Homer and SeqMiner
Genome_build: Hg19
Supplementary_files_format_and_content: ENCODE narrowPeak: Narrow (or Point-Source) Peaks format. See https://genome.ucsc.edu/FAQ/FAQformat.html

molecule: genomic DNA

growth_protocol: Cells were grown in 10% FBS

extract_protocol:
Chromatin was isolated and sheared. Following antibodies were used; HNF4G (Sigma; HPA005438 or Proteintech; 25801-1-AP); H3K4me1 (Abcam; ab8895); H3K27ac (Abcam; ab4729); AR (Abcam, ab108341); FOXA1 (Abcam; ab5089). Magnetic protein A/G beadswere used to collect immunoprecipitates. The immunoprecipate was washed and eluted using standing conditions.
Purified ChIP DNA was blunt-ended, ligated to adaptors, amplified with 8-12-cycles of PCR, and sequenced.

treatment_protocol: Cells were harvested in log phase growth

tag: hnf4g status

value: knockdown

tag: ip

value: Input

tag: cell line


title: 22Rv1_Veh_INPUT

value: wildtype


title: LNCaP_HNF4G_INPUT

value: overexpression

value: LNCaP


title: 22Rv1_Veh_Foxa1 IP

source_name: 22rV1HNF4Gsh_Foxa1 IP


title: 22Rv1_Veh_H3K4me1 IP

source_name: 22rV1HNF4Gsh_H3K4me1 IP


title: 22Rv1_Veh_AR IP

source_name: 22rV1HNF4Gsh_AR IP

value: AR


title: 22Rv1_Dox_H3K4me1 IP

source_name: 22rV1HNF4Gsh-Dox_H3K4me1 IP


title: 22Rv1_Veh_HNF4G IP

source_name: 22rV1HNF4Gs_HNF4G IP


title: 22Rv1_Veh_H3K27acetyl IP

source_name: 22rV1HNF4Gsh_H3K27acetyl IP


title: 22Rv1_Dox_H3K27acetyl IP

source_name: 22rV1HNF4Gsh-Dox_H3K27acetyl IP


title: Mimic control rep2


title: LNCaP_Vec_H3K4me1 IP

source_name: LNCaP_H3K4me1 IP


title: LNCaP_Vec_HNF4G IP

source_name: LNCaP_HNF4G IP


title: LNCaP_HNF4G_H3K4me1 IP

source_name: LNCaP/HNF4G_H3K4me1 IP


title: LNCaP_HNF4G_HNF4G IP

source_name: LNCaP/HNF4G_HNF4G IP


title: 22Rv1_Dox_HNF4G IP

source_name: 22rV1HNF4Gsh-Dox_HNF4G IP


title: LNCaP_Vec_INPUT


title: 22Rv1_Dox_AR IP

source_name: 22rV1HNF4Gsh-Dox_AR IP


title: LNCaP_Vec_H3K27acetyl IP

source_name: LNCaP_H3K27acetyl IP


title: LNCaP_HNF4G_H3K27acetyl IP

source_name: LNCaP/HNF4G_H3K27acetyl IP


title: LNCaP_Vec_Foxa1 IP

source_name: LNCaP_Foxa1 IP


title: LNCaP_HNF4G_Foxa1 IP

source_name: LNCaP/HNF4G_Foxa1 IP


title: LNCaP_Vec_AR IP

source_name: LNCaP_AR IP


title: Mock rep1

source_name: Vascular endothelial cells


title: LNCaP_HNF4G_AR IP

source_name: LNCaP/HNF4G_AR IP


title: 22Rv1_Dox_Foxa1 IP

source_name: 22rV1HNF4Gsh-Dox_Foxa1 IP


title: Mimic rep1


title: LNCaP/AR_HNF4G_CSS_Day32_Rep1

source_name: LNCaP/AR

growth_protocol: Cells were grown in media containing charcoal stripped-serum and cells were harvested at Day 9, Day32 of growth.

value: LNCaP/AR

tag: day


title: LNCaP/AR_HNF4G_CSS_Day32_Rep2

source_name: LNCaP/Ar


title: LNCaP/AR_HNF4G_CSS_Day9_Rep2


title: LNCaP/AR_Vec_CSS_Day9_Rep2


title: LNCaP-HNF1A-Rep1

data_processing:
The sequenced reads from fastq files were mapped to hg19 using STAR and and downstream processing was done usig cuffquant
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: LNCaP

tag: hnf1a status


title: LNCaP-Vec-Rep2


title: LNCaP-HNF1A-Rep2


title: 22Rv1_siSCR


title: LNCaP-Vec-Rep1


title: 22Rv1_siHNF1A


title: brain_gl60j_rep2

first: Carolyn

last: Morrison

address: 540 First Ave

department: Skirball Institute

institute: NYU School of Medicine

description: D.mel. W3L brain gl60j 25C

data_processing:
sequencing adapters and low quality bases were removed with Trimmomatic v0.33 with paramaters TruSeq3-PE-2.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20
trimmed reads were aligned to the Drosophila reference genome dm3 with Tophate v2.2.1 using default parameters
gene expression was calculated from aligned reads with Cufflinks v2.2.1 with default parameters using the RefSeq genome annotation for Drosophila genome build dm3
Differential gene expression was computed between genotypes with the Cufflinks/cuffdiff protocol v2.2.1
Genome_build: Drosophila melanogaster dm3
Supplementary_files_format_and_content: processed data is provided in an Excel spreadsheet with gene expression values normalized as FPKM valules by Cufflinks v2.2.1

organism: Drosophila melanogaster

growth_protocol: Grown on molasses food at 25C

extract_protocol:
TriZol, DNase treatment, RNeasy clean-up, Sodium Acetate precipitation
Illumina TruSeq RNA v2 sample preparation kit

treatment_protocol: Dissected in 0.1M Phosphate Buffer

value: brain

tag: sample type

value: D.mel. W3L brain gl60j 25C


title: brain_gl60j_rep3

description: D.mel. W3L brain gl60j 25C

tag: tissue


title: GC_CELL

city: Richmond

first: Barbara

middle: D.

last: Boyan

state: VA

address: 601 W. Main St.

department: School of Engineering

institute: Virginia Commonwealth University

description: micro RNA

data_processing:
miARma v 1.6
Quality: prefix=pre
Aligner: bowtie2, bowtielength=17, bowtieparameters = -N 1
ReadCount: seqid=ID, featuretype=miRNA
Genome_build: NCBI Rnor_6.0
Supplementary_files_format_and_content: files were generated using miARma-Seq

organism: Rattus norvegicus

source_name: Growth Zone Chondrocyte Cells

growth_protocol: fourth passage chondrocytes were grown out to full confluence in T-175 flasks using Dulbecco's modified Eagle's medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Life Technologies), 50 parts/mL penicillin/streptomycin and 50 mg/mL ascorbic acid (Sigma-Aldrich). Cell culture medium was changed 24hrs after plating and then at 72hr intervals.

extract_protocol:
MVs were isolated from chondrocyte cultures by differential centrifugation of the trypsin digested cell layer (briefly: after trypsinization - 0.25% Trypsin-EDTA - for 10 min, 1xDPBS containing 10% exosome-free FBS was added to stop the reaction. The MVs were isolated by sequential centrifugation at 500 g for 5min, 21,000 g for 20 min and 184,000 g for 70 min. The MV pellets were washed with 0.9% NaCl and recentrifuged at 184,000 g for 70 min.)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Growth Zone Chondrocyte

tag: passage

tag: cell source

value: costochondral cartilage


title: RC_CELL

description: micro RNA

source_name: Resting Zone Chondrocyte Cells

value: Resting Zone Chondrocyte


title: Chicken_testis_M_rep3

city: Heidelberg

first: Maria

last: Warnefors

address: Center for Molecular Biology of Heidelberg University (ZMBH)

country: Germany

institute: University of Heidelberg

data_processing:
After adapter trimming, reads were filtered to only retain those in the size span 15-28 bp.
We mapped all reads to the relevant genomes with Bowtie release 1.1.2, using a series of decreasingly stringent settings to allow for post-transcriptional modifications. In the first round we allowed for 0 mismatches and did not trim any bases from the 3’ end. Next, we mapped all the unmapped reads from the previous round, after trimming first 1 and then 2 bases from the 3’ end. Finally, we repeated the procedure while allowing for 1 mismatch. Reads that could not be mapped with any setting and reads with more than 10 hits (using the first setting where any hits were found) were discarded.
Expression (read counts) was determined for multi-map groups (MMGs) corresponding to one or more mature miRNAs (see main publication for details on miRNAs and MMGs).
Genome_build: mm10
Genome_build: monDom5
Genome_build: galGal5
Supplementary_files_format_and_content: .bed file (the fifth column contains the read count)

organism: Gallus gallus

source_name: Testis

extract_protocol:
Total RNA was extracted from 10 to 20 mg of flash frozen tissue using the Qiagen RNeasy Micro Kit with lysis buffer RLT/40mM DTT and RWT wash buffer,  and the Qiagen miRNeasy Mini Kit according to the manufacturer’s instructions. Small RNA fraction was purified from 0.5 – 2 μg total RNA by denaturing polyacrylamide gel electrophoresis.
Small RNA libraries were prepared for sequencing using the NEXTflex Small RNA-Seq Kit v2 (NF) according to the manufacturer’s instructions. For two of the samples, libraries were also prepared with the lllumina TruSeq Small RNA Library Prep Kit (IL) according to Illumina's instructions and the HD protocol (HD) developed by Sorefan et al, 2012 (DOI: 10.1186/1758-907X-3-4). Libraries were sequenced on an Illumina HiSeq 2500 System.

tag: Sex

value: M

tag: replicate

tag: protocol

value: NF

value: Testis


title: mmu_FUS_RNASeq_hFUSWT_3

city: Baltimore

first: Manolis

last: Maragkakis

state: MD

address: 251 Bayview Blvd

institute: National Institute on Aging

data_processing:
CLIP-Seq and Ribo-Seq adapter trim: the adaptor sequences were trimmed from the reads using cutadapt (v1.12). The adaptor AGGGAGGACGATGCGG was trimmed from the 5’-end of reads and GTGTCAGTCACTTCCAGCGGTCGTATGCCGTCTTCTGCTTG was trimmed from the 3’-end allowing for 0.25 error rate. Only reads longer than 15-nt after adaptor trimming were retained. RNA-Seq adapter trim: The adaptor sequences were trimmed from the reads using the cutadapt software in paired-end mode. The adaptor AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC was trimmed from the 3’-end of mate 1 reads and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA was trimmed from the 3’-end of mate 2 reads allowing for 0.25 error rate.
CLIP-Seq and Ribo-Seq read alignment: reads were aligned to the mouse genome (mm9) using the STAR aligner (v2.4.1c) and the following parameters --outFilterMultimapScoreRange 0 --alignIntronMax 50000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.9 --sjdbOverhang 100. Reads mapping to areas annotated by RepeatMasker as ribosomal RNAs or tRNAs were excluded from further analysis. RNA-Seq read alignment: Paired-end alignment was performed using STAR with the same parameters as for CLIP and Ribo-Seq.
Aligned reads were loaded into a SQLite3 database for further processing with CLIPSeqTools (v0.1.7) and annotated with information whether they overlap with elements from RepeatMasker (downloaded from UCSC) and genes (from UCSC gene model annotation file).
Gene counts were measured using CLIPSeqTools
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are TAB delimited files quantifying the number of reads in each gene. Files contain the following columns: gene_name, gene_location, gene_length, gene_count, gene_count_per_nt, gene_exonic_count, gene_exonic_length, gene_exonic_count_per_nt, gene_intronic_count, gene_intronic_length, gene_intronic_count_per_nt

organism: Mus musculus

source_name: Neurons

growth_protocol: Mouse embryonic stem cells (ES, E14Tg2A.4) were maintained in ES medium on gelatinized plates without feeder cells. Neuronal differentiation was performed as described previously (Wichterle et al., 2009). Cells were maintained into ADFNB+GDNF.

extract_protocol:
For CLIP samples, UV crosslinked RNA bound to the exogenous protein was isolated from immunoprecipitated sample with anti-FLAG antibody (CellSignaling, #2368). For RNA-seq, total RNA was isolated from cells expressing exogenous protein and ribosomal and transfer RNA were depleted with Ribo-Zero Gold kit (Illumina). For Ribo-seq, the ribosome protected RNA fragment (RPF) between 25 to 35 nt in size were collected from cells expressing exogenous protein according to a previous report (Ingolia NT et al, Nat Protc. 2012).
For CLIP-seq, library preparation was performed as described in Nakaya et al, RNA, 2013. Briefly, protein bound RNA was ligated with a 3'-linker with biotin by T4 RNA ligase and then treated with T4 PNK (NEB) and extracted from protein. Then, a 5'-linker was ligated and amplified by RT-PCR. For RNA-seq, total RNA was prepared as above and the library was prepared using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). For Ribo-seq, Ribosome protected fragments (RPFs) were used as input and library was prepared as described in the RNA-seq library preparation in Nakaya et al, RNA, 2013. Briefly, a 3'-linker with biotin was ligated to the RPFs and purified with streptoavidin attached beads and then a 5'-linker was ligated on the beads. Following several wash, the RNA on beads was used for RT-PCR as template. The following sequences need to be trimmed from raw reads: For CLIP-Seq and Ribo-Seq "GTGTCAGTCACTTCCAGCGGTCGTATGCCGTCTTCTGCTTG" needs to be trimmed from the 3'end. For RNA-Seq "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" and "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA" needs to be trimmed from the 3'end of read 1 and read 2 respectivelly.

treatment_protocol: NFLAG-hFUSWT or NFLAG-hFUSR495X were expressed in ES cell derived neurons by lentivirus system and cells were treated with DOX to induce expression of the exogenous protein along with Geneticin to select the cells infected with virus. Control cells had no treatment.

value: ES cell derived neurons

tag: strain

tag: molecule type

value: total RNA

tag: lentiviral transfuction

value: FLAG-tagged human R495X


title: EZH2_ChIPSeq

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

country: China

institute: Peking University

data_processing:
read alignment software: Bowtie with -v 2 -m 1 --best --strata
peak calling: MACS with pvalue cutoff 1e-3 and model fold 4,30
Genome_build: hg19
Supplementary_files_format_and_content: *.clean_hg19.bed files are mapping results by Bowtie. The six lines are: chromosome, start, end, number of mismatch, 0 and strand.
Supplementary_files_format_and_content: *_VS_I_p-3_mfold4_peaks.bed files are peaks got by MACS. The five lines are: chromosome, start, end,name and -10*log10(pvalue) for the peak region.

source_name: Colon cancer cells

growth_protocol: human colon cancer cell line HCT116 was maintained in DMEM medium supplemented with 10% FBS in a humidified incubator containing 5% CO2.

extract_protocol: Libraries of ChIP samples were prepared according to a modified version of the Illumina Genomic DNA protocol, as described previously (Mikkelsen et al., 2007).

treatment_protocol: In EsiM group, HCT116 cells were treated with MTA2 RNAi oligonucleotides. The RNAi oligonucleotides were transfected into cells by using the Lipofectamine 2000 transfection kit (Invitrogen) according to the manufacturer’s instructions. The final concentration of the siRNA molecules is 10 nM and cells were harvested 48 hours later. There is no treatment in other three groups.

tag: chip antibody

value: EZH2 (Abcam, ab3748)


title: Chicken_testis_M_rep2


title: EZH2siMTA2_ChIPSeq


title: MTA2_ChIPSeq

value: MTA2 (Santa Cruz, sc-28731)


title: GC_MV

description: micro RNA

source_name: Growth Zone Chondrocyte Matrix Vesicles

tag: cell type

value: Growth Zone Matrix Vesicle


title: Chicken_testis_M_rep1


title: Chicken_ovary_F_rep3

source_name: Ovary

value: F

value: Ovary


title: Chicken_ovary_F_rep2


title: Chicken_liver_M_rep3

source_name: Liver

value: Liver


title: Chicken_ovary_F_rep1


title: Chicken_liver_M_rep2


title: LNCaP/AR_Vec_CSS_Day9_Rep1

value: LNCaP/AR


title: brain_gl60j_rep1

description: D.mel. W3L brain gl60j 25C

value: brain

value: D.mel. W3L brain gl60j 25C


title: RC_MV

description: micro RNA

source_name: Resting Zone Chondrocyte Matrix Vesicles

value: Resting Zone Matrix Vesicle

value: costochondral cartilage


title: mmu_FUS_RNASeq_hFUSWT_2


title: IgG_ChIPSeq

value: IgG  (Santa Cruz, sc-2027)


title: Chicken_liver_M_rep1

value: M

value: NF


title: mmu_FUS_RNASeq_hFUSR495X_3

value: ES cell derived neurons


title: brain_WT_rep2

description: D.mel. W3L brain WT 25C

source_name: W3L_ brain_Wild-Type

value: D.mel. W3L brain WT 25C


title: mmu_FUS_RNASeq_Ctrl_2

value: total RNA

value: wild type FUS


title: Chicken_liver_F_rep2


title: Chicken_liver_F_rep3


title: brain_WT_rep3

description: D.mel. W3L brain WT 25C


title: Chicken_heart_M_rep3

source_name: Heart

value: Heart


title: Chicken_liver_F_rep1


title: wing_WT_rep3

description: D.mel. W3L wing disc WT 25C

source_name: W3L_wing disc_Wild-Type

value: wing disc

value: D.mel. W3L wing disc WT 25C


title: Chicken_heart_M_rep1


title: brain_WT_rep1

description: D.mel. W3L brain WT 25C


title: mmu_FUS_RNASeq_hFUSR495X_2

value: FLAG-tagged human R495X


title: Chicken_heart_F_rep3

value: F


title: wing_WT_rep2

description: D.mel. W3L wing disc WT 25C


title: SpleenVehicle16

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

data_processing:
The reads were aligned with STAR (version 2.4.0c), and genes annotated in Gencode v18 were quantified with featureCounts (v1.4.3-p1). Normalization and differential expression was done with the Bioconductor package DESeq2.
Supplementary_files_format_and_content: DESEQ2 normalized counts for genes.

source_name: RNA Isolated from portion of the spleen from a chronically treated Towne's mouse with HPMC for seven weeks

growth_protocol: Atopic Dermatitis-like disease was induced by epicutaneous treatment with HDM extract (10 μg/mouse and treatment) and SEB (500 ng/mouse and treatment) given in 2 cycles on days 1 and 4, and 14 and 17, on the shaved and tape-stripped back skin over a 23 day period according to established protocols.  In some experiments, animals were treated i.p. with 200 μg anti-TWEAK or IgG (total volume 200 ul) twice weekly throughout the experiment. Psoriasis-like disease was induced by daily application of 2.5% Imiquimod cream or vehicle control on the shaved back for 8 days.  Animals were treated subcutaneously in the rostral portion of the back with 75 or 200 μg of recombinant murine TWEAK as a N-terminal tagged Fc/IgG-fusion protein or control vehicle (irrelevant IgG) in 200 μl PBS, twice weekly over a 14-day period.

extract_protocol:
Total RNA was harvested using Trizol (Thermo Fisher Scientific) DNAse treated (Qiagen) and cleaned with the RNeasy mini extraction kit (Qiagen) according to manufacturer's recommendations.
500 ng RNA was used as starting input to Illumina TruSeq mRNA stranded library construction according to the manufacturers recommendation. High quality libraries were then pooled and sequenced on an Illumina HiSeq 2500

treatment_protocol: Townes mice, 8–10 weeks old, were dosed with 100 mg/kg DMF or vehicle by PO once daily for 6 days a week for a duration of 7 weeks.

value: Spleen

tag: age

value: 7 weeks

tag: treatment

value: Vehicle


title: wing_WT_rep1

description: D.mel. W3L wing disc WT 25C


title: Chicken_heart_M_rep2


title: mmu_FUS_RNASeq_Ctrl_1


title: Chicken_brain_M_rep3

source_name: Brain

value: Brain


title: Chicken_heart_F_rep1


title: SpleenVehicle15


title: Chicken_brain_M_rep2


title: eye_WT_rep3

description: D.mel. W3L eye disc WT 25C

source_name: W3L_eye disc_Wild-Type

value: eye disc

value: D.mel. W3L eye disc WT 25C


title: Chicken_heart_F_rep2


title: Chicken_brain_F_rep3


title: SpleenVehicle14


title: Chicken_brain_M_rep1

value: M


title: Chicken_brain_F_rep2

value: NF


title: SpleenVehicle13


title: Opossum_testis_M_rep3

organism: Monodelphis domestica

value: Testis


title: brain_Gl_ME_gl60j_rep3

description: insc>Gl in D. mel. W3L gl60j brain

value: D.mel. W3L brain Gl ME gl60j 25C


title: Opossum_testis_M_rep1


title: SpleenVehicle12


title: Opossum_ovary_F_rep3

value: Ovary


title: Opossum_testis_M_rep2


title: brain_Gl_ME_gl60j_rep2

description: insc>Gl in D. mel. W3L gl60j brain


title: Opossum_ovary_F_rep2


title: Opossum_liver_M_rep2

value: Liver


title: brain_Gl_ME_gl60j_rep1

description: insc>Gl in D. mel. W3L gl60j brain


title: SpleenVehicle9


title: SpleenVehicle10


title: Opossum_ovary_F_rep1


title: wing_Gl_ME_rep3

description: UbxFLP; Gl clones in D.mel. W3L wing disc

source_name: W3L_wing disc_Gl_MisExp

value: D.mel. W3L wing disc Gl ME 25C


title: SpleenDMF8

source_name: RNA Isolated from portion of the spleen from a chronically treated Towne's mouse with DMF for seven weeks

value: DMF


title: LNCaP/AR_HNF4G_CSS_Day9_Rep1

source_name: LNCaP/AR

tag: cell line

value: LNCaP/AR


title: SpleenDMF7


title: Opossum_liver_F_rep1


title: wing_Gl_ME_rep2

value: wing disc


title: Opossum_heart_M_rep3

value: Heart


title: wing_Gl_ME_rep1


title: Chicken_brain_F_rep1

value: F


title: eye_WT_rep1

description: D.mel. W3L eye disc WT 25C


title: Opossum_heart_M_rep2


title: SpleenDMF6

value: Spleen

value: 7 weeks


title: Opossum_heart_M_rep1


title: Opossum_liver_M_rep3


title: Opossum_heart_F_rep2


title: Opossum_heart_F_rep1


title: Opossum_heart_F_rep3


title: Opossum_liver_F_rep3


title: SpleenDMF5


title: SpleenDMF4


title: Opossum_brain_M_rep3

value: Brain


title: Opossum_brain_F_rep3


title: eye_WT_rep2

description: D.mel. W3L eye disc WT 25C

value: eye disc


title: Opossum_brain_M_rep2


title: Opossum_liver_M_rep1


title: Opossum_liver_F_rep2


title: Opossum_brain_M_rep1


title: SpleenDMF1


title: Opossum_brain_F_rep2


title: Opossum_brain_F_rep1


title: LiverVehicle16

source_name: RNA Isolated from lobe of liver from a chronically treated Towne's mouse with HPMC vehicle for seven weeks

value: Vehicle


title: LiverVehicle15


title: SpleenDMF3


title: LiverVehicle14


title: PDAC.05

city: Charlestown

first: Joseph

last: Franses

address: 149 13th Street

department: Medical Oncology

institute: Massachusetts General Hospital

data_processing:
initial quality control: FASTQC
alignment: STAR aligner v2.4.0h
duplicate read marking: PICARD
duplicate read removal: SAMTOOLS
quantification of read counts: Htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing absolute read counts

source_name: PDAC_peripheral blood

extract_protocol:
Purified CECs were flash frozen in RNAlater and stored at -80 deg C. RNA was later extracted in batches using the RNEasy micro kit (Qiagen).
Nextera XT DNA library preparation kit (Illumina)

tag: subject status

value: pancreatic ductal adenocarcinoma (PDAC)

value: peripheral blood

value: Circulating epithelial cells (CECs)


title: PDAC.04


title: PDAC.06


title: PDAC.03


title: SpleenVehicle11


title: LiverVehicle13


title: LiverVehicle11


title: LiverVehicle12


title: LiverVehicle10


title: IPMN.28

source_name: IPMN_high-risk_peripheral blood

value: intraductal papillary mucinous neoplasm (IPMN), high-risk


title: PDAC.02


title: PDAC.01


title: IPMN.27


title: LiverDMF8

source_name: RNA Isolated from lobe of liver from a chronically treated Towne's mouse with DMF for seven weeks


title: PDAC.07


title: IPMN.11


title: LiverDMF5


title: IPMN.23


title: IPMN.07

source_name: IPMN_low-risk_peripheral blood

value: intraductal papillary mucinous neoplasm (IPMN), low-risk


title: LiverDMF6

value: Liver


title: IPMN.22


title: dopamine_input_rep_2

city: Toronto

first: John

last: Calarco

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: whole animal

data_processing:
Mapped to C. elegans genome WS235 using STAR alignment software (Dobin et al., 2012).
Gene-centered counts for all genes were obtained using the HTSeq package for whole animal input libraries and cell type-enriched cDNA libraries (Anders et al., 2015, Anders and Huber, 2010).
Gene counts were re-scaled using upper quartile normalization, and fold changes (TRAP immuno-precipitation counts / input counts) were calculated for genes with conservatively detectable expression (RPKM value >= 1 in the input or IP).
Relative tissue enrichment was calculated by comparing fold change values across relevant tissue or neuron types, where the tissue or cell type with the highest fold change value was normalized to 100%.
Genome_build: C. elegans genome WS235
Supplementary_files_format_and_content: Excel file contains raw input and IP (TRAP) Htseq reads and calculated RPKMs

organism: Caenorhabditis elegans

source_name: whole animal input polyA+

growth_protocol: Bleach-synchronized animals were grown at 22Cº in standard NGM 15-cm plates seeded with OP50-1. L4 larvae were collected 46-48 h past L1 release.

extract_protocol:
TRI reagent (Sigma T9424).
Standard protocol in TruSeq RNA Library Kit (Illumina RS-122-2001)


title: IPMN.33


title: IPMN.31


title: serotonin_input_rep_2

description: whole animal


title: dopamine_input_rep_1

description: whole animal


title: serotonin_input_rep_1

description: whole animal


title: LiverDMF3


title: LiverDMF1


title: neuronal_input_rep_2

description: whole animal


title: neuronal_input_rep_1

description: whole animal


title: LiverVehicle9


title: IPMN.30


title: intestine_input_rep_2

description: whole animal


title: Adipose ILC1 1.2

first: Christina

last: Leslie

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FastQC was used to assess sequencing quality
Reads were mapped to the mm10 genome using HiSat2 using the following parameters: -t --no-unal --known-splicesite-infile -x -1 -2.  Genomic index/splice sites/exons were created in HiSat2 using GRCm38.p5 from ENSEMBL along with GRCm38.p5, Release M13, from GENCODE
Gene count table was produced using Rsubread, options isPairedEnd = TRUE, requireBothEndsMapped = TRUE, minOverlap = 80, countChimericFragments = FALSE
Technical replicates were merged into single samples by summing the counts from each replicate.  B13 and H17 should be combined; B17 and H20 should be combined.
Genome_build: mm10
Supplementary_files_format_and_content: gene count table after merging technical replicates (csv)

source_name: Adipose

extract_protocol:
Lymphocytes were harvested as described in manuscript. RNA was isolated by TRIzol extraction followed by SMARTer amplification per manufacturer's instructions.
Library was constructed using standard Illumina protocols and TruSeq SBS Kit v3 (Illumina).


title: Adipose ILC1 2


title: LiverDMF7


title: muscle_input_rep_2

description: whole animal


title: Adipose ILC1 1.1


title: HOXA13 Overexpression control RNA-seq rep3

city: Los Angeles

first: Zhifei

last: Luo

state: CA

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

description:
Overexpression_DESeq2.txt
TPM.txt

data_processing:
RNA-seq data was inspected by FastQC and trimmed using Trimmomatic version 0.35. Reads were mapped to human genome GRCh37 using STAR version 2.5.2b with default settings.
Alignment results were processed for gene quantification using featureCounts version 1.5.1 with the strand-specific option
Differentially expressed genes were determined using DESeq2 version 1.14.1
TPM values for each gene were calculated by RSEM v1.3.0
The quality of each Hi-C library was checked with FastQC and HICUP version 0.5.842. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions (5kb, 10kb, 20kb, 40kb, 100kb). The matrices were normalized using the iterative correction method (iced python library). For the identification of topologically associating domains (TADs), the normalized Hi-C contact matrices, binned with 40kb resolution were used and the domains were called using the Domain caller. Intra-chromosomal significant loops (50kb-10Mb range) were selected with the 5kb resolution contact count matrices using the Fit-Hi-C (false discovery rate (FDR) < 0.05). Hi-C chromatin interaction heatmaps with 5kb resolution was visualized in the 3D Genome Browser (http://biorxiv.org/content/early/2017/02/27/112268). To increase the sequencing depth, two replicates were pooled and processed as above described.
Genome_build: GRCh37
Supplementary_files_format_and_content: TPM values and differential expression; Hi-C contact matrices

source_name: HOXA13 Overexpression control

growth_protocol: RWPE-1 cells were cultured in Keratinocyte Serum Free Medium (Thermo Fisher Scientific, cat. no. 17005-042) without antibiotics. To passage the cells, 0.05% trypsin-0.02% EDTA solution was used and the trypsinization was stopped by adding Dulbecco's phosphate-buffered saline containing 2% FBS. Cells were grown at 37 °C with 5% CO2 for under 20 passages. The cell line identity was confirmed using the STR cell line authentication method at the Norris Comprehensive Cancer Center Media Core and was shown to be free of mycoplasma using the universal mycoplasma detection kit (ATCC 30-1012K).

extract_protocol:
RNA was prepared using TRIzol reagent (Thermal Fisher Scientific, cat. no. 15596018). In situ Hi-C experiments were performed in RWPE-1 cells following the original protocol by Rao et al with minor modifications. Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). Hi-C library was amplified with 14 cycles of PCR using Illumina primers. Each library was sequenced with 75bp paired-end for ~500M read pairs using Illumina HiSeq 2000.
The RNA-seq libraries were made using KAPA stranded mRNA-seq kits (KAPK Biosystems, cat. no. kk8421) according to manufacturer’s instructions
In situ HiC experiments were performed in RWPE-1 cells following the original protocol by Rao et al with minor modifications. HiC was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. HiC material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). HiC library was amplified with 14 cycles of PCR using Illumina primers.

treatment_protocol: For overexpression, RWPE-1 cells were transfected with equal amounts of a HOXA13 expression vector (GeneCopoeiaTM cat. no. EX-I0919-M14) or the corresponding control plasmid expressing eGFP (GeneCopoeiaTM cat. no. EX-EGFP-M14) and harvested 48 hours later. Cells were analyzed by FACS to identify GFP-positive cells and the top 10% eGFP positive cells from 3 control and 3 HOXA13-expressing flasks were collected by cell sorting and subjected to RNA isolation, followed by RNA-seq analysis.

value: prostate cell line RWPE1

value: Gene Overexpression

tag: genotype/variation

value: wild type


title: IPMN.25


title: intestine_input_rep_1

description: whole animal


title: HOXA13 Overexpression control RNA-seq rep2

description:
Overexpression_DESeq2.txt
TPM.txt


title: LiverDMF4

value: DMF


title: muscle_input_rep_1

description: whole animal


title: IPMN.24


title: IPMN.20


title: IPMN.21


title: dopamine_TRAP_rep_2

description: TRAP IP mRNA

source_name: immunoprecipitated mRNA from whole animal lysate


title: IPMN.17


title: HOXA13 Overexpression control RNA-seq rep1

description:
Overexpression_DESeq2.txt
TPM.txt


title: dopamine_TRAP_rep_1

description: TRAP IP mRNA


title: Adipose mNK 1.1

value: mNK


title: HOXA13 Overexpression RNA-seq rep2

description:
Overexpression_DESeq2.txt
TPM.txt

source_name: HOXA13 Overexpression

value: HOXA13 Overexpression


title: Adipose mNK 2


title: IPMN.16


title: Peritoneal Cavity ILC1 2

source_name: Peritoneal Cavity


title: serotonin_TRAP_rep_2

description: TRAP IP mRNA


title: IPMN.15


title: serotonin_TRAP_rep_1

description: TRAP IP mRNA


title: IPMN.14


title: TRβ_WT_PBS_rep2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: ChIP-enriched DNA

data_processing:
Aligment to mm9 using STAR
Differential H3K27ac binding identified using DESeq2.
Bedgraphs were generated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Liver

extract_protocol:
Crosslinked sonicated chromatin was IP'ed using antibodies against H3K27Ac and DNA was extracted by phenol/choloroform.
H3K27ac ChIP-seq libraries were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.

treatment_protocol: WT, TRβ-KO , TRβGS and TRβ147F mice were rendered hypothyroid at the age of 10 to 11 weeks with an iodine-deficient diet (LID) (TD.95007, Harlan-Teklad, USA), 0.05% 2-mercapto-1-methylimidazole (MMI) and 1% potassium perchlorate (Sigma-Aldrich) administered in the drinking water. After three weeks, mice were separated into T3 treatment and control groups for each genotype. T3 treated animals received T3 (Sigma-Aldrich) 20 μg/100 g BW i.p. once. The mice were euthanized with CO2 six hours after the single dose of T3. Livers were subsequently isolated and frozen in liquid nitrogen.

tag: trβ status

value: TRβ WT

value: H3K27ac, Abcam, ab4729


title: neuronal_TRAP_rep_2

description: TRAP IP mRNA


title: Peritoneal Cavity mNK 2


title: Peritoneal Cavity ILC1 1


title: TRβ_WT_PBS_rep1

description: ChIP-enriched DNA

tag: tissue


title: Peritoneal Cavity mNK 1


title: IPMN.13


title: neuronal_TRAP_rep_1

description: TRAP IP mRNA


title: Adipose mNK 1.2


title: IPMN.06


title: TRβ_WT_T3_rep2

description: ChIP-enriched DNA


title: intestine_TRAP_rep_2

description: TRAP IP mRNA


title: TRβ_147F_PBS_rep2

description: ChIP-enriched DNA

value: TRβ_147F (abrogates non-canonical TRβ function).


title: TRβ_WT_T3_rep1

description: ChIP-enriched DNA


title: HD.10

source_name: HD_peripheral blood

value: healthy donor (HD)


title: HOXA13 Overexpression RNA-seq rep3

description:
Overexpression_DESeq2.txt
TPM.txt


title: Liver ILC1 1


title: Liver ILC1 3


title: TRβ_147F_PBS_rep1

description: ChIP-enriched DNA


title: HD.11


title: intestine_TRAP_rep_1

description: TRAP IP mRNA


title: HD.09


title: Liver ILC1 2


title: muscle_TRAP_rep_2

description: TRAP IP mRNA


title: HD.08

description: HD.LL


title: muscle_TRAP_rep_1

description: TRAP IP mRNA


title: HOXA13 Overexpression RNA-seq rep1

description:
Overexpression_DESeq2.txt
TPM.txt


title: Liver mNK 3


title: TaT1

city: La Jolla

first: Pamela

middle: L

last: Mellon

address: 9500 Gilman Dr

institute: UCSD

description:
Cell lines were generated from tumors obtained from mice with a transgene expressing the SV40 T-antigen
Alarid, Development, 1996

data_processing:
Sequencing was done using the HiSeq 2000 sequencer (Illumina).
The resulting sequences were aligned to the mouse genome using the Illumina Consensus Assessment of Sequence and Variation (CASAVA) software program.
Genome_build: NCBI Build 37

source_name: thyrotrope cell line

growth_protocol: Cells were cultured in DMEM with 4.5% glucose (Mediatech Inc., Herndon, VA), 10% fetal bovine serum (Gemini Bio, West Sacramento, CA), and 1x penicillin-streptomycin (Life Technologies, Inc./Invitrogen, Grand Island, NY) in 5% CO2 at 37°C. Cells were seeded on 10 cm dishes (Nunc, Roskilde, Denmark) and harvested at subconfluency.

extract_protocol:
RNA was isolated from the cells using TRIzol® (Invitrogen, Grand Island, NY), as per the manufacturer’s instructions, and treated with Turbo DNA-free DNase (Ambion, Life Technology, USA). The RNA integrity (RNA Integrity Number ≥ 9) and quantity was determined on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).
cDNA libraries were created using the TruSeq™ RNA Sample Prep-v2 (Illumina, San Diego, CA).

tag: Stage

value: mature

value: CB6F1/J mice


title: TRβ_147F_T3_rep1

description: ChIP-enriched DNA


title: Liver mNK 2


title: HD.06

value: peripheral blood


title: aT3-1

description:
Cell lines were generated from tumors obtained from mice with a transgene expressing the SV40 T-antigen
Windle, Mol Endo 1990

source_name: intermediate gonadotrope cell line

value: embryonic


title: TRβ_147F_T3_rep2

description: ChIP-enriched DNA


title: HD.07

value: Circulating epithelial cells (CECs)


title: TRβ_GS_PBS_rep1

description: ChIP-enriched DNA

value: TRβ GS (DNA binding mutant)


title: TRβ_GS_PBS_rep2

description: ChIP-enriched DNA

value: Liver


title: aT1-1

source_name: immature gonadotrope cell line


title: LbT2

source_name: mature gonadotrope cell line


title: Liver mNK 1


title: Spleen ILC1 3

source_name: Spleen


title: Spleen ILC1 2


title: NIH-3T3

description: Jainchill, J. of Virology, 1969

source_name: embryonic fibroblast

value: Swiss


title: Spleen ILC1 1


title: HD.01

description: HD.DL


title: HD.02

description: HD.DM


title: TRβ_GS_T3_rep2

description: ChIP-enriched DNA


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_4B

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
RNASeq: Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse GRCm38 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) applying transcript length correction and 75th percentile normalisation.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following 56 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-56) log2 RPKM values for each sample

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 4B

extract_protocol:
Total RNA libraries (ribozero) were made using 200ng-1μg RNA at the Sanger Institute Illumina bespoke pipeline
RNA was isolated using TriReagent (Sigma) and treated with DNAseI (Ambion DNA-free DNA Cat #1311027) using manufacturers instructions
Total RNA libraries (ribozero) were made using 200ng-1μg RNA at the Sanger Institute Illumina bespoke pipeline

tag: background strain

value: ESC

tag: genotype

value: Wildtype


title: Spleen mNK 5


title: TRβ_KO_PBS_rep2

description: ChIP-enriched DNA

value: TRβ knock-out


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_4A

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 4A


title: Valproic_Acid_3

city: Dresden

first: Guruchandar

last: Arulmozhivarman

address: Fetscherstraße 74

department: Hematology department

institute: TU Dresden - Faculty of Medicine

data_processing:
basecalling: bcl2fastq 2.1.17.4
alignment: alignment of single-end data against hg38 with gsnap version 2015-12-31; splice sites were supported by using Ensembl version 81 (gsnap -d hg38 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-81.ss.hg38.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.5.0 (-a EnsemblGene-81.hg38.TR.gtf -s 2 -Q 1) and the Ensembl version 81 gtf file
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.hg38.e81.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 2 Conditions and their 4 replicates

source_name: G-CSF mobilized peripheral blood stem cells

extract_protocol:
CD34+ cells were re-isolated and  total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

value: CD34+ hematopoietic stem and progenitor cells

tag: culture period-in vitro

value: 5 days-valproic acid treated

tag: type

value: in vitro expanded CD34+ cells


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_3B

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 3B


title: TRβ_KO_PBS_rep1

description: ChIP-enriched DNA

tag: strain

value: H3K27ac, Abcam, ab4729


title: Spleen mNK 3

value: mNK


title: TRβ_KO_T3_rep1

description: ChIP-enriched DNA


title: Valproic_Acid_2


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_2B

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 2B


title: TRβ_KO_T3_rep2

description: ChIP-enriched DNA


title: TRβ_GS_T3_rep1

description: ChIP-enriched DNA


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_2A

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 2A


title: PBS_3

value: 5 days-PBS control treated


title: Spleen mNK 1


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_1B

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 1B


title: PBS_2


title: PBS_1


title: Liver mNK

data_processing:
FastQC was used to assess sequencing quality
Reads were mapped to the mm10 genome using bowtie2 using the following parameters: --no-mixed --no-discordant
Total reads were read using the countBam function from the R package Rsamtools v 1.26.2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files scaled to tags per million

extract_protocol:
Lymphocytes were harvested as described in manuscript. Fresh cells were prepared as previously described (Buenrostro et al., 2013).
Library was constructed using standard Illumina protocols and TruSeq SBS Kit v3 (Illumina).


title: Spleen mNK 4


title: Valproic_Acid_4


title: Mouse_brain_M_rep2_HD

source_name: Brain

tag: Sex

value: M

tag: replicate

tag: protocol

value: HD

value: Brain


title: RNA_Seq_E14_Dicer_CTR_Dnmt1KO_2A

source_name: RNA Seq E14 Dicer CTR Dnmt1KO 2A

tag: cell type


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_1A

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 1A


title: Liver ILC1

source_name: Liver


title: Valproic_Acid_1


title: Mouse_liver_F_rep1_HD

value: F


title: Spleen mNK 2


title: RNA_Seq_E14_Dicer_CTR_Dnmt1KO_1A

source_name: RNA Seq E14 Dicer CTR Dnmt1KO 1A


title: Mouse_liver_F_rep1_IL

value: IL


title: RNA_Seq_E14_Dicer_CTR_Dnmt1_CTR_3A

source_name: RNA Seq E14 Dicer CTR Dnmt1 CTR 3A


title: PBS_4


title: Mouse_testis_M_rep3

source_name: Testis

value: NF

value: Testis


title: RNA_Seq_E14_Dicer_KO_Dnmt1KO_2A

source_name: RNA Seq E14 Dicer KO Dnmt1KO 2A

value: Dicer/Dnmt1 -/-


title: Spleen CD8 T

source_name: Spleen


title: RNA_Seq_E14_Dicer_KO_Dnmt1KO_1B

source_name: RNA Seq E14 Dicer KO Dnmt1KO 1B

value: ESC


title: RNA_Seq_E14_Dicer_KO_Dnmt1KO_1A

source_name: RNA Seq E14 Dicer KO Dnmt1KO 1A


title: Mouse_testis_M_rep1


title: RNA_Seq_E14_Dicer_CTR_Dnmt1KO_2B

source_name: RNA Seq E14 Dicer CTR Dnmt1KO 2B


title: Mouse_ovary_F_rep3

source_name: Ovary

value: Ovary


title: ChIP-seq_H3K9me3_DNMT1_KO_DICER_KO

data_processing:
ChIP-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bowtie; Read counts over 2kb tiles were normalised per million reads and log2 transformed.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated ChIPseq data file is tab delimited and contains the following 29 columns: (1) Chromosome; (2) Start; (3) End; (4-29) log2 readcount for each sample

source_name: ChIP-seq H3K9me3 DNMT1 KO DICER KO

extract_protocol:
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)

tag: chip antibody

value: anti-H3K9me3; Active Motif, MABI 0319


title: Mouse_testis_M_rep2


title: RNA_Seq_E14_Dicer_CTR_Dnmt1KO_1B

source_name: RNA Seq E14 Dicer CTR Dnmt1KO 1B


title: Mouse_brain_M_rep2_IL


title: ChIP-seq_H3K9me2_DNMT1_CTR_DICER_KO

source_name: ChIP-seq H3K9me2 DNMT1 CTR DICER KO

value: Dicer -/-

value: anti-H3K9me2; Abcam ab1220


title: ChIP-seq_H3K27me3_DNMT1_CTR_DICER_KO

source_name: ChIP-seq H3K27me3 DNMT1 CTR DICER KO

value: anti-H3K27me3; Active Motif, 39155


title: Mouse_liver_M_rep3

value: Liver


title: ChIP-seq_H3K27me3_DNMT1_KO_DICER_KO

source_name: ChIP-seq H3K27me3 DNMT1 KO DICER KO


title: Mouse_ovary_F_rep1


title: ChIP-seq_H3K9me2_DNMT1_KO_DICER_KO

source_name: ChIP-seq H3K9me2 DNMT1 KO DICER KO


title: Mouse_liver_F_rep2


title: Mouse_liver_M_rep2


title: Mouse_liver_M_rep1


title: Mouse_liver_F_rep3


title: RNA_Seq_E14_Dicer_KO_Dnmt1KO_2B

source_name: RNA Seq E14 Dicer KO Dnmt1KO 2B


title: Mouse_heart_M_rep3

source_name: Heart

value: Heart


title: WT-LPS-Rep3

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
base calling: Casava1.8
read alignment, RNA-seq data: TopHat 2.0.8
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

extract_protocol:
Total RNA was isolated with the Thermo Scientific GeneJET RNA Purification Kit. The RNA samples were checked for quality using Bio-Analyzer 2100 (Agilent Technologies, San Diego, CA, USA) and Qubit RNA assay kit. 1.5 mg of total RNA from each sample was used to prepare library using ScriptSeq Complete Kit (Epicentre Inc, Madison, WI, USA) according to manufacturer’s protocol.
ScriptSeq Complete Kit

tag: agent

value: LPS


title: WT-LPS-Rep2


title: WT-Rep3


title: ChIP-seq_H3K9me3_DNMT1_CTR_DICER_KO

source_name: ChIP-seq H3K9me3 DNMT1 CTR DICER KO


title: Mouse_liver_F_rep1

source_name: Liver


title: WT-Rep2


title: WT-Rep1


title: Mouse_heart_F_rep3


title: Mouse_ovary_F_rep2


title: Mouse_heart_M_rep2

value: M


title: Mouse_heart_M_rep1


title: Mouse_brain_M_rep3

source_name: Brain


title: Mouse_heart_F_rep1


title: Mouse_brain_M_rep2


title: ASO2-Rep3


title: ASO2-Rep2


title: Mouse_brain_M_rep1


title: WT-LPS-Rep1


title: Mouse_heart_F_rep2


title: ASO2-Rep1


title: ASO1-Rep3


title: ASO2-LPS-Rep3


title: ASO2-LPS-Rep1


title: ASO2-LPS-Rep2


title: Mouse_brain_F_rep3


title: Mouse_brain_F_rep1


title: Mouse_brain_F_rep2


title: ASO1-Rep1


title: ASO1-LPS-Rep2


title: ASO1-LPS-Rep3


title: ASO1-LPS-Rep1


title: m471

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Immuno-precipitated RNA

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: mouse miR-471-5p–transfected Sertoli cell line TM4

growth_protocol: Cells were grown in DMEM medium with 5% CO2.

extract_protocol:
IP RNAs were obtained following standard RNA IP protocol (Millipore Magna-RIP RNA-Binding Protein Immunoprecipitation Kit)
RNA libraries were prepared for sequencing using Illumina TruSeq protocols

treatment_protocol: cells were transfected with miR-471-5p mimic or scramble and after 48 h, cells were subjected to RNA immunoprecipitation using Ago2 antibody

tag: growth protocol

value: Cells were grown in DMEM supplemented with 10%FBS

tag: treatment prototcol

tag: antibody


title: TAL1 ChIPseq WT FLK

city: Birmingham

first: Maarten

last: Hoogenkamp

state: West Midlands

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
All the reads were filltered for the phred score higher then 30
RNA-Seq reads were mapped using TopHat 2.0.9; ChIP-seq and DHS-Seq were mapped using Bowtie 1.1.2
Duplicate reeads were marked for ChIPseq and DHS-seq using Mark Duplicate reads (Galaxy Version 1.56.0)
ChIP-seq and DHS-Seq peaks were called using MACS2 (Galaxy Version 2.1.1.20160309.0) using parameers -t --format=BAM --gsize 2150570000 --bw 250 --mfold 5 50 --bdg --qvalue 0.05
Transcripts were assembled using Cufflinks 2.0.0 based on the reference genome with quartile normalisation and effective length correction. A combined gtf file was produced using Cuffmerge 2.1.1 and used for determination of the differential gene expression using Cuffdiff 2.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Flk-1+ cells

extract_protocol:
RNA extraction using collumns; AmPure beads for the ChIP-Seq; Qiagen MinElute for the DHS-seq
According to Illumina Sample Preparation Kit

value: ES cell derived Flk-1+ cells

value: WT

value: TAL1 (Santa Cruz sc-12984X)


title: LMO2 ChIPseq  WT FLK

value: LMO2 (R&D systems AF2726)


title: LMO2 ChIPseq LMO2KO FLK


title: ESC_H3K9me3_WT_Rep3

first: Yixian

last: Zheng

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

data_processing:
All RNA-seq samples were sequenced on an Illumina Hi-Seq 2000 using paired-end 100-bp mode. The resulting paired-end reads were trimmed to 75-bp paired-end reads as the last 25 bp had low sequencing quality. Then the reads were then mapped to the mouse genome mm9 using Tophat 2.1.0 (Kim et al., 2013a), and we used the Gencode gtf file (vM1) as known transcripts (-G option). We used htseq-count (Anders et al., 2015) to count reads on genes defined by the Gencode gtf file. Only genes in the “lincrna” and “protein coding” types were considered.
Chip-seq libraries were sequenced on an IlluminaHi-seq 2000 with single-end 50-bp mode. The reads were mapped to the mm9 genome using Bowtie 1.1.2 (Langmead et al., 2009) with "-v 2 -m 1" option. Bedgraph files for genome browser view were generated using custom script.
For HiC data, trimming, mapping, pair-matching and filtering were done using the HiCUP software (Wingett et al., 2015), The interaction read number beween each two 20-Kb windows are counted.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file showing counts of RNA-seq reads on each gene
Supplementary_files_format_and_content: gzipped bedgraoh file showing ChIP-seq read density (RPKM)
Supplementary_files_format_and_content: tab-delimited text file showing interaction read counts between each two 20-Kb windows.

source_name: embryonic stem cells

growth_protocol: The derivation of wild-type and lamin-TKO mESCs were described in our previous publication (Kim et al., 2013b). WT and TKO mESCs were cultured using the same method as described (Kim et al., 2013b) for Hi-C, ChIP-seq, and RNA-seq experiments. For FISH, mESC stocks, which were prepared from the mESCs expanded on feeder cells, were thawed and grown using 0.1% gelatin-coated plates in the absence of feeder cells with KO-DMEM medium (Invitrogen) containing 15% fetal bovine serum (FBS, Invitrogen), 100 μM β-mercaptoethanol (Invitrogen), 2 mM Glutamax, 0.1 mM nonessential amino acids, 50 μg/ml penicillin/streptomycin, and 1,000 units/ml LIF (Millipore). When the cells became ~70% confluent, they were passaged to a new plate and incubated for 30 min at 37°C in 5% CO2 to allow the attachment of the residue feeder cells to the bottom of the plate.

extract_protocol:
4 x 106 TKO or WT mESCs were harvested and fixed as described in the Hi-C method section. The crosslinked cells were resuspended in Nucleus/Chromatin Preparation (NCP) buffer I [10 mMHepes, pH 6.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100 and 1x protease inhibitors (Roche)] and incubated at 4oC for 10 min with gentle rotation. The suspension was centrifuged at 2,000g for 5 min. The pellets were resuspended in NCP buffer II (10 mM Hepes, pH 6.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1x protease inhibitors), followed by centrifugation. The pellets were resuspended in SDS lysis buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 1% SDS and 1x protease inhibitors). The suspension was sonicated with a Bioruptor sonicator (Diagenode) to break chromatin DNA into about 200 bp in size. The sonicated DNA was diluted 10-fold with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris, pH 8.1, and 167 mM NaCl). To precipitate chromatin, 40 μl protein A-Dynabeads (Life Technologies, 10001D) resuspended in 0.5 ml ChIP binding buffer (0.01% Tween-20 in 1x PBS) were incubated with 4 mg of antibodies for each IP at 4oC for 6 h. After washing with ChIP binding buffer, the beads were incubated with diluted sonicated chromatin DNA suspension overnight, continuously rotating. The beads were sequentially washed with low salt wash buffer (20 mM Tris pH 8.1, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 150 mM NaCl), high salt wash buffer (20 mM Tris pH 8.1, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 500 mM NaCl), LiCl buffer (10 mM Tris, pH8.0, 250 mM LiCl, 1% IGEPA CA630 (NP40), 1% Sodium deoxycholate, and 1 mM EDTA), and TE buffer. To reverse crosslinking, the beads were incubated with elution buffer (10 mM Tris, pH 8.0, 1% SDS, 1 mM EDTA and 0.2 mg/μl Proteinase K) at 65oC overnight. Supernatant was collected, extracted with Phenol:Chloroform (1:1), and precipitated with ethanol. The pellets were washed with 75% ethanol, air-dried and resuspended in 10 mM Tris (pH 8.0). DNA concentration was determined with a Quant-iTDS DNA kit (Life Tech, Q-33120).
1 ~ 400 ng of DNA were used to prepare ChIP-seq libraries with a TruSeq DNA prep kit (Illumina) according to the manufacturer’s recommendation

value: wildtpye

value: Abcam, ab8898


title: control

description: Immuno-precipitated RNA

source_name: mouse scramble–transfected Sertoli cell line TM4

value: Testis

value: Scramble transfected


title: RNAseq LMO2KO HE1

molecule: polyA RNA

source_name: haemogenic endothelium1

value: ES cell derived HE1 cells


title: TAL1 ChIPseq LMO2KO FLK


title: DHSseq WT FLK


title: LDB1 ChIPseq LMO2KO FLK

value: Ldb1 (Abcam ab96799)


title: DHSseq LMO2KO FLK


title: RNAseq WT HE1

source_name: haemogenic endothelium 1


title: ESC_H3K9me3_WT_Rep1

value: ESC


title: ESC_H3K9me3_TKO_Rep3

value: lamin-B1/B2/A triple knockout


title: LDB1 ChIPseq WT FLK


title: ASO1-Rep2


title: ribozero mRNA emb-4(hc60) rep2

first: Julie

middle: M

last: Claycomb

state: ON

address: MaRS Centre, West Tower 661 University Ave, Room 1535

department: Department of Molecular Genetics

description:
mRNA.alignments.txt
ribozero_MJ60_20_2_R1

data_processing:
The adapters were trimmed from the reads using cutadapt (version 1.10). RIP-seq data and mRNA-seq data were all mapped to C. elegans genome, version ce10/WS220, using bowtie2 with default parameters. Small RNA-seq data were aligned to C. elegans genome, version ce10/WS220, using STAR (version STAR_2.3.0e.OSX_x86_64) with following parameters: --outFilterMismatchNoverLmax 0.05 -- outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 1 -- alignIntronMax 1.
Reads mapping ribosomal loci were removed from every alignment file. RIP-seq and mRNA-seq aligned reads  mapping to protein coding genes were summarized on the gene level using featureCounts (v1.5.1). Small RNA reads mapping rRNA loci were removed, and only aligned reads 17nt - 30nt long with proper 5' nucleotide (A,G,C,T) were kept for downstream analysis. For differential analysis of small RNAs mapping to protein coding genes, only antisense mapping reads were counted (using multiBamCov function in bedtools v2.25.0) and expressed as PPM values. Only genes with min average value of 5 PPM were considered in the analysis.
Genome_build: ce10/WS220
Supplementary_files_format_and_content: Tab delimited txt files with abundance measurements expressed as either RPKM values (RIP-seq data), PPM values (small RNA-seq data), or values extracted from DEseq2 (mRNA-seq data).
RIP.alignment.genebody.txt (abundance measurements calculated for entire gene body)
RIP.alignment.exons.txt (abundance measurements calculated for exons)
RIP.alignment.introns.txt (abundance measurements calculated for introns)
smallRNA.alignments.txt (abundance measurements calculated for entire gene body)
mRNA.alignments.txt (abundance measurements calculated for entire gene body)

source_name: ribozero mRNA emb-4(hc60)

growth_protocol: Worms were propagated at 14°C then shifted to 20°C for one generation.

extract_protocol:
TriReagent was used to extract total RNA, followed by ethanol precipitation. Quantification and crude assessment of RNA quality was performed using Qubit HS RNA kit (Invitrogen).
For mRNA library preparation, 4 μg of total RNA were treated with DNase I (Invitrogen), ethanol precipitated and quantified with the Qubit HS RNA kit (Invitrogen). 1 μg of DNase treated RNA was used for rRNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina). Library preparation was executed as described by the Truseq Stranded mRNA Sample Preparation Kit manual (Illumina). Samples were quantified by the Qubit HS DNA kit (Invitrogen), pooled and sent for sequencing.
For small RNA, poly(A) mRNA, and ribozero mRNA, worms were frozen in 3-5 volumes of Tri-Reagent (MRC), broken apart using a Wheaton Dounce Homogenizer, vortexed for 10 minutes at RT, then 10% BCP was added, vortexed for an additional 5 min at RT, then centrifuged at 13kXg for 5 minutes. The supernatant was transferred to a new tube, and precipitated with Isopropanol. RNA quality and concentration were assessed using Nanodrop and Qubit quantification.
1 μg of total RNA was used for small RNA library preparation using the Truseq Small RNA Library Prep Kit (Illumina), following the protocol provided by the manufacturer. For mRNA library preparation, 4 μg of total RNA were treated with DNase I (Invitrogen), ethanol precipitated and quantified with the Qubit HS RNA kit (Invitrogen). 1 μg of DNase treated RNA was used for each of rRNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina) and Poly-A selection (Truseq Stranded mRNA Sample Preparation Kit). Library preparation was executed as described by the Truseq Stranded mRNA Sample Preparation Kit manual (Illumina). For RIPs, up to 2 μg of each sample were treated with DNase I (Invitrogen). DNase-treated RNA was then phenol-chloroform extracted, ethanol precipitated and re-quantified using Qubit HS RNA kit (Invitrogen), as well as examined for quality by BioAnalyzer (Agilent). 600 μg of DNase-treated RNA were used for subsequent sample preparation. Ribosomal RNAs were removed from each sample using Ribo-Zero Gold rRNA Removal Kit (Illumina), as per the manufacturer’s protocol. The remaining RNA was ethanol precipitated and prepared for sequencing using Truseq Stranded mRNA Sample Preparation Kit (Illumina), following the protocol provided by the manufacturer.

tag: developmental stage

value: Young Adults

tag: tissue

value: whole worm


title: ESC_H3K9me3_WT_Rep2


title: ribozero mRNA emb-4(hc60) rep1

description:
mRNA.alignments.txt
ribozero_MJ60_20_1_R1


title: ribozero mRNA WT rep2

description:
mRNA.alignments.txt
ribozero_N2_20_2_R1

source_name: ribozero mRNA WT

value: wild type (N2)


title: ribozero mRNA WT rep1

description:
mRNA.alignments.txt
ribozero_N2_20_1_R1


title: ESC_H3K9me3_TKO_Rep2


title: RNAseq LMO2KO FLK


title: ESC_H3K9me3_TKO_Rep1


title: ESC_H3K4me3_WT_Rep3

value: Cell Signaling, 9751


title: poly(A) mRNA emb-4(hc60) rep1

description:
mRNA.alignments.txt
AMY_polA_mRNA_N2_MJ60_AR005_R1

source_name: poly(A) mRNA emb-4(hc60)

extract_protocol:
TriReagent was used to extract total RNA, followed by ethanol precipitation. Quantification and crude assessment of RNA quality was performed using Qubit HS RNA kit (Invitrogen).
For mRNA library preparation, 4 μg of total RNA were treated with DNase I (Invitrogen), ethanol precipitated and quantified with the Qubit HS RNA kit (Invitrogen). 1 μg of DNase treated RNA was used for Poly-A selection (Truseq Stranded mRNA Sample Preparation Kit). Library preparation was executed as described by the Truseq Stranded mRNA Sample Preparation Kit manual (Illumina). Samples were quantified by the Qubit HS DNA kit (Invitrogen), pooled and sent for sequencing.
For small RNA, poly(A) mRNA, and ribozero mRNA, worms were frozen in 3-5 volumes of Tri-Reagent (MRC), broken apart using a Wheaton Dounce Homogenizer, vortexed for 10 minutes at RT, then 10% BCP was added, vortexed for an additional 5 min at RT, then centrifuged at 13kXg for 5 minutes. The supernatant was transferred to a new tube, and precipitated with Isopropanol. RNA quality and concentration were assessed using Nanodrop and Qubit quantification.
1 μg of total RNA was used for small RNA library preparation using the Truseq Small RNA Library Prep Kit (Illumina), following the protocol provided by the manufacturer. For mRNA library preparation, 4 μg of total RNA were treated with DNase I (Invitrogen), ethanol precipitated and quantified with the Qubit HS RNA kit (Invitrogen). 1 μg of DNase treated RNA was used for each of rRNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina) and Poly-A selection (Truseq Stranded mRNA Sample Preparation Kit). Library preparation was executed as described by the Truseq Stranded mRNA Sample Preparation Kit manual (Illumina). For RIPs, up to 2 μg of each sample were treated with DNase I (Invitrogen). DNase-treated RNA was then phenol-chloroform extracted, ethanol precipitated and re-quantified using Qubit HS RNA kit (Invitrogen), as well as examined for quality by BioAnalyzer (Agilent). 600 μg of DNase-treated RNA were used for subsequent sample preparation. Ribosomal RNAs were removed from each sample using Ribo-Zero Gold rRNA Removal Kit (Illumina), as per the manufacturer’s protocol. The remaining RNA was ethanol precipitated and prepared for sequencing using Truseq Stranded mRNA Sample Preparation Kit (Illumina), following the protocol provided by the manufacturer.


title: poly(A) mRNA emb-4(hc60) rep2

description:
mRNA.alignments.txt
AMY_polA_mRNA_N2_MJ60_AR006_R1


title: WGBS_Seq_E14_d9.2_DNMT1KO

data_processing:
WGBS: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts.
Genome_build: NCBIM37
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol:
DNA was isolated from samples using Qiaamp kit from Qiagen
WGBS-Seq was performed as described previously (Ficz et al., 2013) with 12 cycles of PCR amplification using Kapa Uracil Polymerase (Kapa Biosystems)

tag: background strain

value: Dnmt1 KO


title: poly(A) mRNA WT rep2

description:
mRNA.alignments.txt
AMY_polA_mRNA_N2_MJ60_AR015_R1

source_name: poly(A) mRNA WT


title: poly(A) mRNA WT rep1

description:
mRNA.alignments.txt
AMY_polA_mRNA_N2_MJ60_AR014_R1


title: WGBS_Seq_E14_d9.2_control

tag: genotype

value: Wildtype


title: ESC_H3K4me3_WT_Rep1


title: WGBS_Seq_E14_d9.1_DNMT1KO


title: WGBS_Seq_E14_d9.1_control


title: WGBS_Seq_E14_d6.1_DNMT1KO


title: small RNA emb-4(hc60) rep1

description:
smallRNA.alignments.txt
small_RNA_MJ60_20_1_R1

source_name: small RNA emb-4(hc60)

extract_protocol:
TriReagent was used to extract total RNA, followed by ethanol precipitation. Quantification and crude assessment of RNA quality was performed using Qubit HS RNA kit (Invitrogen).
For small RNA library preparation, 1 μg of total RNA was used following the Truseq Small RNA Library Prep Kit (Illumina) protocol. The resulting PCR product DNA was size selected (PAGE 8% gel, 150bp), eluted overnight (10 mM Tris-Cl pH7.5, 1 mM EDTA, 0.3 M NaCl), and then precipitated with 20μg glycogen and 1 volume of isopropanol. The recovered cDNA was resuspended in 30μl ultrapure water and quantified using Qubit HS DNA kit (Invitrogen). All samples were pooled in equal amounts into a 20nM solution and sent for sequencing.
For small RNA, poly(A) mRNA, and ribozero mRNA, worms were frozen in 3-5 volumes of Tri-Reagent (MRC), broken apart using a Wheaton Dounce Homogenizer, vortexed for 10 minutes at RT, then 10% BCP was added, vortexed for an additional 5 min at RT, then centrifuged at 13kXg for 5 minutes. The supernatant was transferred to a new tube, and precipitated with Isopropanol. RNA quality and concentration were assessed using Nanodrop and Qubit quantification.
1 μg of total RNA was used for small RNA library preparation using the Truseq Small RNA Library Prep Kit (Illumina), following the protocol provided by the manufacturer. For mRNA library preparation, 4 μg of total RNA were treated with DNase I (Invitrogen), ethanol precipitated and quantified with the Qubit HS RNA kit (Invitrogen). 1 μg of DNase treated RNA was used for each of rRNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina) and Poly-A selection (Truseq Stranded mRNA Sample Preparation Kit). Library preparation was executed as described by the Truseq Stranded mRNA Sample Preparation Kit manual (Illumina). For RIPs, up to 2 μg of each sample were treated with DNase I (Invitrogen). DNase-treated RNA was then phenol-chloroform extracted, ethanol precipitated and re-quantified using Qubit HS RNA kit (Invitrogen), as well as examined for quality by BioAnalyzer (Agilent). 600 μg of DNase-treated RNA were used for subsequent sample preparation. Ribosomal RNAs were removed from each sample using Ribo-Zero Gold rRNA Removal Kit (Illumina), as per the manufacturer’s protocol. The remaining RNA was ethanol precipitated and prepared for sequencing using Truseq Stranded mRNA Sample Preparation Kit (Illumina), following the protocol provided by the manufacturer.


title: ESC_H3K4me3_TKO_Rep2


title: ESC_H3K4me3_TKO_Rep3


title: small RNA emb-4(hc60) rep2

description:
smallRNA.alignments.txt
small_RNA_MJ60_20_2_R1


title: small RNA WT rep2

description:
smallRNA.alignments.txt
small_RNA_N2_20_2_R1

source_name: small RNA WT


title: ESC_H3K4me3_TKO_Rep1


title: ESC_H3K4me1_WT_Rep3

value: Abcam, ab8895


title: RNAseq WT FLK

value: ES cell derived Flk-1+ cells

value: WT


title: RNAseq TAL1KO FLK


title: WGBS_Seq_E14_d6.1_control


title: ESC_H3K4me1_TKO_Rep3


title: small RNA WT rep1

description:
smallRNA.alignments.txt
small_RNA_N2_20_1_R1


title: ESC_H3K4me1_TKO_Rep2


title: ESC_H3K4me1_WT_Rep2

value: wildtpye


title: WGBS_Seq_E14_d3.2_DNMT1KO


title: WGBS_Seq_E14_d3.2_control


title: ESC_H3K4me1_WT_Rep1


title: Input

description:
RIP.alignment.genebody.txt
RIP.alignment.exons.txt
RIP.alignment.introns.txt
Input

source_name: Input

extract_protocol:
EMB-4 RNA IPs (RIPs), were performed on extracts from gravid adult N2 worms, using 50 μl anti-EMB-4 (7K3-12, 80ng/μl). To preserve RNA integrity, 1:100 Superase-In was added to DROSO Complete buffer prior to lysate preparation, as well as to any additional DROSO complete buffer added to each IP. 4x5 mg IPs were set up for each sample (anti-EMB-4 and no antibody control). After pre-clearing, incubation with antibody and collection of immunocomplexes, beads were washed 5x5 min and all four IPs were pooled for each sample prior to the last wash. 10% of the beads were saved for IP validation by Western Blot. The remaining 90% were resuspended in 4x volume of TriReagent and RNA extraction was performed. The extracted RNA was precipitated overnight at -80°C. The Qubit HS RNA kit (Invitrogen) was used to quantify the extracted RNA and up to 2 μg of each sample were treated with DNase I (Invitrogen). DNase-treated RNA was then phenol-chloroform extracted, ethanol precipitated and re-quantified using Qubit HS RNA kit (Invitrogen), as well as examined for quality by BioAnalyzer (Agilent). 600 μg of DNase-treated RNA were used for subsequent sample preparation. Ribosomal RNAs were removed from each sample using Ribo- Zero Gold rRNA Removal Kit (Illumina), as per the manufacturer’s protocol. The remaining RNA was ethanol precipitated and prepared for sequencing using Truseq Stranded mRNA Sample Preparation Kit (Illumina), following the protocol provided by the manufacturer. The resulting PCR product DNA was quantified using the Qubit HS DNA kit (Invitrogen) and all samples were pooled in equal amounts into a 20nM solution and sequenced.
For small RNA, poly(A) mRNA, and ribozero mRNA, worms were frozen in 3-5 volumes of Tri-Reagent (MRC), broken apart using a Wheaton Dounce Homogenizer, vortexed for 10 minutes at RT, then 10% BCP was added, vortexed for an additional 5 min at RT, then centrifuged at 13kXg for 5 minutes. The supernatant was transferred to a new tube, and precipitated with Isopropanol. RNA quality and concentration were assessed using Nanodrop and Qubit quantification.
1 μg of total RNA was used for small RNA library preparation using the Truseq Small RNA Library Prep Kit (Illumina), following the protocol provided by the manufacturer. For mRNA library preparation, 4 μg of total RNA were treated with DNase I (Invitrogen), ethanol precipitated and quantified with the Qubit HS RNA kit (Invitrogen). 1 μg of DNase treated RNA was used for each of rRNA depletion (Ribo-Zero Gold rRNA Removal Kit, Illumina) and Poly-A selection (Truseq Stranded mRNA Sample Preparation Kit). Library preparation was executed as described by the Truseq Stranded mRNA Sample Preparation Kit manual (Illumina). For RIPs, up to 2 μg of each sample were treated with DNase I (Invitrogen). DNase-treated RNA was then phenol-chloroform extracted, ethanol precipitated and re-quantified using Qubit HS RNA kit (Invitrogen), as well as examined for quality by BioAnalyzer (Agilent). 600 μg of DNase-treated RNA were used for subsequent sample preparation. Ribosomal RNAs were removed from each sample using Ribo-Zero Gold rRNA Removal Kit (Illumina), as per the manufacturer’s protocol. The remaining RNA was ethanol precipitated and prepared for sequencing using Truseq Stranded mRNA Sample Preparation Kit (Illumina), following the protocol provided by the manufacturer.

value: Gravid Adults

tag: ip antibody

value: none (Total input RNA from same lysates used for RIPs)


title: Mock IP

description:
RIP.alignment.genebody.txt
RIP.alignment.exons.txt
RIP.alignment.introns.txt
Mock IP

source_name: Mock IP

value: Mock IP (using no antibody with Protein A/G agarose beads from Santa Cruz Biotecnology Co.)


title: WGBS_Seq_E14_d3.1_DNMT1KO


title: WGBS_Seq_E14_d1.2_DNMT1KO


title: ESC_H3K4me1_TKO_Rep1


title: WGBS_Seq_E14_d1.2_control


title: WD no_hormone_4h replicate 3

first: Natalie

middle: Anne

last: Dye

address: Pfotenhauerstrasse 108

institute: MPI-CBG

description:
Sample name: no_hormone_3
Column header name in gene_fpkms_by_replicate.txt: no_hormone_2

data_processing:
Reads were trimmed with cutadapt
Trimmed Reads were mapped using tophat2
Abundance estimation was performed using cufflinks
Genome_build: BDGP5
Supplementary_files_format_and_content: FPKM for each replicate

source_name: 96hr wing discs (WD)

growth_protocol: Wild type OregonR flies were grown at low density at 25C on standard food containing cornmeal, molasses agar and yeast extract. Larvae were collected for dissection at 96hr after egg laying, washed thoroughly with water and surface sterilized with 70% ethanol. Hormone free media for culture was as follows: Grace's media (Sigma G9771) prepared without Sodium Bicarbonate but with 5mM BisTris; pH adjusted to 6.7; + 5% fetal bovine serum (Invitrogen 10270098) + Penicillin/Streptomycin (Sigma P4333, diluted to 1X in media). Hormone was added just prior to the start of the experiment. 20-hydroxyecdysone (Sigma H5142) was added as a 1000x dilution from an ethanol stock solution (final 20nM in media). Bovine insulin (Sigma I6634) was added as a 2000x dilution from an acidified water stock solution (final 5ug/ml in media). Discs were dissected in hormone-free media, and then immediately transferred to the media for culture. Dissections were performed within 45min, and the middle of that window was considered to be time 0hr. Discs were cultured in a volume of 500ul/~15 discs at 25C. No_culture discs were taken from the initial timepoint (96hr AEL) and frozen in liquid nitrogen within 30min of dissection.

extract_protocol:
RNA was isolated using a Qiagen RNeasy Mini kit. Samples were lysed by vortexing for 20-30sec in Buffer RLT + 2-mercaptoethanol on ice. Manufacturer's instructions were followed. Ethanol precipitation was subsequantly performed to achieve greater purification. mRNA was isolated from 1ug of total RNA using poly-dT enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Final elution was in 15ul of 2x first strand cDNA synthesis buffer.
NEBNext Ultra Directional RNA Library Prep Kit was used after chemical fragmentation of the sample at 94C for 15min. Custom adaptors were used for ligation and then depleted using an XP bead purification (Beckman Coulter) with a ratio of 1:1. Indexing was achieved during PCR enrichment using amplification primers carrying the index sequence. Two more XP bead purifications were done, and then the samples were quantified with Qubit dsDNA HS Assay Kit (Invitrogen).

treatment_protocol: At the given times specified for each sample, discs were removed from the culture vessel in a volume of 10-15ul and transferred to a microfuge tube. Samples were rapidly frozen in liquid nitrogen and stored at -80C until all replicates were collected.

value: OregonR

tag: hormone for culture

tag: length of culture

value: WD


title: ESC_H3K4me3_WT_Rep2

value: ESC


title: WGBS_Seq_E14_d1.1_DNMT1KO


title: WGBS_Seq_E14_d1.1_control


title: WD without culture replicate 3

description:
Sample name: no_culture_3
Column header name in gene_fpkms_by_replicate.txt: no_culture_2

tag: strain


title: WD no_hormone_4h replicate 2

description:
Sample name: no_hormone_2
Column header name in gene_fpkms_by_replicate.txt: no_hormone_1


title: WGBS_Seq_E14_d3.1_control


title: WD without culture replicate 1

description:
Sample name: no_culture_1
Column header name in gene_fpkms_by_replicate.txt: no_culture_0


title: EMB-4 IP

description:
RIP.alignment.genebody.txt
RIP.alignment.exons.txt
RIP.alignment.introns.txt
EMB-4 IP

source_name: EMB-4 IP

value: Immunoprecipitated RNA using EMB-4 Antibody clone 7K3-12 at 80ng/μ and Protein A/G agarose beads from Santa Cruz Biotechnolog Co.


title: ESC_H3K27me3_WT_Rep4

value: Millipore, 07-449


title: WD no_hormone_4h replicate 1

description:
Sample name: no_hormone_1
Column header name in gene_fpkms_by_replicate.txt: no_hormone_0


title: WD in insulin_9h replicate 3

description:
Sample name: insulin_9h_3
Column header name in gene_fpkms_by_replicate.txt: insulin_9h_2

value: 5ug/ml bovine insulin


title: ESC_H3K27me3_WT_Rep3


title: WD in insulin_9h replicate 2

description:
Sample name: insulin_9h_2
Column header name in gene_fpkms_by_replicate.txt: insulin_9h_1


title: ESC_H3K27me3_WT_Rep1


title: WGBS_Seq_E14_d11.1_control